48 results on '"Pavan Bachireddy"'
Search Results
2. Mechanisms of response and resistance to combined decitabine and ipilimumab for advanced myeloid disease
- Author
-
Livius Penter, Yang Liu, Jacquelyn O. Wolff, Lin Yang, Len Taing, Aashna Jhaveri, Jackson Southard, Manishkumar Patel, Nicole M. Cullen, Kathleen L. Pfaff, Nicoletta Cieri, Giacomo Oliveira, Seunghee Kim-Schulze, Srinika Ranasinghe, Rebecca Leonard, Taylor Robertson, Elizabeth A. Morgan, Helen X. Chen, Minkyung H. Song, Magdalena Thurin, Shuqiang Li, Scott J. Rodig, Carrie Cibulskis, Stacey Gabriel, Pavan Bachireddy, Jerome Ritz, Howard Streicher, Donna S. Neuberg, F. Stephen Hodi, Matthew S. Davids, Sacha Gnjatic, Kenneth J. Livak, Jennifer Altreuter, Franziska Michor, Robert J. Soiffer, Jacqueline S. Garcia, and Catherine J. Wu
- Subjects
Immunology ,Cell Biology ,Hematology ,Biochemistry - Abstract
The challenge of eradicating leukemia in patients with acute myelogenous leukemia (AML) after initial cytoreduction has motivated modern efforts to combine synergistic active modalities including immunotherapy. Recently, the ETCTN/CTEP 10026 study tested the combination of the DNA methyltransferase inhibitor decitabine together with the immune checkpoint inhibitor ipilimumab for AML/myelodysplastic syndrome (MDS) either after allogeneic hematopoietic stem cell transplantation (HSCT) or in the HSCT-naïve setting. Integrative transcriptome-based analysis of 304 961 individual marrow-infiltrating cells for 18 of 48 subjects treated on study revealed the strong association of response with a high baseline ratio of T to AML cells. Clinical responses were predominantly driven by decitabine-induced cytoreduction. Evidence of immune activation was only apparent after ipilimumab exposure, which altered CD4+ T-cell gene expression, in line with ongoing T-cell differentiation and increased frequency of marrow-infiltrating regulatory T cells. For post-HSCT samples, relapse could be attributed to insufficient clearing of malignant clones in progenitor cell populations. In contrast to AML/MDS bone marrow, the transcriptomes of leukemia cutis samples from patients with durable remission after ipilimumab monotherapy showed evidence of increased infiltration with antigen-experienced resident memory T cells and higher expression of CTLA-4 and FOXP3. Altogether, activity of combined decitabine and ipilimumab is impacted by cellular expression states within the microenvironmental niche of leukemic cells. The inadequate elimination of leukemic progenitors mandates urgent development of novel approaches for targeting these cell populations to generate long-lasting responses. This trial was registered at www.clinicaltrials.gov as #NCT02890329.
- Published
- 2023
3. Supplementary Figures 1-3 from Definition of an Enhanced Immune Cell Therapy in Mice That Can Target Stem-Like Lymphoma Cells
- Author
-
Steve H. Thorne, Dean W. Felsher, Pavan Bachireddy, Alice C. Fan, Tobi Schmidt, Robert S. Negrin, Rachel Sikorski, and Christopher H. Contag
- Abstract
Supplementary Figures 1-3 from Definition of an Enhanced Immune Cell Therapy in Mice That Can Target Stem-Like Lymphoma Cells
- Published
- 2023
4. Expansion of a CD8+ Temra Population and Activating T-Cell Interactions Characterize the Graft Versus Leukemia Response in Relapsed AML
- Author
-
Katie Maurer, Cameron Y. Park, Mehdi Borji, Shouvik Mani, Jackson Southard, Samouil L. Farhi, Domenic Abbondanza, Shuqiang Li, Kenneth J. Livak, Jerome Ritz, Robert J. Soiffer, Pavan Bachireddy, Catherine J. Wu, and Elham Azizi
- Subjects
Immunology ,Cell Biology ,Hematology ,Biochemistry - Published
- 2022
5. Molecular and cellular features of CTLA-4 blockade for relapsed myeloid malignancies after transplantation
- Author
-
Matthew S. Davids, Robert J. Soiffer, Emma S. Hathaway, F. Stephen Hodi, Pavan Bachireddy, Magdalena Thurin, Vincent T. Ho, Wandi Zhang, Sarah Nikiforow, Nicoletta Cieri, Jerome Ritz, Stacey Gabriel, Mariano Severgnini, Aashna Jhaveri, X. Shirley Liu, Haesook T. Kim, Jingxin Fu, Kenneth J. Livak, Sacha Gnjatic, Scott J. Rodig, Alexandra Savell, Philippe Armand, Catherine J. Wu, Teddy Huang, Joseph H. Antin, Corey Cutler, Carrie Cibulskis, Livius Penter, Shuqiang Li, Howard Streicher, Donna Neuberg, Srinika Ranasinghe, Matthew Nazzaro, Yi Zhang, Emily M. Thrash, Helen X. Chen, John Koreth, and Seunghee Kim-Schulze
- Subjects
Male ,Myeloid ,BLOOD COMMENTARY ,medicine.medical_treatment ,Immunology ,Ipilimumab ,Hematopoietic stem cell transplantation ,CD8-Positive T-Lymphocytes ,Biochemistry ,medicine ,Humans ,CTLA-4 Antigen ,Gene Expression Regulation, Leukemic ,business.industry ,Allogeneic Cells ,Hematopoietic Stem Cell Transplantation ,Cell Biology ,Hematology ,Immune checkpoint ,Neoplasm Proteins ,Blockade ,Transplantation ,medicine.anatomical_structure ,Leukemia, Myeloid ,CTLA-4 ,Cancer research ,Female ,Nivolumab ,business ,medicine.drug - Abstract
Relapsed myeloid disease after allogeneic stem cell transplantation (HSCT) remains largely incurable. We previously demonstrated the potent activity of immune checkpoint blockade in this clinical setting with ipilimumab or nivolumab. To define the molecular and cellular pathways by which CTLA-4 blockade with ipilimumab can reinvigorate an effective graft-versus-leukemia (GVL) response, we integrated transcriptomic analysis of leukemic biopsies with immunophenotypic profiling of matched peripheral blood samples collected from patients treated with ipilimumab following HSCT on the Experimental Therapeutics Clinical Trials Network 9204 trial. Response to ipilimumab was associated with transcriptomic evidence of increased local CD8+ T-cell infiltration and activation. Systemically, ipilimumab decreased naïve and increased memory T-cell populations and increased expression of markers of T-cell activation and costimulation such as PD-1, HLA-DR, and ICOS, irrespective of response. However, responding patients were characterized by higher turnover of T-cell receptor sequences in peripheral blood and showed increased expression of proinflammatory chemokines in plasma that was further amplified by ipilimumab. Altogether, these data highlight the compositional T-cell shifts and inflammatory pathways induced by ipilimumab both locally and systemically that associate with successful GVL outcomes. This trial was registered at www.clinicaltrials.gov as #NCT01822509.
- Published
- 2021
6. A multicenter phase 1 study of nivolumab for relapsed hematologic malignancies after allogeneic transplantation
- Author
-
Yi Bin Chen, Edward D. Ball, Robert J. Soiffer, Vincent T. Ho, Pavan Bachireddy, Corey Cutler, David Avigan, Asad Bashey, Catherine J. Wu, Howard Streicher, Michael Mazzeo, Jerome Ritz, Alexandra Savell, Edwin P. Alyea, Frederick L. Locke, Haesook T. Kim, Philippe Armand, Caitlin Costello, Adrienne Anderson, Alex F. Herrera, Sarah Nikiforow, Rodrigo O. Maegawa, Alexander P. Boardman, Augustine Weber, and Matthew S. Davids
- Subjects
Adult ,Male ,Oncology ,medicine.medical_specialty ,Programmed Cell Death 1 Receptor ,Immunology ,Graft vs Host Disease ,Kaplan-Meier Estimate ,Biochemistry ,Antineoplastic Agents, Immunological ,Recurrence ,Internal medicine ,medicine ,Humans ,Prospective Studies ,Treatment Failure ,Adverse effect ,Prospective cohort study ,Aged ,Transplantation ,business.industry ,Hematopoietic Stem Cell Transplantation ,Retrospective cohort study ,Cell Biology ,Hematology ,Middle Aged ,Allografts ,medicine.disease ,Clinical trial ,Nivolumab ,Graft-versus-host disease ,Hematologic Neoplasms ,Toxicity ,Female ,business - Abstract
Programmed cell death-1 (PD-1)/programmed death ligand-1 blockade may potentially augment graft-vs-tumor effects following allogeneic hematopoietic cell transplantation (alloHCT), but retrospective studies of anti–PD-1 therapy reported substantial toxicity from graft-versus-host-disease (GVHD). Here, we report the results of a prospective clinical trial of PD-1 blockade for relapsed hematologic malignancies (HMs) after alloHCT (NCT01822509). The primary objective in this phase 1 multicenter, investigator-initiated study was to determine maximum tolerated dose and safety. Secondary objectives were to assess efficacy and immunologic activity. Patients with relapsed HMs following alloHCT were eligible. Nivolumab was administered every 2 weeks until progression or unacceptable toxicity, starting with a 1-mg/kg cohort, with planned deescalation based on toxicity to a 0.5-mg/kg cohort. Twenty-eight patients were treated (n = 19 myeloid, n = 9 lymphoid). Median age was 57 years (range 27-76), and median time from alloHCT to enrollment was 21 months (range 5.6-108.5). Two of 6 patients treated at 1 mg/kg experienced dose-limiting toxicity (DLT) from immune-related adverse events (irAEs). Twenty-two patients were treated at 0.5 mg/kg, and 4 DLTs occurred, including 2 irAEs and 2 with fatal GVHD. The overall response rate in efficacy-evaluable patients was 32% (8/25). With a median follow-up of 11 months, the 1-year progression-free survival and overall survival were 23% and 56%, respectively. In this first prospective clinical trial of an anti–PD-1 antibody for post–alloHCT relapse, GVHD and irAEs occurred, requiring dose deescalation, with only modest antitumor activity. Further studies of anti–PD-1 therapy post–alloHCT may require specific toxicity mitigation strategies. This trial was registered at www.clinicaltrials.gov as #NCT 01822509.
- Published
- 2020
7. Coevolving JAK2V617F+relapsed AML and donor T cells with PD-1 blockade after stem cell transplantation: an index case
- Author
-
Satyen H. Gohil, Teddy Huang, Dominik Schmidt, F. Stephen Hodi, Kenneth J. Livak, Donna Neuberg, Catherine J. Wu, Emily M. Thrash, Mariano Severgnini, Robert Zeiser, Livius Penter, Pavan Bachireddy, and Shuqiang Li
- Subjects
Myeloid ,medicine.medical_treatment ,T cell ,T-Lymphocytes ,Population ,Programmed Cell Death 1 Receptor ,Hematopoietic stem cell transplantation ,hemic and lymphatic diseases ,medicine ,Humans ,Transplantation, Homologous ,education ,education.field_of_study ,business.industry ,Hematopoietic Stem Cell Transplantation ,Hematology ,Stimulus Report ,Blockade ,Transplantation ,Leukemia, Myeloid, Acute ,medicine.anatomical_structure ,Cancer research ,Leukocytes, Mononuclear ,Nivolumab ,Stem cell ,business - Abstract
Key Points Index case of nivolumab response associated with altered circulating T-cell composition and heterogeneous PD-L1 expression on AML blasts.Single-cell approaches provide complementary insight into cellular mechanisms of response and resistance to transplant/checkpoint blockade., Visual Abstract, Relapse of myeloproliferative neoplasms (MPNs) after allogeneic hematopoietic stem cell transplantation (HSCT) is associated with poor outcomes, as therapeutic approaches to reinstate effective graft-versus-leukemia (GVL) responses remain suboptimal. Immune escape through overexpression of PD-L1 in JAK2V617F-mutated MPN provides a rationale for therapeutic PD-1 blockade, and indeed, clinical activity of nivolumab in relapsed MPN post-HSCT has been observed. Elucidation of the features of response following PD-1 blockade in such patients could inform novel therapeutic concepts that enhance GVL. Here, we report an integrated high-dimensional analysis using single-cell RNA sequencing, T-cell receptor sequencing, cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), and assay for transposase-accessible chromatin using sequencing (scATAC-seq), together with mass cytometry, in peripheral blood mononuclear cells collected at 6 timepoints before, during, and after transient response to PD-1 blockade from an index case of relapsed MPN following HSCT. Before nivolumab infusion, acute myeloid leukemia (AML) blasts demonstrated high expression of chemokines, and T cells were characterized by expression of interferon-response genes. This baseline inflammatory signature disappeared after nivolumab infusion. Clinical response was characterized by transient expansion of a polyclonal CD4+ T-cell population and contraction of an AML subpopulation that exhibited megakaryocytic features and elevated PD-L1 expression. At relapse, the proportion of the AML subpopulation with progenitor-like features progressively increased, suggesting coevolution of AML blasts and donor-derived T cells. We thus demonstrate how single-cell technologies can provide complementary insight into cellular mechanisms underlying response to PD-1 blockade, motivating future longitudinal high-dimensional single-cell studies of GVL responses in relapsed myeloid disease.
- Published
- 2021
8. Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma
- Author
-
Patrick C. Lee, Shuqiang Li, Charles H. Yoon, Jing Sun, Jason Pyrdol, Zoe B. Ciantra, J. Bryan Iorgulescu, Jinyan Liu, Donna E. Leet, Anita Giobbie-Hurder, Donna Neuberg, Satyen H. Gohil, Teddy Huang, Edward F. Fritsch, Wandi Zhang, Adrienne M. Luoma, Mohamed Uduman, Siranush Sarkizova, Kai W. Wucherpfennig, Giacomo Oliveira, Dan H. Barouch, Liudmila Elagina, Nir Hacohen, Oriol Olive, Lars Rønn Olsen, Zhuting Hu, Elizabeth I. Buchbinder, Derin B. Keskin, Sachet A. Shukla, Robert A. Redd, Bradley L. Pentelute, Patrick A. Ott, Scott J. Rodig, Catherine J. Wu, Keerthi Shetty, Kenneth J. Livak, Pavan Bachireddy, Rosa Lundbye Allesøe, Rebecca L. Holden, Lauren Peter, and Juliet Forman
- Subjects
0301 basic medicine ,integumentary system ,business.industry ,medicine.medical_treatment ,T cell ,General Medicine ,General Biochemistry, Genetics and Molecular Biology ,Neoantigen Peptide ,Article ,Vaccination ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Immune system ,medicine.anatomical_structure ,Cancer immunotherapy ,Antigen ,SDG 3 - Good Health and Well-being ,030220 oncology & carcinogenesis ,Immunology ,Medicine ,Cytotoxic T cell ,business ,Memory T cell - Abstract
Personal neoantigen vaccines have been envisioned as an effective approach to induce, amplify and diversify antitumor T cell responses. To define the long-term effects of such a vaccine, we evaluated the clinical outcome and circulating immune responses of eight patients with surgically resected stage IIIB/C or IVM1a/b melanoma, at a median of almost 4 years after treatment with NeoVax, a long-peptide vaccine targeting up to 20 personal neoantigens per patient ( NCT01970358 ). All patients were alive and six were without evidence of active disease. We observed long-term persistence of neoantigen-specific T cell responses following vaccination, with ex vivo detection of neoantigen-specific T cells exhibiting a memory phenotype. We also found diversification of neoantigen-specific T cell clones over time, with emergence of multiple T cell receptor clonotypes exhibiting distinct functional avidities. Furthermore, we detected evidence of tumor infiltration by neoantigen-specific T cell clones after vaccination and epitope spreading, suggesting on-target vaccine-induced tumor cell killing. Personal neoantigen peptide vaccines thus induce T cell responses that persist over years and broaden the spectrum of tumor-specific cytotoxicity in patients with melanoma. Personalized neoantigen vaccination in patients with melanoma elicits durable and specific memory T cell clones that have cytotoxic gene signatures and can diversify to include nonvaccine neoantigen specificities.
- Published
- 2021
9. Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to the graft-versus-leukemia effect
- Author
-
Pavan Bachireddy, Nathan Mathewson, Samuel S. Freeman, Arman W. Mohammad, Nikolaos Barkas, Donna Neuberg, Gad Getz, Natalie Bavli, Kendell Clement, Juliet Forman, Jennifer R. Brown, Thomas J. Kipps, Liudmila Elagina, Christina Ennis, Vincent T. Ho, Sachet A. Shukla, Edwin P. Alyea, Jerome Ritz, Robert J. Soiffer, Ignaty Leshchiner, Laura Z. Rassenti, Catherine J. Wu, Vinhkhang N Nguyen, Derin B. Keskin, Peter V. Kharchenko, Andreas Gnirke, and Satyen H. Gohil
- Subjects
Homologous ,Lymphoma ,medicine.medical_treatment ,Chronic lymphocytic leukemia ,Cell ,Graft vs Host Disease ,Graft vs Leukemia Effect ,Hematopoietic stem cell transplantation ,Human leukocyte antigen ,Medical and Health Sciences ,Article ,Transcriptome ,Rare Diseases ,HLA Antigens ,Stem Cell Research - Nonembryonic - Human ,immune system diseases ,hemic and lymphatic diseases ,Genetics ,medicine ,Transplantation, Homologous ,Humans ,Epigenetics ,Chronic ,Cancer ,Transplantation ,Chemotherapy ,Leukemia ,business.industry ,Hematopoietic Stem Cell Transplantation ,B-Cell ,Hematology ,General Medicine ,Biological Sciences ,Stem Cell Research ,medicine.disease ,Leukemia, Lymphocytic, Chronic, B-Cell ,Lymphocytic ,surgical procedures, operative ,medicine.anatomical_structure ,Cancer research ,Stem Cell Research - Nonembryonic - Non-Human ,Stem cell ,business - Abstract
Leukemic relapse remains a major barrier to successful allogeneic hematopoietic stem cell transplantation (allo-HSCT) for aggressive hematologic malignancies. The basis for relapse of advanced lymphoid malignancies remains incompletely understood and may involve escape from the graft-versus-leukemia (GvL) effect. We hypothesized that for patients with chronic lymphocytic leukemia (CLL) treated with allo-HSCT, leukemic cell-intrinsic features influence transplant outcomes by directing the evolutionary trajectories of CLL cells. Integrated genetic, transcriptomic, and epigenetic analyses of CLL cells from 10 patients revealed that the clinical kinetics of post-HSCT relapse are shaped by distinct molecular dynamics. Early relapses after allo-HSCT exhibited notable genetic stability; single CLL cell transcriptional analysis demonstrated a cellular heterogeneity that was static over time. In contrast, CLL cells relapsing late after allo-HSCT displayed notable genetic evolution and evidence of neoantigen depletion, consistent with marked single-cell transcriptional shifts that were unique to each patient. We observed a greater rate of epigenetic change for late relapses not seen in early relapses or relapses after chemotherapy alone, suggesting that the selection pressures of the GvL bottleneck are unlike those imposed by chemotherapy. No selective advantage for human leukocyte antigen (HLA) loss was observed, even when present in pretransplant subpopulations. Gain of stem cell modules was a common signature associated with leukemia relapse regardless of posttransplant relapse kinetics. These data elucidate the biological pathways that underlie GvL resistance and posttransplant relapse.
- Published
- 2020
10. Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy
- Author
-
Catherine J. Wu, Shuqiang Li, Dana Pe'er, Jerome Ritz, Pavan Bachireddy, Christina Ennis, Robert J. Soiffer, Zi-Ning Choo, Vinhkhang N Nguyen, Cassandra Burdziak, Elham Azizi, Kenneth J. Livak, Donna Neuberg, and Edwin P. Alyea
- Subjects
Tumor microenvironment ,T cell ,medicine.medical_treatment ,T-cell receptor ,Cancer ,Immunotherapy ,Biology ,medicine.disease ,Donor lymphocyte infusion ,Leukemia ,medicine.anatomical_structure ,Immune system ,medicine ,Cancer research - Abstract
Immune therapies have transformed the cancer therapeutic landscape but fail to benefit most patients. To elucidate the underlying mechanisms by which T cells mediate elimination of leukemia, we generated a high-resolution map of longitudinal T cell dynamics within the same tumor microenvironment (TME) during response or resistance to donor lymphocyte infusion (DLI), a widely used immunotherapy for relapsed leukemia. We analyzed 87,939 bone marrow-derived single T cell transcriptomes, along with chromatin accessibility and single T cell receptor clonality profiles, by developing novel machine learning tools for integrating longitudinal and multimodal data. We found that pre-treatment enrichment and post-treatment rapid, durable expansion of ‘terminal’ (TEX) and ‘precursor’ (TPEX) exhausted subsets, respectively, defined DLI response. A contrasting, heterogeneous pattern of T cell dysfunction marked DLI resistance. Unexpectedly, TPEX cells that expanded in responders did not arise from the infusion product but instead from both pre-existing and novel clonotypes recruited to the TME. Our unbiased dissection of the TME using a Bayesian method, Symphony, defined the T cell circuitry underlying effective human anti-leukemic immune responses that may be broadly relevant to other exhaustion antagonists across cancers. Finally, we provide a general analysis paradigm for exploiting temporal single-cell genomic profiling for deep understanding of therapeutic scenarios beyond oncology.
- Published
- 2020
11. Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to graft-versus-leukemia
- Author
-
Jennifer R. Brown, Robert J. Soiffer, Christina Ennis, Gad Getz, Kendell Clement, Liudmila Elagina, Andreas Gnirke, Jerome Ritz, Peter V. Kharchenko, Edwin P. Alyea, Nikolas Barkas, Sachet A. Shukla, Samuel S. Freeman, Juliet Forman, Arman W. Mohammad, Laura Z. Rassenti, Satyen H. Gohil, Ignaty Leshchiner, Donna Neuberg, Thomas J. Kipps, Vincent T. Ho, Pavan Bachireddy, Vinhkhang N Nguyen, Catherine J. Wu, and Natalie Bavli
- Subjects
0303 health sciences ,Chemotherapy ,medicine.medical_treatment ,Chronic lymphocytic leukemia ,Human leukocyte antigen ,Hematopoietic stem cell transplantation ,Biology ,medicine.disease ,3. Good health ,Transcriptome ,03 medical and health sciences ,Leukemia ,surgical procedures, operative ,0302 clinical medicine ,immune system diseases ,hemic and lymphatic diseases ,030220 oncology & carcinogenesis ,medicine ,Cancer research ,Epigenetics ,Stem cell ,030304 developmental biology - Abstract
Resistance to the graft-versus-leukemia (GvL) effect remains the major barrier to successful allogeneic hematopoietic stem cell transplantation (allo-HSCT) for aggressive hematologic malignancies. The basis of GvL resistance for advanced lymphoid malignancies remains incompletely understood. We hypothesized that for patients with chronic lymphocytic leukemia (CLL) treated with allo-HSCT, leukemic cell-intrinsic features shape GvL outcomes by directing the evolutionary trajectories of CLL cells. Integrated genetic, transcriptomic and epigenetic analyses of CLL cells from 10 patients revealed that the clinical kinetics of post- HSCT relapse are shaped by distinct molecular dynamics and suggest that the selection pressures of the GvL bottleneck are unlike those imposed by chemotherapy. No selective advantage for HLA loss was observed, even when present in pre-transplant subpopulations. Regardless of post-transplant relapse kinetics, gain of stem cell modules was a common signature associated with leukemia relapse. These data elucidate the biological pathways that underlie GvL resistance and post-transplant relapse.One Sentence SummaryWe find that the clinical kinetics of chronic lymphocytic leukemia relapse after stem cell transplant are underwritten by distinct genetic and epigenetic evolutionary trajectories and suggest that the selection pressures of the post-transplant, immunologic bottleneck are unlike those imposed by chemotherapy.
- Published
- 2020
12. Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer
- Author
-
Sachet A. Shukla, Wandi Zhang, Annie Apffel, Irwin Jungreis, Susan Klaeger, Aviv Regev, Bo Li, François Aguet, Zhe Ji, Tamara Ouspenskaia, Christina R. Hartigan, Nir Hacohen, Yuen Ting Chow, Catherine J. Wu, Gad Getz, Siranush Sarkizova, Travis Law, Phuong M. Le, Giacomo Oliveira, Steven A. Carr, Manolis Kellis, Derin B. Keskin, Karl R. Clauser, Hasmik Keshishian, Elena Christian, Binyamin A. Knisbacher, and Pavan Bachireddy
- Subjects
Open reading frame ,biology ,Antigen ,Cancer immunotherapy ,medicine.medical_treatment ,MHC class I ,Proteome ,biology.protein ,medicine ,Ribosome profiling ,Computational biology ,Major histocompatibility complex ,Epitope - Abstract
Tumor epitopes – peptides that are presented on surface-bound MHC I proteins - provide targets for cancer immunotherapy and have been identified extensively in the annotated protein-coding regions of the genome. Motivated by the recent discovery of translated novel unannotated open reading frames (nuORFs) using ribosome profiling (Ribo-seq), we hypothesized that cancer-associated processes could generate nuORFs that can serve as a new source of tumor antigens that harbor somatic mutations or show tumor-specific expression. To identify cancer-specific nuORFs, we generated Ribo-seq profiles for 29 malignant and healthy samples, developed a sensitive analytic approach for hierarchical ORF prediction, and constructed a high-confidence database of translated nuORFs across tissues. Peptides from 3,555 unique translated nuORFs were presented on MHC I, based on analysis of an extensive dataset of MHC I-bound peptides detected by mass spectrometry, with >20-fold more nuORF peptides detected in the MHC I immunopeptidomes compared to whole proteomes. We further detected somatic mutations in nuORFs of cancer samples and identified nuORFs with tumor-specific translation in melanoma, chronic lymphocytic leukemia and glioblastoma. NuORFs thus expand the pool of MHC I-presented, tumor-specific peptides, targetable by immunotherapies.
- Published
- 2020
- Full Text
- View/download PDF
13. Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer
- Author
-
Karl R. Clauser, Gad Getz, Wandi Zhang, Elena Christian, Siranush Sarkizova, Susan Klaeger, Bo Li, Yuen Ting Chow, Annie Apffel, Sune Justesen, Binyamin A. Knisbacher, François Aguet, Pavan Bachireddy, Catherine J. Wu, Aviv Regev, Christina R. Hartigan, Nir Hacohen, Sarah Chen, Irwin Jungreis, Zhe Ji, Hasmik Keshishian, Sachet A. Shukla, Phuong M. Le, Steven A. Carr, Tamara Ouspenskaia, Giacomo Oliveira, Travis Law, Manolis Kellis, and Derin B. Keskin
- Subjects
medicine.medical_treatment ,Biomedical Engineering ,Bioengineering ,Computational biology ,Major histocompatibility complex ,Applied Microbiology and Biotechnology ,Epitope ,Mass Spectrometry ,Immune system ,Antigen ,Antigens, Neoplasm ,MHC class I ,medicine ,Humans ,Ribosome profiling ,Melanoma ,biology ,Histocompatibility Antigens Class I ,Cancer ,Immunotherapy ,medicine.disease ,biology.protein ,Molecular Medicine ,Peptides ,Biotechnology - Abstract
Tumor-associated epitopes presented on MHC-I that can activate the immune system against cancer cells are typically identified from annotated protein-coding regions of the genome, but whether peptides originating from novel or unannotated open reading frames (nuORFs) can contribute to antitumor immune responses remains unclear. Here we show that peptides originating from nuORFs detected by ribosome profiling of malignant and healthy samples can be displayed on MHC-I of cancer cells, acting as additional sources of cancer antigens. We constructed a high-confidence database of translated nuORFs across tissues (nuORFdb) and used it to detect 3,555 translated nuORFs from MHC-I immunopeptidome mass spectrometry analysis, including peptides that result from somatic mutations in nuORFs of cancer samples as well as tumor-specific nuORFs translated in melanoma, chronic lymphocytic leukemia and glioblastoma. NuORFs are an unexplored pool of MHC-I-presented, tumor-specific peptides with potential as immunotherapy targets. New tumor epitopes are discovered by ribosome profiling and immunopeptidome mass spectrometry.
- Published
- 2020
14. Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy
- Author
-
Nicoletta Cieri, Donna Neuberg, Shuqiang Li, Neil G. Ruthen, Dana Pe'er, Haesook T. Kim, Christina Ennis, Robert J. Soiffer, Jerome Ritz, Cameron Y. Park, Zhongqi Ge, Vinhkhang N Nguyen, Katie Maurer, Zi-Ning Choo, Pavan Bachireddy, Edwin P. Alyea, Satyen H. Gohil, Derin B. Keskin, Cassandra Burdziak, Kenneth J. Livak, Elham Azizi, and Catherine J. Wu
- Subjects
T-Lymphocytes ,medicine.medical_treatment ,T cell ,Gene regulatory network ,ATAC-seq ,Biology ,Lymphocyte Activation ,Immunotherapy, Adoptive ,Article ,General Biochemistry, Genetics and Molecular Biology ,Donor lymphocyte infusion ,Clonal Evolution ,Cell therapy ,Transcriptome ,medicine ,Humans ,Transplantation, Homologous ,Longitudinal Studies ,Leukemia ,Immunotherapy ,medicine.disease ,Tissue Donors ,medicine.anatomical_structure ,Lymphocyte Transfusion ,Cancer research ,Neoplasm Recurrence, Local ,Stem Cell Transplantation - Abstract
Summary To elucidate mechanisms by which T cells eliminate leukemia, we study donor lymphocyte infusion (DLI), an established immunotherapy for relapsed leukemia. We model T cell dynamics by integrating longitudinal, multimodal data from 94,517 bone marrow-derived single T cell transcriptomes in addition to chromatin accessibility and single T cell receptor sequencing from patients undergoing DLI. We find that responsive tumors are defined by enrichment of late-differentiated T cells before DLI and rapid, durable expansion of early differentiated T cells after treatment, highly similar to “terminal” and “precursor” exhausted subsets, respectively. Resistance, in contrast, is defined by heterogeneous T cell dysfunction. Surprisingly, early differentiated T cells in responders mainly originate from pre-existing and novel clonotypes recruited to the leukemic microenvironment, rather than the infusion. Our work provides a paradigm for analyzing longitudinal single-cell profiling of scenarios beyond adoptive cell therapy and introduces Symphony, a Bayesian approach to infer regulatory circuitry underlying T cell subsets, with broad relevance to exhaustion antagonists across cancers.
- Published
- 2021
15. Local and Systemic Effects of Immune Checkpoint Blockade on Relapsed Myeloid Malignancies Following Allogeneic Hematopoietic Stem Cell Transplantation
- Author
-
Wandi Zhang, Srinika Ranasinghe, Donna Neuberg, Kenneth J. Livak, Jerome Ritz, Robert J. Soiffer, Livius Penter, Yi Zhang, Satyen H. Gohil, Shuqiang Li, Teddy Huang, Haesook T. Kim, Pavan Bachireddy, Robert Zeiser, Nicoletta Cieri, Alexandra Savell, X. Shirley Liu, Catherine J. Wu, and Matthew S. Davids
- Subjects
Oncology ,education.field_of_study ,medicine.medical_specialty ,Myeloid ,business.industry ,medicine.medical_treatment ,Immunology ,Population ,Ipilimumab ,Cell Biology ,Hematology ,Hematopoietic stem cell transplantation ,Biochemistry ,Transplantation ,Kite Pharma ,Immunophenotyping ,medicine.anatomical_structure ,Internal medicine ,Medicine ,Nivolumab ,education ,business ,medicine.drug - Abstract
Relapse after allogeneic hematopoietic stem cell transplantation (HSCT) remains an unmet medical need. The ETCTN 9204 study evaluated in 71 study subjects if immune checkpoint blockade with anti-CTLA-4 (Ipilimumab (Ipi), n = 43) or anti-PD-1 (Nivolumab (Nivo), n = 28) antibodies could stimulate graft-versus-leukemia (GvL) responses in this setting. We focused mainly on patients (pts) with relapsed AML/MDS, which constituted the majority of pts (n = 38; 54%). Ipi induced both long-term complete remissions (CR; n = 3) and transient CRs (TR; n = 3), while Nivo did not generate any CRs, but 4 patients demonstrated partial remissions (PR). To define the molecular features associated with response to Ipi, we performed bulk transcriptomic analyses of formalin-fixed paraffin-embedded biopsies of sites of AML/MDS involvement (n = 35) collected before and after Ipi treatment from 13 pts. Our analysis of matched pre- and post-Ipi samples of patients with CRs identified 50 differentially expressed genes. By gene ontology analysis, these were enriched for signatures of 'lymphocyte activation' and 'antigen-receptor signaling'. Principal component analysis using these genes separated post-Ipi CR samples as a distinct cluster, transcriptionally apart from pre-Ipi CR samples and from non-responder (NR, n = 15) pre and post-Ipi samples. Of note, post-Ipi CR samples were similar to both pre- and post-Ipi TR samples as well as samples from GvHD/toxicity biopsies (n = 9). Consistent with these findings, we detected increased CD8+ T cell abundance post-Ipi in CR but not NR samples with CIBERSORTx (pre vs post, median score 0.043 vs. 0.56, p < 0.01). Likewise, reconstruction of T cell receptor (TCR) CDR3 sequences using the tool TRUST showed an increase in TCR clonotypes per million reads post-Ipi in CR samples (pre vs post, median 0.33 vs. 1.65, p < 0.05). In sum, response to CTLA-4 blockade is characterized by transcriptional evidence of T cell infiltration and activation within the tumor microenvironment, with similar gene programs observed in the setting of GvHD. To determine if the changes within tissue sites following Ipi are also observed in peripheral blood (PB), we analyzed the immunophenotype and TCR repertoire of T cells from serially collected PB samples from pts with AML/MDS (n = 14) or non-myeloid malignancy (n = 6). In responders and non-responders, exposure to Ipi was associated with decreased naïve, increased effector memory, and increased expression of HLA-DR on central memory T cells (p < 0.05), consistent with T cell differentiation and activation. From 9 of 14 AML/MDS pts (CR = 4, NR = 5), bulk TCR sequencing before and after 1 cycle of Ipi yielded 572,017 PB TCR sequences. Only 776 clonotypes demonstrated significant change in frequency, and these TCRs were detected in greater proportion among responders (613/776 versus NR 163/776, p < 0.01). Thus, Ipi alters the differentiation states of circulating T cells irrespective of response and leads to higher TCR repertoire turnover in CR patients. Of the AML patients achieving PR following Nivo, we also observed transcriptional evidence of CD8+ T cell infiltration in one patient. This signature, however, was not detected in a second such patient. In a separate instance, we had the opportunity to dissect the molecular features of a partial response in a patient with JAK2V617F+ secondary AML following Nivo through single-cell RNA and ATAC-sequencing (scRNA-seq and scATAC-seq, 10x Genomics) of PB mononuclear cells collected serially across 6 timepoints. In total, we analyzed the transcriptomes and chromatin accessibility data from of 27,777 and 28,713 individual cells, respectively. At time of response, non-exhausted CD4+ T cells expanded while both exhausted CD8+ T cells and a malignant subpopulation with increased expression of PD-L1 and features of megakaryocytic differentiation preferentially contracted. The subsequent expansion of a PD-L1- malignant population at progression suggests that decreased leukemic PD-L1 expression was associated with relapse. Altogether, these data highlight the molecular and cellular features of successful reinvigoration of GvL using CTLA-4 blockade, from increased local T cell infiltration and activation in the leukemic microenvironment to peripheral T cell turnover. In addition, the selection of therapy-resistant subclones after PD-1 blockade underscores the need for further high-resolution studies of GvL responses. Disclosures Zeiser: Novartis: Honoraria; Incyte: Honoraria; Malinckrodt: Honoraria. Ritz:Rheos Medicines: Consultancy; LifeVault Bio: Consultancy; Infinity Pharmaceuticals: Consultancy; Falcon Therapeutics: Consultancy; Avrobio: Consultancy; Kite Pharma: Research Funding; Talaris Therapeutics: Consultancy; Equillium: Research Funding; Amgen: Research Funding; TScan Therapeutics: Consultancy. Neuberg:Madrigak Pharmaceuticals: Current equity holder in publicly-traded company; Celgene: Research Funding; Pharmacyclics: Research Funding. Soiffer:alexion: Consultancy; Gilead: Consultancy; Be the Match/ National Marrow Donor Program: Membership on an entity's Board of Directors or advisory committees; Rheos Therapeutics: Consultancy; Juno: Membership on an entity's Board of Directors or advisory committees; Novartis: Consultancy; Mana Therapeutics: Consultancy; Precision Bioscience: Consultancy; VOR Biopharma: Consultancy; Kiadis: Membership on an entity's Board of Directors or advisory committees; Cugene: Consultancy; Celgene: Membership on an entity's Board of Directors or advisory committees. Liu:GV20 Oncotherapy: Consultancy, Membership on an entity's Board of Directors or advisory committees; 3DMed Care: Consultancy; Sanofi: Research Funding; Takeda: Research Funding. Davids:AbbVie: Consultancy; Gilead Sciences: Consultancy; Sunesis: Consultancy; BeiGene: Consultancy; AstraZeneca: Consultancy, Research Funding; Syros Pharmaceuticals: Consultancy; Research to Practice: Honoraria; Pharmacyclics: Consultancy, Research Funding; TG Therapeutics: Consultancy, Research Funding; Verastem: Consultancy, Research Funding; Adaptive Biotechnologies: Consultancy; Janssen: Consultancy; Surface Oncology: Research Funding; Novartis: Consultancy, Research Funding; MEI Pharma: Consultancy, Research Funding; Genentech: Consultancy, Research Funding; Eli Lilly: Consultancy; Zentalis: Consultancy; Celgene: Consultancy; Bristol Myers Squibb: Research Funding; Merck: Consultancy; Ascentage Pharma: Consultancy, Research Funding. Wu:Pharmacyclics: Research Funding; BionTech: Current equity holder in publicly-traded company. OffLabel Disclosure: Ipilimumab and Nivolumab were tested in the setting of relapsed hematological malignancies after allogeneic stem cell transplantation.
- Published
- 2020
16. A large peptidome dataset improves HLA class I epitope prediction across most of the human population
- Author
-
Letitia Li, Thomas Eisenhaure, Derin B. Keskin, William J. Lane, Hasmik Keshishian, Nir Hacohen, Tamara Ouspenskaia, Christina R. Hartigan, Sune Justesen, Phuong M. Le, Steven A. Carr, Ioannis K. Zervantonakis, Karl R. Clauser, Pavan Bachireddy, David A. Braun, Keith L. Ligon, Jennifer M. Rosenbluth, Wandi Zhang, Catherine J. Wu, Travis Law, Guang Lan Zhang, Giacomo Oliveira, Jonathan Stevens, Susan Klaeger, and Siranush Sarkizova
- Subjects
Proteasome Endopeptidase Complex ,Proteome ,Population ,Amino Acid Motifs ,Biomedical Engineering ,Bioengineering ,Endogeny ,Peptide ,Human leukocyte antigen ,Computational biology ,Biology ,Ligands ,Applied Microbiology and Biotechnology ,Epitope ,Article ,Cell Line ,03 medical and health sciences ,Epitopes ,0302 clinical medicine ,Humans ,Allele ,education ,Databases, Protein ,Alleles ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,education.field_of_study ,Histocompatibility Antigens Class I ,Predictive value ,chemistry ,Genetic Loci ,Molecular Medicine ,Peptides ,030217 neurology & neurosurgery ,Algorithms ,Biotechnology ,Peptide Hydrolases - Abstract
Prediction of HLA epitopes is important for the development of cancer immunotherapies and vaccines. However, current prediction algorithms have limited predictive power, in part because they were not trained on high-quality epitope datasets covering a broad range of HLA alleles. To enable prediction of endogenous HLA class I-associated peptides across a large fraction of the human population, we used mass spectrometry to profile >185,000 peptides eluted from 95 HLA-A, -B, -C and -G mono-allelic cell lines. We identified canonical peptide motifs per HLA allele, unique and shared binding submotifs across alleles and distinct motifs associated with different peptide lengths. By integrating these data with transcript abundance and peptide processing, we developed HLAthena, providing allele-and-length-specific and pan-allele-pan-length prediction models for endogenous peptide presentation. These models predicted endogenous HLA class I-associated ligands with 1.5-fold improvement in positive predictive value compared with existing tools and correctly identified >75% of HLA-bound peptides that were observed experimentally in 11 patient-derived tumor cell lines.
- Published
- 2019
17. Abstract LT008: Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy
- Author
-
Donna Neuberg, Shuqiang Li, Jerome Ritz, Christina Ennis, Edwin P. Alyea, Robert J. Soiffer, Dana Pe'er, Vinhkhang N Nguyen, Kenneth J. Livak, Catherine J. Wu, Pavan Bachireddy, Cassandra Burdziak, Zi Ning Choo, and Elham Azizi
- Subjects
Cancer Research ,Tumor microenvironment ,medicine.medical_treatment ,T cell ,T-cell receptor ,Cancer ,Immunotherapy ,Biology ,medicine.disease ,Donor lymphocyte infusion ,Leukemia ,medicine.anatomical_structure ,Oncology ,Cancer research ,medicine ,Bone marrow - Abstract
Immune therapies have transformed the cancer therapeutic landscape but fail to benefit most patients. To elucidate the underlying mechanisms by which T cells mediate elimination of leukemia, we generated a high-resolution map of longitudinal T cell dynamics within the same tumor microenvironment (TME; bone marrow) during response or resistance to donor lymphocyte infusion (DLI), a widely used immunotherapy for relapsed leukemia. We analyzed 87,939 bone marrow-derived single T cell transcriptomes, along with chromatin accessibility and single T cell receptor clonality profiles, by developing novel machine learning tools for integrating longitudinal and multimodal data. We found that pre-treatment enrichment and post-treatment rapid, durable expansion of ‘terminal’ (TEX) and ‘precursor’ (TPEX) exhausted subsets, respectively, defined DLI response. In contrast to the common, shared pathways marking DLI response, a heterogeneous pattern of T cell dysfunction marked DLI resistance. Unexpectedly, TPEX cells that expanded in responders did not arise from the infusion product but instead from both pre-existing and novel clonotypes recruited to the TME. Further, we introduce a Bayesian method, Symphony, to define the T cell regulatory circuitry and master regulators underlying TEX and TPEX subsets that may be broadly relevant to other exhaustion antagonists across cancers. In conclusion, our data implicate the hierarchy of both TEX and TPEX subsets for immunotherapeutic responses in leukemia, extending the scope of their relevance beyond checkpoint blockade to adoptive cellular therapy. Moreover, our results provocatively suggest that immunologic ‘help’ from DLI, rather than direct transfer of anti-leukemic T cells, drove leukemic remission. Finally, we provide a general analysis paradigm for exploiting temporal single-cell genomic profiling for deep understanding of how immune therapies differentially shape the evolutionary trajectories of the TME in accordance with clinical outcome. Citation Format: Pavan Bachireddy, Elham Azizi, Cassandra Burdziak, Vinhkhang Nguyen, Christina Ennis, Zi- Ning Choo, Shuqiang Li, Kenneth Livak, Donna Neuberg, Robert Soiffer, Jerome Ritz, Edwin Alyea, Dana Pe'er, Catherine Wu. Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy [abstract]. In: Proceedings of the AACR Virtual Special Conference on the Evolving Tumor Microenvironment in Cancer Progression: Mechanisms and Emerging Therapeutic Opportunities; in association with the Tumor Microenvironment (TME) Working Group; 2021 Jan 11-12. Philadelphia (PA): AACR; Cancer Res 2021;81(5 Suppl):Abstract nr LT008.
- Published
- 2021
18. Splicing modulation sensitizes chronic lymphocytic leukemia cells to venetoclax by remodeling mitochondrial apoptotic dependencies
- Author
-
Matthew S. Davids, Fara Faye Regis, Mei Zheng, Michaela Gruber, Jing Sun, Lillian Werner, Laura Z. Rassenti, Jessica Wong, Angela N. Brooks, Anthony Letai, Lili Wang, Catherine J. Wu, Thomas J. Kipps, Michael P. Thomas, Robin Reed, Jing Deng, Matthew Meyerson, Ruben D. Carrasco, Michael Seiler, Ekaterina Kim, Elisa Ten Hacken, Shanye Yin, Jan A. Burger, Amy L. Gill, Pavan Bachireddy, Silvia Buonamici, Rebecca Valentin, Pete Smith, Emanuela M. Ghia, and Donna Neuberg
- Subjects
0301 basic medicine ,Male ,Adoptive cell transfer ,Lymphoma ,Chronic lymphocytic leukemia ,Drug Resistance ,Apoptosis ,Drug Screening Assays ,Transgenic ,chemistry.chemical_compound ,Mice ,immune system diseases ,hemic and lymphatic diseases ,Antineoplastic Combined Chemotherapy Protocols ,80 and over ,MCL1 ,Chronic ,Cancer ,Aged, 80 and over ,Sulfonamides ,Leukemia ,Heterocyclic ,General Medicine ,Hematology ,Middle Aged ,Lymphocytic ,Mitochondria ,medicine.anatomical_structure ,Proto-Oncogene Proteins c-bcl-2 ,RNA splicing ,Apoptosis inhibitors ,Female ,Macrolides ,RNA Splicing Factors ,Transcription ,Research Article ,Adult ,Spliceosome ,Primary Cell Culture ,Mice, Transgenic ,Thiophenes ,Therapeutics ,Biology ,03 medical and health sciences ,Splicing factor ,Bridged Bicyclo Compounds ,Rare Diseases ,Clinical Research ,Proto-Oncogene Proteins ,medicine ,Genetics ,Animals ,Humans ,neoplasms ,B cell ,Aged ,Venetoclax ,Animal ,B-Cell ,Antitumor ,medicine.disease ,Bridged Bicyclo Compounds, Heterocyclic ,Phosphoproteins ,Leukemia, Lymphocytic, Chronic, B-Cell ,Disease Models, Animal ,Alternative Splicing ,030104 developmental biology ,Pyrimidines ,Orphan Drug ,chemistry ,Drug Resistance, Neoplasm ,Disease Models ,Mutation ,Cancer research ,Spliceosomes ,Epoxy Compounds ,Neoplasm ,Myeloid Cell Leukemia Sequence 1 Protein ,Drug Screening Assays, Antitumor - Abstract
The identification of targetable vulnerabilities in the context of therapeutic resistance is a key challenge in cancer treatment. We detected pervasive aberrant splicing as a characteristic feature of chronic lymphocytic leukemia (CLL), irrespective of splicing factor mutation status, which was associated with sensitivity to the spliceosome modulator, E7107. Splicing modulation affected CLL survival pathways, including members of the B cell lymphoma-2 (BCL2) family of proteins, remodeling antiapoptotic dependencies of human and murine CLL cells. E7107 treatment decreased myeloid cell leukemia-1 (MCL1) dependence and increased BCL2 dependence, sensitizing primary human CLL cells and venetoclax-resistant CLL-like cells from an Eμ-TCL1-based adoptive transfer murine model to treatment with the BCL2 inhibitor venetoclax. Our data provide preclinical rationale to support the combination of venetoclax with splicing modulators to reprogram apoptotic dependencies in CLL for treating venetoclax-resistant CLL cases.
- Published
- 2018
19. A Novel Approach To Identify Genetic Signatures Of Clinical Outcome To Ipilimumab
- Author
-
Sachet A. Shukla, Pavan Bachireddy, and Catherine J. Wu
- Subjects
Oncology ,medicine.medical_specialty ,business.industry ,Internal medicine ,medicine ,Ipilimumab ,business ,Outcome (game theory) ,medicine.drug - Published
- 2018
20. Clinical and Immunologic Activity of Ipilimumab Following Decitabine Priming in Post-Allogeneic Transplant and Transplant-Naïve Patients with Relapsed or Refractory Myelodysplastic Syndromes and Acute Myeloid Leukemia: A Multi-Center Phase 1, Two-Arm, Dose-Escalation Study
- Author
-
Jacqueline S. Garcia, Howard Streicher, Michael K Keng, Robert J. Soiffer, Corey Cutler, Mariano Severgnini, Stephanie Andrews, Eric S. Winer, Matthew S. Davids, Jerome Ritz, Ryan C. Brennick, Yael Flamand, Marlise R. Luskin, Alexandra Savell, Ana Lako, Yohei Arihara, Claire Manuszak, Andreas Kantartzis, Richard Stone, Benjamin Tomlinson, Edwin P. Alyea, Vincent T. Ho, Nicole Cullen, Lillian Werner, Myrna Nahas, Pavan Bachireddy, David P. Steensma, R. Coleman Lindsley, Andrew M. Brunner, Catherine J. Wu, Scott J. Rodig, Martha Wadleigh, Samer K. Khaled, Donna Neuberg, Daniel J. DeAngelo, and Ilene Galinsky
- Subjects
Oncology ,medicine.medical_specialty ,business.industry ,Myelodysplastic syndromes ,medicine.medical_treatment ,Immunology ,Myeloid leukemia ,Decitabine ,Ipilimumab ,Cell Biology ,Hematology ,medicine.disease ,Biochemistry ,Transplantation ,Photopheresis ,Refractory ,Internal medicine ,medicine ,business ,Febrile neutropenia ,medicine.drug - Abstract
Background: Patients (pts) with MDS or AML who relapse after allogeneic transplantation (allo-HCT) have a very poor prognosis. Hypomethylating agents (HMA) and checkpoint blockade with the anti-CTLA4 blocking antibody ipilimumab (IPI) have each induced responses with acceptable toxicity in AML pts who relapse after allo-HCT. We hypothesized that adding decitabine (DAC) would improve response compared with IPI alone by activating and promoting T cell-mediated anti-leukemic immune reactivity. We are conducting a multicenter phase I study (CTEP 10026) of DAC plus IPI in pts with R/R MDS/AML in both post allo-HCT and transplant-naïve settings to assess safety and estimate efficacy. Methods: The primary objective is to determine the maximum tolerated dose (MTD) or RP2D of combination DAC + IPI in pts with R/R MDS/AML who are post allo-HCT (Arm A) or transplant-naïve (Arm B). Cohorts of 3-6 are sequentially enrolled in 3 dose levels (DL) of IPI using a 3+3 design with expansion in each arm; DLs 0-2 are 3, 5 and 10 mg/kg, respectively. Eligibility for both arms: relapsed AML (extramedullary or ≥ 5% blasts) or R/R MDS (≥ 5% blasts) or unfit elderly AML; Arm A only: ≥ 2 wks off systemic immunosuppressive (IS) therapy, T cell chimerism ≥ 20%, and no prior acute GVHD ≥ gr III. DLT is defined as ≥ gr 3 non-heme, ≥ gr 3 acute GVHD or ≥ gr 3 steroid-refractory immune-related adverse events (AEs) occurring within 8 weeks from first IPI dose. Epigenetic priming with DAC lead-in cycle 0 was followed by combination cycles of DAC + IPI. DAC is given at 20 mg/m2 days 1-5 q 28 days. IPI is given on day 1 of cycles 1-4 and every other cycle in cycles 5-12. Pts who discontinued study either in cycle 0 or DLT period without IPI-toxicity were replaced. Arm A opened after safety was confirmed at DL0 in Arm B. Results: As of June 9, 2019, 26 pts (15M, 11 F) have enrolled in this on-going trial. Of the 12 pts (11 AML and 1 MDS) enrolled in Arm A (post allo-HCT), median age was 66.5 (range 29-74) and 9 had previously received HMA. 7 of 8 pts in DL0 (1 progressed in cycle 0) and 3 of 4 pts in DL1 (1 died from pneumonia in cycle 0) received DAC + IPI. DL0 was expanded to 6 to confirm safety without DLT. Median treatment duration after first IPI dose was 5 cycles (range 1-7); 4 pts continue on trial. Common AEs were gr 1-2 dyspnea (n=4), gr 1-3 fatigue (n=4), and gr 1-2 fever (n=4). Gr 3 AEs were febrile neutropenia (n=2), pneumonia (n=1), and candidemia (n=1). Gr 1 immune-related dermatitis (n=1) reversed with steroids. Acute GVHD was not observed. Moderate-severe chronic GVHD was noted in 2 pts mainly involving skin, which was responsive to photopheresis and oral IS. Though 1 CR and 1 marrow CR have been observed at DL0, dose-escalation up to DL2 is on-going to determine MTD. Of the 14 pts (11 AML and 3 MDS) enrolled in Arm B (transplant naïve), median age was 75.5 (range 34-82) and 9 had previously received HMA. 4 of 6 pts in DL0 (1 progressed and 1 withdrew in cycle 0), 3 of 5 pts in DL1 (2 withdrew in cycle 0) and 3 of 3 pts in DL2 received DAC + IPI. Median treatment duration after first IPI dose was 4 cycles (range 1-8); 3 pts remain on study. Common AEs were gr 1-3 fatigue (n=9), gr 1-2 anorexia (n=5), and gr 3 febrile neutropenia (n=8). Immune-related gr 2 colitis (n=1) and gr 2/3 (n=4) dermatitis were all steroid-responsive. Of the 10 pts who received at least one IPI dose, 5 (50%) achieved an objective response including 3 CR, 1 CRi and 1 PR. All responses were observed in AML pts, including 1 with only skin involved. Expansion to confirm MTD is underway. No treatment-related deaths or DLTs were observed in either Arm. Reasons for discontinuation after IPI: progression (n=9), proceeding to allo-HCT or DLI (n=2), withdrawal (n=1), stroke due to underlying atrial fibrillation (n=1) and disseminated nocardiosis (n=1). In both Arms, multiplex immunofluorescence (MIF) staining of BM biopsies revealed a higher density of CD3+CD4+ cells after 4 cycles of DAC + IPI in 4 responders (R) compared to 4 non-responders (NR) (p=0.0433). Longitudinal MIF IHC in an Arm B responder identified the increasing presence of a tumor immune infiltrate composed of CD3+CD8+GZMB+ T cells prior to achieving CR (Fig 1). Conclusions: Combination DAC + IPI is tolerable and has encouraging clinical activity in post allo-HCT and transplant naïve pts with R/R MDS/AML. Ongoing studies focus on comparing the immunologic and genetic characteristics of the tumor immune infiltrate in each cohort to understand the contribution of alloimmunity to treatment response. Disclosures Garcia: Abbvie: Research Funding; Genentech: Research Funding. Keng:agios: Membership on an entity's Board of Directors or advisory committees. Brunner:Jazz Pharma: Membership on an entity's Board of Directors or advisory committees; Forty Seven Inc: Membership on an entity's Board of Directors or advisory committees; Novartis: Research Funding; Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Astra Zeneca: Research Funding. Khaled:Omeros: Consultancy; Alexion: Consultancy, Speakers Bureau; Daiichi Sankyo: Other: Travel support. Steensma:H3 Biosciences: Other: Research funding to institution, not investigator.; Arrowhead: Equity Ownership; Onconova: Consultancy; Stemline: Consultancy; Aprea: Research Funding; Pfizer: Consultancy; Summer Road: Consultancy; Astex: Consultancy. Winer:Jazz Pharmaceuticals, Pfizer: Consultancy. Cutler:Omeros: Consultancy; Kadmon: Consultancy; BiolineRx: Other: DSMB; Cellect: Other: DSMB; Kalytera: Other: DSMB; ElsaLys: Consultancy; Genentech: Consultancy; Pharmacyclics: Consultancy; Fate Therapeutics: Consultancy; Incyte: Consultancy; Jazz: Consultancy; BMS: Consultancy. Ho:Omeros Corporation: Membership on an entity's Board of Directors or advisory committees; Jazz Pharmaceuticals: Research Funding; Jazz Pharmaceuticals: Consultancy. Neuberg:Madrigal Pharmaceuticals: Equity Ownership; Pharmacyclics: Research Funding; Celgene: Research Funding. Lindsley:Takeda Pharmaceuticals: Consultancy; Jazz Pharmaceuticals: Research Funding; Medlmmune: Research Funding. Galinsky:ABIM: Other: Member of specialty oncology board; Merus Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; AbbVie Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Pfizer Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees. Ritz:TScan Therapeutics: Consultancy; LifeVault Bio: Consultancy; Kite Pharma: Research Funding; Talaris Therapeutics: Consultancy; Draper Labs: Consultancy; Avrobio: Consultancy; Celgene: Consultancy; Merck: Research Funding; Equillium: Research Funding; Aleta Biotherapeutics: Consultancy. Davids:AbbVie, Acerta Pharma, Adaptive, Biotechnologies, Astra-Zeneca, Genentech, Gilead Sciences, Janssen, Pharmacyclics, TG therapeutics: Membership on an entity's Board of Directors or advisory committees; AbbVie, Astra-Zeneca, Genentech, Janssen, MEI, Pharmacyclics, Syros Pharmaceuticals, Verastem: Consultancy; Acerta Pharma, Ascentage Pharma, Genentech, MEI pharma, Pharmacyclics, Surface Oncology, TG Therapeutics, Verastem: Research Funding; Research to Practice: Honoraria. Wu:Pharmacyclics: Research Funding; Neon Therapeutics: Other: Member, Advisory Board. Stone:AbbVie, Actinium, Agios, Argenx, Arog, Astellas, AstraZeneca, Biolinerx, Celgene, Cornerstone Biopharma, Fujifilm, Jazz Pharmaceuticals, Amgen, Ono, Orsenix, Otsuka, Merck, Novartis, Pfizer, Sumitomo, Trovagene: Consultancy; Argenx, Celgene, Takeda Oncology: Other: Data and Safety Monitoring Board/Committee: ; Novartis, Agios, Arog: Research Funding. DeAngelo:Blueprint: Consultancy, Research Funding; Novartis: Consultancy, Research Funding; Abbvie: Research Funding; Glycomimetics: Research Funding; Amgen, Autolus, Celgene, Forty-seven, Incyte, Jazzs, Pfizer, Shire, Takeda: Consultancy. Soiffer:Jazz: Consultancy; Gilead, Mana therapeutic, Cugene, Jazz: Consultancy; Juno, kiadis: Membership on an entity's Board of Directors or advisory committees, Other: DSMB; Kiadis: Other: supervisory board; Mana therapeutic: Consultancy; Cugene: Consultancy. OffLabel Disclosure: Combination of ipilimumab and decitabine for MDS/AML treatment for patients who are post-transplant or transplant naive
- Published
- 2019
21. Distinct Evolutionary Patterns in Chronic Lymphocytic Leukemia (CLL) during Resistance to Graft-Versus-Leukemia (GvL)
- Author
-
Peter V. Kharchenko, Jerome Ritz, Gad Getz, Samuel S. Freeman, Jennifer R. Brown, Donna Neuberg, Christina Ennis, Ignaty Leshchiner, Pavan Bachireddy, Satyen H. Gohil, Natalie Bavli, Vincent T. Ho, Nikolas Barkas, Kendell Clement, Catherine J. Wu, Liudmila Elagina, Edwin P. Alyea, Robert J. Soiffer, Vinhkhang N Nguyen, and Sachet A. Shukla
- Subjects
Graft-vs-Leukemia Effect ,business.industry ,Chronic lymphocytic leukemia ,Immunology ,Cancer ,Cell Biology ,Hematology ,Human leukocyte antigen ,medicine.disease ,Biochemistry ,Chemotherapy regimen ,Leukemia ,medicine ,Cancer research ,Stem cell ,business ,Protein p53 - Abstract
The factors mediating GvL resistance following allogeneic stem cell transplant (SCT) in lymphoid malignancies remain incompletely characterized. Because cell-intrinsic features shape chemotherapeutic relapse, we hypothesized that they also shape GvL outcomes by influencing evolutionary trajectories of CLL relapse after reduced intensity conditioning SCT (RIC). We identified 9 heavily pre-treated patients (pts) (range: 1-5 therapies, median: 3) with various times to CLL relapse after RIC (range: 83-1825 days), of which 8 had at least partial responses before relapse. To define evolutionary trajectories, we generated paired whole-exome and RNA sequencing data from purified CLL cells pre/post-RIC, using MuTect2 and ABSOLUTE algorithms to identify somatic alterations (SAs) and corresponding cancer cell fractions (CCFs). 5 pts had clonal SAs in TP53 and/or SF3B1 pre-SCT, and no single SA was specific to post-RIC. Furthermore, we found no SAs nor altered expression of HLA class I/II or b2M in either baseline or post-RIC samples. However, we found 6 relapse pairs to exhibit complex branched evolution involving CCF shifts of at least 0.2 in subclonal and clonal SAs whereas 3 pairs showed genomic stability. Clonal evolution was associated with longer time to relapse (Wilcoxon, p=0.02; median 798 versus 304 days) as well as complete response (p=0.05), suggesting that GvL immune escape may be facilitated by clonal evolution. To determine the phenotypic consequences of clonal evolution, we examined single cell transcriptomes using scRNAseq from paired pre/post-RIC CLL cells from 2 pts with early (304, 442 days; "ERs") and 2 pts with late (1801, 1825 days; "LRs") relapses after RIC. Using the inDrop platform, we profiled a median of 3560 CLL cells/pt (range: 2254-5278). Clustering using Seurat revealed marked transcriptional stability after RIC in ERs whereas dramatic shifts in gene expression programs were observed in LRs. Single cell trajectory analysis using Monocle identified ordered biological processes through which LRs, but not ERs, progressed. Branched expression analysis revealed multiple patient specific pathways defining LRs, including within chromatin regulators (EBF1, BANK1), oncogenic pathways (AFF3, DENND4A) and ribosomal biosynthesis (EEF1G, NACA). Thus, genetic evolution in LRs results in distinct phenotypic consequences. To directly link SAs with transcriptional outcomes, we interrogated scRNAseq data for known SAs identified by WES. In one LR, loss of a CLL cancer driver (RPS15mut) was observed in two of three post-RIC transcriptional clusters, either through deletion of chr.19p (where RPS15 resides) or reversion to the wildtype allele (implying loss of heterozygosity). In addition, genomic and transcriptional loss of HLA genes were detectable in pre-RIC clusters that failed to expand at relapse in both LRs, suggesting that pre-existing HLA loss does not provide a selective advantage for CLL relapse after RIC, consistent with our bulk analyses. These data highlight how scRNAseq can delineate genetic selection pressures within subpopulations of a single patient. To investigate whether epigenetic dysregulation underlies these genetic changes, we measured locally disordered methylation (LDM), a known epigenetic mechanism of CLL genetic variability. Genome-wide methylome profiles revealed increases in LDM in LRs compared to ERs for various genomic regions (Kruskal-Wallis (KW), p Altogether, these data highlight important features of GvL resistance in CLL: 1) GvL selective pressure, shown by LRs, can shape evolutionary trajectories through genotypic alterations that directly exert phenotypic consequences; 2) alterations in HLA genes have less influence in CLL than in myeloid malignancies; and 3) GvL immune editing may select for epigenetic variability that facilitates evasion through stem-like states. Disclosures Brown: Octapharma: Consultancy; Novartis: Consultancy; Loxo: Consultancy, Research Funding; Kite: Consultancy, Research Funding; Janssen: Honoraria; Invectys: Other: other; Gilead: Consultancy, Research Funding; Genentech/Roche: Consultancy; Dynamo Therapeutics: Consultancy; Catapult Therapeutics: Consultancy; BeiGene: Consultancy; AstraZeneca: Consultancy; Acerta Pharma: Consultancy; Morphosys: Other: Data safety monitoring boards ; Sun Pharmaceuticals, Inc: Research Funding; Sun: Research Funding; Verastem: Consultancy, Research Funding; TG Therapeutics: Consultancy; Teva: Honoraria; Sunesis: Consultancy; Pharmacyclics: Consultancy; Pfizer: Consultancy. Getz:MuTect, ABSOLTUE, MutSig and POLYSOLVER: Patents & Royalties: MuTect, ABSOLTUE, MutSig and POLYSOLVER; IBM: Research Funding; Pharmacyclics: Research Funding. Ho:Jazz Pharmaceuticals: Consultancy; Jazz Pharmaceuticals: Research Funding; Omeros Corporation: Membership on an entity's Board of Directors or advisory committees. Neuberg:Celgene: Research Funding; Pharmacyclics: Research Funding; Madrigal Pharmaceuticals: Equity Ownership. Soiffer:Gilead, Mana therapeutic, Cugene, Jazz: Consultancy; Jazz: Consultancy; Kiadis: Other: supervisory board; Mana therapeutic: Consultancy; Cugene: Consultancy; Juno, kiadis: Membership on an entity's Board of Directors or advisory committees, Other: DSMB. Ritz:TScan Therapeutics: Consultancy; Equillium: Research Funding; Merck: Research Funding; Kite Pharma: Research Funding; Aleta Biotherapeutics: Consultancy; Celgene: Consultancy; Avrobio: Consultancy; LifeVault Bio: Consultancy; Draper Labs: Consultancy; Talaris Therapeutics: Consultancy. Wu:Neon Therapeutics: Other: Member, Advisory Board; Pharmacyclics: Research Funding.
- Published
- 2019
22. T Cell Determinants of Response and Resistance to PD-1 Blockade in Richter's Transformation
- Author
-
Aina Zurita Martinez, Donna Neuberg, William G. Wierda, Lars Rønn Olsen, Gad Getz, Nitin Jain, Peter V. Kharchenko, Shuqiang Li, Kenneth Livak, Ana Lako, Scott J. Rodig, Catherine J. Wu, Camilla Koldbæk Lemvigh, Ignaty Leshchiner, Giacomo Oliveira, Erin M. Parry, Lillian Werner, Annabelle J. Anandappa, Pavan Bachireddy, Noelia Purroy, Satyen H. Gohil, and Teddy Huang
- Subjects
Chemistry ,T cell ,Chronic lymphocytic leukemia ,Immunology ,T-cell receptor ,Cell Biology ,Hematology ,medicine.disease ,Biochemistry ,Richter's transformation ,medicine.anatomical_structure ,Cancer research ,medicine ,Pd 1 blockade ,Bone marrow specimen ,health care economics and organizations - Abstract
Despite advances in the treatment of chronic lymphocytic leukemia (CLL), the transformation of CLL to an aggressive lymphoma, or Richter's transformation (RT), remains a clinical challenge, as it responds poorly to standard therapies and shortens survival. Recent studies demonstrate that RT, but not underlying CLL, responds to PD-1 checkpoint blockade (CPB) with an overall response rate of 43-65%. Given the central role of T cells in anti-tumor immunity, we hypothesized that differences in T cell populations underlie response and resistance to CPB in RT. We focused on a discovery cohort of 6 patients with RT (4 responders, 2 non-responders) and 2 patients with relapsed/refractory CLL enrolled on a study in which patients were initiated with anti-PD1 therapy (nivolumab 3 mg/kg every 2 weeks), with subsequent concurrent ibrutinib (420 mg daily)(NCT 02420912). We examined a total of 15 serial study marrow specimens collected at treatment initiation and 3 month response evaluation, as well as 2 healthy marrow donors. To systematically discover the T cell populations and states associated with CPB response in RT, we performed single-cell RNA-sequencing (scRNA-seq, 10x Genomics) of non-lymphoma (CD5-CD19-) cells isolated by flow cytometry from marrow samples. A total of 60,727 T and NK cells were captured with average detection of 1001 genes/cell. Using the novel joint clustering approach Conos, 11 transcriptionally distinct clusters of lymphocytes were identified. We first contrasted baseline RT/CLL with normal marrow and observed differences across T cell populations, which we confirmed through the examination of publicly available marrow scRNA-seq data from 28 healthy donors. Compared to normal marrow, RT/CLL marrow was enriched for cytotoxic populations, including both CD8 effector/effector memory (E/EM) (p=0.001, t-test) and cytotoxic CD4 (p=0.001) T cells as well as for cells expressing multiple exhaustion markers, including PDCD1, LAG3 and TIGIT (p=0.001). In contrast, normal marrow contained increased T cells with a naïve-like phenotype (p=0.06). When we focused on the pre-treatment samples from RT patients, RT responders had a larger CD8 E/EM population (p=0.04) and fewer T regulatory cells (p=0.006, t-test) than RT non-responders. Using DESeq2 to compare clusters from all samples, we evaluated if there were differences in gene expression between RT responders and non-responders. CD8 E/EM T cells of RT non-responders showed increased expression of TOX, a recently uncovered master regulator of cell exhaustion (padj =0.00016), while this cell subtype in RT responders upregulated a contrasting program of activating transcription factors as well as the co-stimulatory gene CD226 (padj =0.04). As for CD4 T cells, RT responders revealed an enriched cytotoxic gene program compared to RT non-responders (padjPRF1 5.9 x 10-10, GZMH 6.0 x 10-6, NKG7 6.4 x 10-19). To investigate whether response to CPB therapy for RT was associated with changes in the T cell receptor (TCR) repertoire, and to obtain protein-level validation of transcriptional signatures, we performed single-cell TCR sequencing with paired gene and protein expression (10x Genomics) on pre- and post-therapy samples from a RT responder and a non-responder. Indeed, we confirmed our gene expression findings, including validation of cytotoxic CD4 T cells and the enrichment of CD226 protein in E/EM CD8 T cells in the RT responder. TCR clonal expansion was observed in the RT responder at baseline with persistence of enriched clonotypes following CPB, suggesting the presence of tumor-reactive T cell clones. In contrast, the RT non-responder displayed higher TCR diversity with enriched clonotypes showing increased exhaustion post-CPB (p In conclusion, we identified marrow T cell populations enriched in RT patients and described distinct T cell transcriptional programs that delineate RT responders from non-responders. We have thus discovered candidate gene biomarkers that may identify patients likely to respond to CPB therapies and uncovered a CD8 E/EM T cell population that is likely to underlie response to PD-1 CPB. Disclosures Getz: Pharmacyclics: Research Funding; IBM: Research Funding; MuTect, ABSOLTUE, MutSig and POLYSOLVER: Patents & Royalties: MuTect, ABSOLTUE, MutSig and POLYSOLVER. Neuberg:Celgene: Research Funding; Madrigal Pharmaceuticals: Equity Ownership; Pharmacyclics: Research Funding. Rodig:Bristol Myers Squib: Consultancy, Honoraria, Other: Travel Expenses, Speakers Bureau; Kite, a Gilead Company: Research Funding; Affirmed: Research Funding; Merck: Research Funding. Wierda:KITE pharma: Research Funding; Gilead Sciences: Research Funding; AbbVie: Research Funding; Acerta Pharma Inc: Research Funding; Genentech: Research Funding; GSK/Novartis: Research Funding; Pharmacyclics LLC: Research Funding; Sunesis: Research Funding; Miragen: Research Funding; Oncternal Therapeutics Inc.: Research Funding; Cyclcel: Research Funding; Loxo Oncology Inc.: Research Funding; Janssen: Research Funding; Xencor: Research Funding; Juno Therapeutics: Research Funding. Jain:AbbVie: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Verastem: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Incyte: Research Funding; AstraZeneca: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Servier: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Cellectis: Research Funding; Janssen Pharmaceuticals, Inc.: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Pharmacyclics, an AbbVie company: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Precision Biosciences: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Adaptive Biotechnologies: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Pfizer: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; ADC Therapeutics: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Genentech: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; BMS: Research Funding. Wu:Neon Therapeutics: Other: Member, Advisory Board; Pharmacyclics: Research Funding.
- Published
- 2019
23. Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade
- Author
-
Andreas Gnirke, Bastian Schilling, Qian Zhan, Dirk Schadendorf, Alexander Meissner, Taha Merghoub, Levi A. Garraway, George F. Murphy, Patrick Ryan Potts, Nir Hacohen, Ying Huang, Patrick C. Lee, Diana Miao, Clyde Bango, Arman W. Mohammad, Christine G. Lian, Catherine J. Wu, Jedd D. Wolchok, Daniel Gusenleitner, Eliezer M. Van Allen, Derin B. Keskin, Donna Neuberg, Pavan Bachireddy, Rupert Langer, Christina Galonska, Kendell Clement, Zachary J. Cartun, Jeffrey S. Weber, Alexandra Snyder, Mehrtash Babadi, F. Stephen Hodi, and Sachet A. Shukla
- Subjects
0301 basic medicine ,Male ,Skin Neoplasms ,medicine.medical_treatment ,Medizin ,chemical and pharmacologic phenomena ,Mice, Transgenic ,General Biochemistry, Genetics and Molecular Biology ,Article ,Epigenesis, Genetic ,03 medical and health sciences ,Mice ,Antigens, Neoplasm ,Cell Line, Tumor ,Neoplasms ,medicine ,Autophagy ,Animals ,Humans ,CTLA-4 Antigen ,610 Medicine & health ,Melanoma ,Germ-Line Mutation ,biology ,Gene Expression Profiling ,Antibodies, Monoclonal ,hemic and immune systems ,Immunotherapy ,DNA Methylation ,medicine.disease ,Ipilimumab ,Immune checkpoint ,Ubiquitin ligase ,Blockade ,Gene expression profiling ,030104 developmental biology ,CTLA-4 ,biology.protein ,Cancer research ,570 Life sciences ,Female ,Melanoma-Specific Antigens - Abstract
CTLA-4 immune checkpoint blockade is clinically effective in a subset of patients with metastatic melanoma. We identify a subcluster of MAGE-A cancer-germline antigens, located within a narrow 75 kb region of chromosome Xq28, that predicts resistance uniquely to blockade of CTLA-4, but not PD-1. We validate this gene expression signature in an independent anti-CTLA-4-treated cohort and show its specificity to the CTLA-4 pathway with two independent anti-PD-1-treated cohorts. Autophagy, a process critical for optimal anti-cancer immunity, has previously been shown to be suppressed by the MAGE-TRIM28 ubiquitin ligase in vitro. We now show that the expression of the key autophagosome component LC3B and other activators of autophagy are negatively associated with MAGE-A protein levels in human melanomas, including samples from patients with resistance to CTLA-4 blockade. Our findings implicate autophagy suppression in resistance to CTLA-4 blockade in melanoma, suggesting exploitation of autophagy induction for potential therapeutic synergy with CTLA-4 inhibitors.
- Published
- 2018
- Full Text
- View/download PDF
24. Oncogenes and the Initiation and Maintenance of Tumorigenesis
- Author
-
Constadina Arvanitis, Pavan K. Bendapudi, Pavan Bachireddy, and Dean W. Felsher
- Subjects
Genetically modified mouse ,Angiogenesis ,Cell ,Mutant ,Cancer ,Biology ,medicine.disease_cause ,Oncogene Addiction ,medicine.disease ,medicine.anatomical_structure ,medicine ,Cancer research ,Carcinogenesis ,Gene - Abstract
Cancer is a complex and multistep process whereby an individual cell acquires a series of mutant gene products culminating in a spectrum of pathophysiologic features including relentless proliferation, growth, blocked differentiation, the inappropriate induction of angiogenesis, tissue invasion, and loss of genomic stability. Given the genetic and biologic complexity of tumorigenesis, it is perhaps surprising that there are circumstances when cancer can be reversed through the repair or inactivation of individual mutant genes. However, recent experiments in transgenic mouse models and clinical results using new pharmacological agents demonstrate that cancer can be treated through the targeted repair and/or inactivation of specific oncogenes. Hence, cancers appear to be dependent upon particular oncogenes to maintain their neoplastic properties, thus exhibiting the phenomena tumor maintenance or oncogene addiction.
- Published
- 2016
25. Abstract 566: Neoantigens from translated unannotated open reading frames in cancer
- Author
-
Siranush Sarkizova, Wandi Zhang, Phuong M. Le, Steven A. Carr, Travis Law, Derin B. Keskin, Tamara Ouspenskaia, Yuen Ting Chow, Elena Christian, Zhe Ji, Pavan Bachireddy, Joshua Gould, Susan Klaeger, Aviv Regev, Catherine J. Wu, Nir Hacohen, Karl R. Clauser, and Bo Li
- Subjects
Untranslated region ,Genetics ,Cancer Research ,Cancer ,Human leukocyte antigen ,Biology ,Major histocompatibility complex ,medicine.disease ,Oncology ,Antigen ,Cancer cell ,MHC class I ,biology.protein ,medicine ,Ribosome profiling - Abstract
Somatic mutations in cancer cells can generate neoantigens which can be recognized by immune cells and trigger an immune response. Patients vaccinated with neoantigen-based peptides display expanded neoantigen-specific T cells, suggesting that this could be a promising avenue for cancer treatment. Currently, neoantigen predictions are based on mutations detected by whole exome sequencing, which covers a pre-determined set of annotated exons, and often falls short for cancers with few somatic mutations. Ribosome profiling (Ribo-seq), which allows to monitor mRNA translation, has predicted a plethora of translated novel unannotated ORFs (nuORFs). Here we hypothesized that nuORFs can provide another source of neoantigens in cancer cells. In particular, we focused on nuORFs in the following categories: 1) nuORFs expressed in healthy and cancer cells, that have acquired tumor-specific somatic mutations; 2) nuORFs upregulated in or specific to cancer cells. To explore this hypothesis, we performed Ribo-seq on primary healthy and cancer cells and cell lines from melanoma, glioblastoma, colon carcinoma and chronic lymphocytic leukemia. Using this extensive dataset, we performed hierarchical ORF prediction analysis to build a database of highest confidence predicted translated nuORFs across healthy and cancer cell types. To determine if peptides from nuORFs can be a source of antigens, we searched our collection of mono-allelic MHC class I immunopeptidome mass spectrometry (MS) spectra from 94 common HLA alleles against our pan-tissue nuORF database. Additionally, we performed MHC class I immunoprecipitation followed by MS on the same cells used for Ribo-seq. We found HLA-presented unmutated peptides derived from thousands of nuORFs, found within, but out-of-frame with annotated protein-coding ORFs, within 5’ and 3’ untranslated regions of annotated protein-coding transcripts, long non-coding RNAs (lncRNAs), pseudogenes, and other RNA species. The HLA-binding motifs of peptides from nuORFs correspond to the expected motifs for given HLA types, indicating that 1) nuORFs are translated and 2) nuORF-derived peptides are presented on MHC I. To identify tumor-specific somatic mutations in nuORFs, we performed whole genome sequencing on patient-matched healthy and cancer cells and mapped somatic mutations to annotated ORFs and nuORFs. Finally, to identify nuORFs upregulated in or specific to cancer cells, we compared translation levels of nuORFs between healthy and cancer cells of the same origin. We found translated nuORFs with cancer-specific somatic mutations and nuORFs highly upregulated in and specific to cancer cells, suggesting that they can give rise to neoantigens. In conclusion, nuORFs are translated, contribute peptides to MHC I presentation, acquire somatic mutations, are expressed in tissue- and cancer-dependent manner and should be considered in the search for neoantigens in cancer. Citation Format: Tamara Ouspenskaia, Travis E. Law, Karl R. Clauser, Susan Klaeger, Derin B. Keskin, Bo Li, Elena Christian, Yuen Ting Chow, Phuong M. Le, Joshua Gould, Zhe Ji, Wandi Zhang, Pavan Bachireddy, Siranush Sarkizova, Nir Hacohen, Steven A. Carr, Catherine J. Wu, Aviv Regev. Neoantigens from translated unannotated open reading frames in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 566.
- Published
- 2019
26. Abstract 3371: Mapping the evolution of T cell states during DLI response and resistance using single-cell data and computational tools
- Author
-
Elham Azizi, Pavan Bachireddy, Vinhkhang N. Nguyen, Shuqiang Li, Donna S. Neuberg, Robert J. Soiffer, Jerome Ritz, Edwin P. Alyea, Dana Pe'er, and Catherine J. Wu
- Subjects
Cancer Research ,Oncology - Abstract
Donor lymphocyte infusion (DLI) is a standard of care and potentially curative immunotherapy for relapsed leukemia after allogeneic hematopoietic stem cell transplant (allo-SCT). Despite low response rates for many leukemias, chronic myelogenous leukemia (CML) has historically exhibited an exquisite DLI sensitivity, and we previously reported that durable response to DLI was associated with reversal of exhaustion of bone marrow (BM) -infiltrating T cells (Bachireddy et al., Blood 2014). Critical questions remain, however, regarding the exact transcriptional states of those T cell subtypes mediating exhaustion, anti-leukemia responses, and resistance to DLI. To map evolving phenotypic T cell states in situ at single cell resolution, we profiled viable cells isolated from cryopreserved BM mononuclear cells from a median of 3 timepoints before and after DLI from 12 patients with relapsed CML after allo-SCT, including 6 long-term responders to DLI (R’s) and 6 nonresponders (NR’s), using single cell RNA sequencing (scRNA-seq). Using our computational tools for processing and analyzing scRNA-seq data (Azizi et al., Cell 2018), we detected 381,462 cells in total derived from 43 unique patient-timepoints that met our quality metrics. Because DLI’s anti-leukemic efficacy derives in large part from T cell activity, we sought a more refined characterization of T cells using our tool Biscuit (Azizi et al., Cell 2018) to merge, normalize and cluster T cells. We observed a marked increase in the number of T cell clusters in post-DLI samples compared to matched pre-DLI samples (p Comparing T cell exhaustion between R vs NR cases, we confirmed increased T cell exhaustion signatures in R-pre T cells. Using factor analysis techniques we found that anergy, dysfunction and tolerance are shared factors driving a subset of T cells that are enriched in NRs, suggesting multiple forms of T cell dysfunction in DLI resistance. We found that the clusters dominated by post-DLI R T cells were characterized by greater diversity of T helper subsets (Th1, Tfh, Th2, Th9, and Th22) and enrichment for exhaustion, type I and II IFN pathways, proinflammatory gene sets and CD8 T cell activation. Clusters dominated by NR T cells displayed increases in Th17 and Treg signatures, anergy and tolerance. These data suggest that (1) pretreatment T cell phenotypic diversity may be important for DLI response; (2) that DLI increases such diversity differently in R’s than in NR’s; (3) while T cell subsets exhibit some overlap pre-therapy, responders and non-responders become increasingly dissimilar post therapy. Citation Format: Elham Azizi, Pavan Bachireddy, Vinhkhang N. Nguyen, Shuqiang Li, Donna S. Neuberg, Robert J. Soiffer, Jerome Ritz, Edwin P. Alyea III, Dana Pe'er, Catherine J. Wu. Mapping the evolution of T cell states during DLI response and resistance using single-cell data and computational tools [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3371.
- Published
- 2019
27. Single Cell T Cell Maps of Donor Lymphocyte Infusion (DLI) Response and Resistance
- Author
-
Jerome Ritz, Robert J. Soiffer, Elham Azizi, Donna Neuberg, Edwin P. Alyea, Dana Pe'er, Pavan Bachireddy, Shuqiang Li, Vinhkhang N Nguyen, and Catherine J. Wu
- Subjects
Transplantation ,Cell type ,business.industry ,T cell ,Cell ,Hematology ,medicine.disease ,Peripheral blood mononuclear cell ,Donor lymphocyte infusion ,CD8A ,medicine.anatomical_structure ,Antigen ,medicine ,Cancer research ,business ,Chronic myelogenous leukemia - Abstract
DLI can eradicate leukemic relapse after allogeneic hematopoietic stem cell transplant (allo-SCT), potentially by reversing T cell exhaustion for chronic myelogenous leukemia (CML). Critical questions remain, however, regarding the exact cellular identities and transcriptional states of those T cell subtypes mediating exhaustion, anti-leukemia responses, and DLI resistance. To map evolving phenotypic T cell states in situ at single cell resolution, we obtained single cell transcriptomes from bone marrow mononuclear cells before/after DLI from 6 responders ("R's") and 6 nonresponders ("NR's") with relapsed CML after T-cell depleted allo-SCT. In total, 381,462 cells derived from 43 unique patient-timepoints met our quality metrics; we curated a set of 62 distinct cell states, from T, B, NK, monocyte, and progenitor subtypes, whose identities were determined by both cell type and timepoint. Because DLI's anti-leukemic efficacy derives largely from T cell activity, we evaluated if DLI response associated with distinct T cell transcriptional phenotypes ("states"). We observed a marked separation of T cell clusters based on clinical outcome and a significant increase in the number of T cell clusters after DLI in matched samples after controlling for cell number (pre vs post, p-value We queried global T cell dysfunction between R's vs NR's, observing increased T cell exhaustion signatures in R-pre T cells, consistent with our previously published findings, but also detecting increased tolerance and anergy in NR-post T cells, suggesting multiple forms of T cell dysfunction in DLI resistance. Anergic and tolerant cells constituted distinct clusters, expressing reduced CD8A/CD4 expression, suggesting decreased antigen responsiveness. We will also infer novel gene regulatory networks driving T cell states and clonal expansion by integrating scRNA-seq data with associated ATAC-seq profiles and scTCR repertoires, using novel computational techniques. These findings will be updated at the meeting. Altogether, these data suggest that (1) pretreatment T cell phenotypic diversity may be important for DLI response; (2) that DLI increases such diversity differentially in R's than in NR's; and (3) even in the absence of clinical response, NR's undergo significant T cell phenotypic remodeling.
- Published
- 2019
28. Clonal and Single Cell Dynamics of Resistance to Graft-Versus-Leukemia (GvL) in Chronic Lymphocytic Leukemia (CLL)
- Author
-
Catherine J. Wu, Vinhkhang N Nguyen, Jerome Ritz, Robert J. Soiffer, Samuel S. Freeman, Donna Neuberg, Pavan Bachireddy, Kendell Clement, Peter V. Kharchenko, Jennifer R. Brown, Liudmila Elagina, Vincent T. Ho, Gad Getz, Edwin P. Alyea, Nikolaos Barkas, Ignaty Leshchiner, and Sachet A. Shukla
- Subjects
medicine.medical_treatment ,Chronic lymphocytic leukemia ,T cell ,Immunology ,Cell Biology ,Hematology ,Hematopoietic stem cell transplantation ,Biology ,medicine.disease ,Biochemistry ,Donor lymphocyte infusion ,Transplantation ,Leukemia ,medicine.anatomical_structure ,Cancer cell ,medicine ,Cancer research ,CD5 - Abstract
Although the GvL effect is the curative basis for allogeneic hematopoietic stem cell transplantation, the key cellular and molecular mechanisms driving GvL sensitivity and resistance remain incompletely understood. Using genomic approaches, we systematically characterized the changes in cellular composition and state of CLL and non-CLL cells in two settings of effective GvL: reduced intensity conditioning regimens (RIC) and donor lymphocyte infusion (DLI). We identified 10 patients with CLL progression after RIC, 6 of whom had complete responses before relapse. To define the evolutionary trajectories of CLL cells after RIC, we generated paired whole-exome sequencing data from pre- and post-RIC CLL cells sorted from PBMCs. We used DNA from autologous CD4+ T cells for germline comparison and the algorithms MuTect2 and ABSOLUTE to identify somatic alterations with corresponding cancer cell fractions (CCFs). 5 of the 10 patients had clonal mutations in TP53 and/or SF3B1 pre-transplant. Mutation burden was higher at baseline than previously described for CLL (mean 29.7 vs 17.9 non-silent SNVs/exome, p1 vs We likewise saw diverse clonal trajectories in 2 index cases of DLI response followed by relapse, either 11 [branched evolution] or 1.5 [linear] years after DLI. To deeply examine co-evolution of CLL and immune cells during DLI-relapse, we performed single cell RNA sequencing of both cell types collected from 4 paired PBMC samples representing either pre- or post-(relapsed)-DLI time points. Using the inDrop platform, we profiled a median of 11,686 (range: 9,101-16,756) cells per sample with a median of 5,363 CD19+ CD5+ expressing CLL cells (range: 3,622-9,463). We first sought to define the transcriptional heterogeneity underlying CLL cells during DLI relapse. Data visualization using t-distributed stochastic neighbor embedding plots revealed broad transcriptional shifts in CLL clusters from pre- to post-DLI and also showed the complexity of transcriptional substructure to more closely relate to a patient's own genomic structure rather than a common CLL phenotype, in contrast to prior studies. DLI-relapsed CLL cells in both patients were marked by upregulation of CXCR4 and members of the RhoGTPase family, suggesting migration capacity and cytoskeletal remodeling to play a role in GvL escape. GO term enrichment analysis identified DLI sensitive CLL cells in these cases to associate with regulation of lipid and lipoprotein metabolism and interferon signaling. We then determined parallel changes in PBMC immune states over time, which were subtle and not related to time point. To determine if the leukemic microenvironment can differentially affect immune states, we profiled, in total, 32,777 single bone marrow mononuclear cells (BMMC) from pre-DLI, during DLI response, and post-DLI relapse for one patient. Unlike PBMCs, BMMC-derived T cells clustered preferentially by time point, then state of differentiation. DLI response induced a pronounced shift in all T cell states, reflected by upregulation of NFKB and PI3K-AKT signaling; a dysfunctional state marked by metallothionein family expression, recently discovered in murine single cell studies, was unique to the post-DLI relapse timepoint in this patient. Altogether, these data suggest that GvL selective pressure can shape genetic evolutionary trajectories; scRNA-seq analysis of the 2 informative DLI cases is consistent with the notion that the CLL microenvironment shapes immune states during GvL response and relapse. Ongoing studies will dissect the molecular pathways governing these trajectories to suggest therapeutic strategies for overcoming GvL resistance. Disclosures Brown: Boehringer: Consultancy; Sunesis: Consultancy; Morphosys: Membership on an entity's Board of Directors or advisory committees; Gilead: Consultancy, Research Funding; Invectys: Membership on an entity's Board of Directors or advisory committees; Janssen: Consultancy; Verastem: Consultancy, Research Funding; Celgene: Consultancy; Beigene: Membership on an entity's Board of Directors or advisory committees; Genentech: Consultancy; Loxo: Consultancy; TG Therapeutics: Consultancy; Sun Pharmaceutical Industries: Research Funding; Roche/Genentech: Consultancy; Acerta / Astra-Zeneca: Membership on an entity's Board of Directors or advisory committees; Abbvie: Consultancy; Pharmacyclics: Consultancy. Ho:Jazz Pharmaceuticals: Consultancy. Soiffer:Jazz Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees. Wu:Neon Therapeutics: Equity Ownership.
- Published
- 2018
29. A Phase I/Ib Study of Nivolumab for Relapsed Hematologic Malignancies after Allogeneic Hematopoietic Cell Transplantation (alloHCT)
- Author
-
Sarah Nikiforow, David Avigan, Matthew S. Davids, Frederick L. Locke, Edward D. Ball, Michael Mazzeo, Philippe Armand, Robert J. Soiffer, Rodrigo O. Maegawa, Catherine J. Wu, Howard Streicher, Yi-Bin Chen, Alexandra Savell, Edwin P. Alyea, Pavan Bachireddy, Caitlin Costello, Haesook T. Kim, Vincent T. Ho, Asad Bashey, Alex F. Herrera, and Corey Cutler
- Subjects
0301 basic medicine ,medicine.medical_specialty ,medicine.medical_treatment ,Immunology ,Population ,Ipilimumab ,Hematopoietic stem cell transplantation ,Biochemistry ,03 medical and health sciences ,0302 clinical medicine ,Internal medicine ,Medicine ,education ,education.field_of_study ,business.industry ,Retrospective cohort study ,Cell Biology ,Hematology ,medicine.disease ,Clinical trial ,Transplantation ,030104 developmental biology ,030220 oncology & carcinogenesis ,Nivolumab ,business ,Progressive disease ,medicine.drug - Abstract
BACKGROUND: Patients (pts) with relapsed hematologic malignancies (HM) after alloHCT are a unique population, given the potential to harness a dormant graft-vs.-tumor effect therapeutically. We previously reported that CTLA-4 blockade with ipilimumab was feasible and active in this population (Davids et al., N Eng J Med, 2016). In retrospective studies, anti-PD1 antibodies were active in pts with relapsed lymphoid malignancies after alloHCT, though with substantial toxcity due to GVHD (Herbaux et al. and Haverkos et al., Blood, 2017). Here, we report on the first prospective clinical trial of PD1 blockade in pts with relapsed HM after alloHCT. METHODS: The primary objectives in this ph I/Ib, multicenter, investigator-initiated, CTEP-sponsored study (CTEP 9204) were to determine MTD and evaluate safety of nivolumab (nivo). Secondary objectives were to assess efficacy and immunologic correlates. Pts with any HM with relapse or persistent disease after alloHCT were eligible. Nivo was initially given to a 1 mg/kg cohort, with planned escalation to a 3 mg/kg cohort or de-escalation to a 0.5 mg/kg cohort depending on toxicities. Nivo was dosed q2 wks until progression or unacceptable toxicity, and disease-specific response evaluations were q4 cycles. RESULTS: A total of 28 pts with relapsed HM after alloHCT were treated. Median age was 57 (range 27-76), and pts had the following HM: AML (n=11), MDS (n=7), Hodgkin lymphoma (HL, n=5), non-Hodgkin lymphoma (NHL, n=3), MPD and CLL (n=1 each). Median number of prior therapies was 2 (range 1-9), and 18/28 (64%) had progressed after at least 1 prior therapy for relapse post alloHCT. The median time from alloHCT to study enrollment was 21 mo. (range 5.7-174 mo.). Six pts were treated initially with nivo 1 mg/kg. Two immune-related adverse events (irAEs) resulted in DLTs, including one pt with sepsis and fatal ARDS, and one pt with new anti-phospholipid antibodies and a fatal thrombotic cerebral vascular accident. Other irAEs included gr3 pneumonitis and transaminitis (n=1 each). One pt had cGVHD (NIH mild). Response was observed in 3/6 pts, including 1 CR (PMBCL) and 2 PR (HL and CMML). Due to the toxicities at 1 mg/kg, a cohort of 8 pts was then treated with nivo 0.5 mg/kg, which was generally well-tolerated, with no DLTs. A phase Ib expansion cohort then accrued 14 more pts at 0.5 mg/kg. Accrual was terminated after 14 pts were treated due to meeting the protocol-defined stopping rule of ≥4 DLTs in the first 15 pts in this cohort. These DLTs included 2 cases of grade III acute GVHD (liver and gut) as well as gr3 elevated bilirubin (n=1) and gr3 transaminitis (n=1) which did not recover to ≤gr1 within 4 wks. The 2 pts with liver dysfunction without histological evidence of GVHD eventually improved, but both pts with GVHD died due to complications from GVHD. Other toxicities included gr4 lipase elevation, gr3 rash, gr3 transaminitis, gr3 orthostatic hypotension, and gr2 seizure in a pt with a known seizure disorder (n=1 each). In the 22 pts treated at nivo 0.5 mg/kg, 10 pts (45%) had new onset or worsening of GVHD, including 1 with aGVHD only, 7 with cGVHD only (3 of whom had baseline cGVHD), and 2 with both acute and cGVHD. Shorter time from alloHCT was significantly associated with higher risk of developing GVHD (p=0.019). The overall response rate in the 19 evaluable pts treated at nivo 0.5 mg/kg was 16%, including 1 pt with HL with CR and 1 pt each with HL and AML achieving PR. Nine pts had stable disease for at least 1 response evaluation, and 7 pts had progressive disease as best response. Studywide, the overall response rate was 24% (6/25), the median number of cycles received was 3 (range 1-25), and 12/28 (43%) had at least 1 dose delay due to toxicity. With a median follow-up of 3.9 mo. (range 1.4-20.9 mo.), the 6 mo. PFS and OS were 39% and 61%, respectively. CONCLUSIONS: In this first prospective clinical trial of an anti-PD1 antibody for relapsed HM post-alloHCT, severe GVHD and irAEs occurred, even at the lower dose of nivo 0.5 mg/kg, leading to early closure due to toxicity. Modest anti-tumor activity was observed mainly in lymphoid malignancies known already to be responsive to anti-PD1 therapy, which may justify further exploration of anti-PD1 therapy in those populations in trials with strategies to mitigate toxicity; however, given the more favorable safety and efficacy profile of anti-CTLA-4 therapy in other HM, our future studies focus on combining ipilimumab with novel partners to improve outcomes. Disclosures Davids: Celgene: Consultancy; MEI Pharma: Consultancy, Research Funding; Verastem: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; TG Therapeutics: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Astra-Zeneca: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Roche/Genentech: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Pharmacyclics: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Merck: Consultancy; BMS: Research Funding; Janssen: Consultancy, Membership on an entity's Board of Directors or advisory committees; Gilead: Membership on an entity's Board of Directors or advisory committees; AbbVie, Inc: Consultancy, Membership on an entity's Board of Directors or advisory committees; Surface Oncology: Research Funding. Costello:Celgene: Consultancy; Takeda: Consultancy; Poseida Therapeutics, Inc.: Research Funding. Herrera:Seattle Genetics: Research Funding; Pharmacyclics: Consultancy, Research Funding; Merck, Inc.: Consultancy, Research Funding; KiTE Pharma: Consultancy, Research Funding; Immune Design: Research Funding; AstraZeneca: Research Funding; Bristol-Myers Squibb: Consultancy, Research Funding; Genentech: Consultancy, Research Funding; Gilead Sciences: Research Funding. Locke:Novartis Pharmaceuticals: Other: Scientific Advisor; Cellular BioMedicine Group Inc.: Consultancy; Kite Pharma: Other: Scientific Advisor. Chen:Incyte: Consultancy, Membership on an entity's Board of Directors or advisory committees; Magenta Therapeutics: Consultancy; REGiMMUNE: Consultancy; Takeda Pharmaceuticals: Consultancy. Nikiforow:Kite Pharma: Consultancy. Ho:Jazz Pharmaceuticals: Consultancy. Wu:Neon Therapeutics: Equity Ownership. Soiffer:Jazz Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees.
- Published
- 2018
30. Mapping the Evolution of T Cell Transcriptional States during DLI Response and Resistance Using Single-Cell Data
- Author
-
Jerome Ritz, Dana Pe'er, Edwin P. Alyea, Pavan Bachireddy, Catherine J. Wu, Robert J. Soiffer, Elham Azizi, Donna Neuberg, Shuqiang Li, and Vinhkhang N Nguyen
- Subjects
Cell type ,T cell ,Immunology ,Cell Biology ,Hematology ,Biology ,Biochemistry ,CD8A ,medicine.anatomical_structure ,Antigen ,Single-cell analysis ,medicine ,Cytotoxic T cell ,Progenitor cell ,Stem cell - Abstract
Donor lymphocyte infusion (DLI) is a potentially curative immune therapy for leukemic relapse after allogeneic hematopoietic stem cell transplant (allo-SCT). We previously reported that durable response to DLI for chronic myelogenous leukemia (CML) was associated with reversal of exhaustion of bone marrow-infiltrating T cells. Critical questions remain, however, regarding the exact cellular identities and transcriptional states of those T cell subtypes mediating exhaustion, anti-leukemia responses, and resistance to DLI. To map evolving phenotypic T cell states in situ at single cell resolution, we profiled viable cells isolated from cryopreserved bone marrow mononuclear cells (BMMCs) from a median of 3 timepoints (range: 2-6) before and after DLI from 12 patients with relapsed CML after T-cell depleted allo-SCT, using single cell RNA sequencing (scRNAseq, via the 10x Genomics Chromium platform). For reference, we also characterized a healthy donor marrow sample. Six of 12 patients were long-term responders to CD8-depleted DLI ("R's") and the remaining 6 were nonresponders ("NR's,"). In total, 381,462 cells derived from 43 unique patient-timepoints met our quality metrics, with a median of 2548 mRNA molecules/cell and 8735 cells/sample. By merging data across the cohort and removing batch effects (using the tool Biscuit), we curated a set of 62 distinct cell states, including subtypes of T, B, NK, monocytes, progenitors and CD34+ stem cells, whose identities were determined by both cell type and time point. We evaluated if response to DLI was associated with distinct T cell transcriptional phenotypes ("states"). We observed a marked increase in the number of T cell clusters in post-DLI samples (mean 41, range: 35-46) compared to matched pre-DLI samples, (mean 38, range: 34-41) after controlling for cell number (p-value We next compared global T cell dysfunction between R vs NR cases by summarizing scores for various dysfunction signatures across all T cells. We again observed increased T cell exhaustion signatures in R-pre T cells but also detected increased tolerance and anergy in NR-post T cells, suggesting multiple forms of T cell dysfunction in DLI resistance. We found that the clusters dominated by post-DLI R T cells were characterized by greater diversity of T helper subsets (Th1, Tfh, Th2, Th9, and Th22) and enrichment for exhaustion, type I and II IFN pathways, proinflammatory gene sets and CD8 T cell activation. Clusters dominated by NR T cells displayed increases in Th17 and Treg signatures, anergy and tolerance. Anergic cells were enriched for Treg signatures and did not share cluster membership with tolerant cells, which did not enrich for a specific subtype. Both types expressed only CD3D without CD8A or CD4, suggesting decreased antigen responsiveness. Single cell analysis of TCR repertoires and co-evolving leukemia cells will be updated at the meeting. Altogether, these data suggest that (1) pretreatment T cell phenotypic diversity may be important for DLI response; (2) that DLI increases such diversity differentially in responders than in nonresponders; and (3) even in the absence of clinical response, nonresponders undergo significant T cell phenotypic remodeling. Further studies will involve functional validation of dysfunctional T cell clusters and identification of therapeutic targets for reversing DLI resistance. Disclosures Soiffer: Jazz Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees. Wu:Neon Therapeutics: Equity Ownership.
- Published
- 2018
31. Ipilimumab for Patients with Relapse after Allogeneic Transplantation
- Author
-
Edward D. Ball, David Avigan, Philippe Armand, Pavan Bachireddy, Nicole R. LeBoeuf, Scott R. Granter, Jason L. Hornick, Joseph H. Antin, Catherine J. Wu, Corey Cutler, Alexander Lukez, John Koreth, Haesook T. Kim, Rebecca Liguori, Michaela Bowden, Michael S. Rooney, Asad Bashey, Vincent T. Ho, Chensheng W. Zhou, Yi-Bin Chen, Caitlin Costello, Robert J. Soiffer, Matthew S. Davids, Jerome Ritz, Mariano Severgnini, Alexandra Savell, Edwin P. Alyea, Scott J. Rodig, Peter McSweeney, F. Stephen Hodi, Masahiro Hirakawa, and Howard Streicher
- Subjects
0301 basic medicine ,Oncology ,Male ,Lymphoma ,medicine.medical_treatment ,T-Lymphocytes ,Hematopoietic stem cell transplantation ,Regenerative Medicine ,T-Lymphocytes, Regulatory ,Medical and Health Sciences ,0302 clinical medicine ,Recurrence ,Stem Cell Research - Nonembryonic - Human ,Monoclonal ,CTLA-4 Antigen ,6.2 Cellular and gene therapies ,Cancer ,Pediatric ,Leukemia ,Hematopoietic Stem Cell Transplantation ,Antibodies, Monoclonal ,General Medicine ,Induction Chemotherapy ,Hematology ,Middle Aged ,Regulatory ,030220 oncology & carcinogenesis ,6.1 Pharmaceuticals ,Hematologic Neoplasms ,Female ,Stem Cell Research - Nonembryonic - Non-Human ,Patient Safety ,Development of treatments and therapeutic interventions ,medicine.drug ,Homologous ,Adult ,medicine.medical_specialty ,Allogeneic transplantation ,Pediatric Cancer ,Clinical Trials and Supportive Activities ,Ipilimumab ,Antibodies ,Article ,03 medical and health sciences ,Rare Diseases ,Transplantation Immunology ,Clinical Research ,Internal medicine ,General & Internal Medicine ,medicine ,Transplantation, Homologous ,Humans ,Adverse effect ,Aged ,Transplantation ,Myeloproliferative Disorders ,5.2 Cellular and gene therapies ,business.industry ,Induction chemotherapy ,Evaluation of treatments and therapeutic interventions ,Leukemia and Lymphoma Society Blood Cancer Research Partnership ,Stem Cell Research ,Immune checkpoint ,Surgery ,CD4 Lymphocyte Count ,Clinical trial ,030104 developmental biology ,Neoplasm Recurrence, Local ,business - Abstract
BackgroundLoss of donor-mediated immune antitumor activity after allogeneic hematopoietic stem-cell transplantation (HSCT) permits relapse of hematologic cancers. We hypothesized that immune checkpoint blockade established by targeting cytotoxic T-lymphocyte-associated protein 4 with ipilimumab could restore antitumor reactivity through a graft-versus-tumor effect.MethodsWe conducted a phase 1/1b multicenter, investigator-initiated study to determine the safety and efficacy of ipilimumab in patients with relapsed hematologic cancer after allogeneic HSCT. Patients received induction therapy with ipilimumab at a dose of 3 or 10 mg per kilogram of body weight every 3 weeks for a total of 4 doses, with additional doses every 12 weeks for up to 60 weeks in patients who had a clinical benefit.ResultsA total of 28 patients were enrolled. Immune-related adverse events, including one death, were observed in 6 patients (21%), and graft-versus-host disease (GVHD) that precluded further administration of ipilimumab was observed in 4 patients (14%). No responses that met formal response criteria occurred in patients who received a dose of 3 mg per kilogram. Among 22 patients who received a dose of 10 mg per kilogram, 5 (23%) had a complete response, 2 (9%) had a partial response, and 6 (27%) had decreased tumor burden. Complete responses occurred in 4 patients with extramedullary acute myeloid leukemia and 1 patient with the myelodysplastic syndrome developing into acute myeloid leukemia. Four patients had a durable response for more than 1 year. Responses were associated with in situ infiltration of cytotoxic CD8+ T cells, decreased activation of regulatory T cells, and expansion of subpopulations of effector T cells in the blood.ConclusionsOur early-phase data showed that administration of ipilimumab was feasible in patients with recurrent hematologic cancers after allogeneic HSCT, although immune-mediated toxic effects and GVHD occurred. Durable responses were observed in association with several histologic subtypes of these cancers, including extramedullary acute myeloid leukemia. (Funded by the National Institutes of Health and others; ClinicalTrials.gov number, NCT01822509.).
- Published
- 2016
32. Arresting the Inflammatory Drive of Chronic Lymphocytic Leukemia with Ibrutinib
- Author
-
Pavan Bachireddy and Catherine J. Wu
- Subjects
0301 basic medicine ,Male ,Cancer Research ,Chronic lymphocytic leukemia ,Cell Communication ,Clinical success ,chemistry.chemical_compound ,Mice ,0302 clinical medicine ,Piperidines ,immune system diseases ,Bone Marrow ,Cell Movement ,T-Lymphocyte Subsets ,hemic and lymphatic diseases ,Tumor Microenvironment ,Aged, 80 and over ,B-Lymphocytes ,Cell Differentiation ,Middle Aged ,Oncology ,030220 oncology & carcinogenesis ,Ibrutinib ,Cytokines ,Female ,Signal transduction ,Inflammation Mediators ,Signal Transduction ,Antineoplastic Agents ,Article ,Immunophenotyping ,03 medical and health sciences ,medicine ,Animals ,Humans ,neoplasms ,Protein Kinase Inhibitors ,Aged ,business.industry ,Adenine ,Macrophages ,Receptor signaling ,medicine.disease ,Leukemia, Lymphocytic, Chronic, B-Cell ,Disease Models, Animal ,030104 developmental biology ,Pyrimidines ,chemistry ,Immunology ,Cancer research ,Pyrazoles ,Th17 Cells ,business - Abstract
Chronic lymphocytic leukemia (CLL) cells depend on microenvironmental interactions for proliferation and survival that are at least partially mediated through B-cell receptor (BCR) signaling. Ibrutinib, a Bruton tyrosine kinase inhibitor, disrupts BCR signaling and leads to the egress of tumor cells from the microenvironment. Although the on-target effects on CLL cells are well defined, the impact on the microenvironment is less well studied. We therefore sought to characterize the in vivo effects of ibrutinib on the tumor microenvironment.Patients received single-agent ibrutinib on an investigator-initiated phase II trial. Serial blood and tissue samples were collected pretreatment and during treatment. Changes in cytokine levels, cellular subsets, and microenvironmental interactions were assessed.Serum levels of key chemokines and inflammatory cytokines decreased significantly in patients on ibrutinib. Furthermore, ibrutinib treatment decreased circulating tumor cells and overall T-cell numbers. Most notably, a reduced frequency of the Th17 subset of CD4(+)T cells was observed concurrent with reduced expression of activation markers and PD-1 on T cells. Consistent with direct inhibition of T cells, ibrutinib inhibited Th17 differentiation of murine CD4(+)T cells in vitro Finally, in the bone marrow microenvironment, we found that ibrutinib disaggregated the interactions of macrophages and CLL cells, inhibited secretion of CXCL13, and decreased the chemoattraction of CLL cells.In conjunction with inhibition of BCR signaling, these changes in the tumor microenvironment likely contribute to the antitumor activity of ibrutinib and may impact the efficacy of immunotherapeutic strategies in patients with CLL. See related commentary by Bachireddy and Wu, p. 1547.
- Published
- 2016
33. Abstract 17: In situ immune expression signatures before and after ipilimumab therapy for relapsed acute myeloid leukemia after allogeneic stem cell transplantation
- Author
-
Robert J. Soiffer, Michaela Bowden, Scott J. Rodig, Chensheng W. Zhou, Michael S. Rooney, Pavan Bachireddy, Catherine J. Wu, Edwin P. Alyea, Vincent T. Ho, Matthew S. Davids, John Koreth, and Joseph H. Antin
- Subjects
Transplantation ,In situ ,Cancer Research ,Immune system ,Oncology ,Cancer research ,medicine ,Myeloid leukemia ,Ipilimumab ,Biology ,Stem cell ,medicine.drug - Abstract
Immune evasion may facilitate hematologic relapse after allogeneic hematopoietic stem cell transplantation (allo-SCT). We recently demonstrated that CTLA4 blockade with ipilimumab reinvigorates a graft-versus-leukemia effect to induce complete remissions of acute myeloid leukemia (AML) relapsing after allo-SCT. Here, we hypothesized that immune subpopulation dynamics and activation states inferred from in situ gene expression changes within the leukemic microenvironment are informative of clinical outcome. We undertook an in situ transcriptomic characterization of paired, pre/post ipilimumab leukemic biopsies from five samples with relapsed, extramedullary AML. We performed a response-to-treatment expression analysis for each patient and found three immune patterns corresponding to three clinical response patterns following ipilimumab (durable response, relapse, and primary resistance). Durable responses were characterized by a diverse infiltration of activated cytotoxic T lymphocytes, B cells, and macrophages. In contrast, primary resistance was associated with both marked infiltration of CD8 T cells deficient in T-cell receptor signaling, activation, or cytolytic activity and absent infiltration of other immune effectors. Interestingly, the sample with transient response and eventual relapse demonstrated pre- and post-treatment immunologically “inflamed” states that were strongly downregulated during clinical relapse. In situ gene expression analyses of leukemic biopsies before and after ipilimumab therapy suggest that specific patterns of immune population dynamics and activation states underlie diverse clinical outcomes. Citation Format: Pavan Bachireddy, Matthew S. Davids, Michael S. Rooney, Michaela Bowden, Chensheng W. Zhou, Scott J. Rodig, Vincent Ho, Joseph Antin, John Koreth, Edwin Alyea, Robert J. Soiffer, Catherine J. Wu. In situ immune expression signatures before and after ipilimumab therapy for relapsed acute myeloid leukemia after allogeneic stem cell transplantation [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr 17.
- Published
- 2017
34. External Beam Radiation Therapy Enhances Local Control in Pigmented Villonodular Synovitis
- Author
-
Phuoc T. Tran, Pavan Bachireddy, Robert B. West, David G. Mohler, Melissa Horoschak, Sarah S. Donaldson, Daniel S. Kapp, and Christopher F. Beaulieu
- Subjects
Adult ,Male ,Cancer Research ,medicine.medical_specialty ,medicine.medical_treatment ,External beam radiation ,Synovitis, Pigmented Villonodular ,Statistics, Nonparametric ,Young Adult ,Synovitis ,medicine ,Humans ,Radiology, Nuclear Medicine and imaging ,Young adult ,Aged ,Retrospective Studies ,Radiation ,business.industry ,Retrospective cohort study ,Middle Aged ,medicine.disease ,Surgery ,Radiation therapy ,Oncology ,Time to recurrence ,Amputation ,Pigmented villonodular synovitis ,Female ,business ,Follow-Up Studies - Abstract
Purpose Pigmented villonodular synovitis (PVNS) is a rare proliferative disorder of the synovium with locally aggressive behavior. We reviewed our experience using radiation therapy in the treatment of PVNS. Materials and Methods Seventeen patients with 18 sites of PVNS were treated with radiation between 1993 and 2007. Cases were retrospectively reviewed for patient information, treatment parameters, complications, and outcome. Seven sites were primary presentations and 11 were recurrent with an average of 2.5 prior surgical interventions. The most common location was the knee joint (67%). Cytoreductive surgery was performed before radiation therapy in 16/18 sites with all having proven or suspected residual disease. Radiation was delivered using 4–15 MV photons with an average total dose 34 Gy (range, 20–36 Gy). Seventeen of 18 sites (94%) had postradiotherapy imaging. Results With average follow-up of 46 months (range, 8–181 months), initial local control was achieved in 75% (12/16) of the sites with prior cytoreductive surgery (mean time to recurrence, 38 months). Ultimate local control was 100% after repeat resection (mean follow-up, 61 months). Two additional sites without prior cytoreductive surgery showed growth after radiotherapy (mean time to documented growth, 10.5 months). Seventeen of the 18 involved joints (94%) were scored as excellent or good PVNS-related function, one site (5%) as fair function, and no site with poor function. No patient required amputation; and there were no Grade 3/4 treatment-related complications. Conclusion Postoperative external beam radiation is effective in preventing disease recurrence and should be offered following maximal cytoreduction to enhance local control in PVNS.
- Published
- 2009
35. Cellular senescence is an important mechanism of tumor regression upon c-Myc inactivation
- Author
-
Chi Hwa Wu, Alper Yetil, Alice C. Fan, Dean W. Felsher, Jan van Riggelen, and Pavan Bachireddy
- Subjects
Senescence ,Multidisciplinary ,Oncogene ,MAP Kinase Signaling System ,Genes, myc ,Biological Sciences ,Biology ,Genes, p53 ,medicine.disease_cause ,Oncogene Addiction ,Chromatin ,Malignant transformation ,Histone H4 ,Mice ,Histone H3 ,Neoplasms ,medicine ,Cancer research ,Animals ,Humans ,Genes, Retinoblastoma ,Carcinogenesis ,Cell aging ,Cellular Senescence ,DNA Damage - Abstract
Oncogene-induced senescence is an important mechanism by which normal cells are restrained from malignant transformation. Here we report that the suppression of the c-Myc (MYC) oncogene induces cellular senescence in diverse tumor types including lymphoma, osteosarcoma, and hepatocellular carcinoma. MYC inactivation was associated with prototypical markers of senescence, including acidic β-gal staining, induction of p16INK4a, and p15INK4b expression. Moreover, MYC inactivation induced global changes in chromatin structure associated with the marked reduction of histone H4 acetylation and increased histone H3 K9 methylation. Osteosarcomas engineered to be deficient in p16INK4a or Rb exhibited impaired senescence and failed to exhibit sustained tumor regression upon MYC inactivation. Similarly, only after lymphomas were repaired for p53 expression did MYC inactivation induce robust senescence and sustained tumor regression. The pharmacologic inhibition of signaling pathways implicated in oncogene-induced senescence including ATM/ATR and MAPK did not prevent senescence associated with MYC inactivation. Our results suggest that cellular senescence programs remain latently functional, even in established tumors, and can become reactivated, serving as a critical mechanism of oncogene addiction associated with MYC inactivation.
- Published
- 2007
36. Sustained regression of tumors upon MYC inactivation requires p53 or thrombospondin-1 to reverse the angiogenic switch
- Author
-
Sandra Ryeom, Matthew J. Rioth, Alice C. Fan, Sylvie Giuriato, Andrew M. Kopelman, Emmanuelle Passegué, Jan van Riggelen, Judah Folkman, Ryan C. Lynch, Dean W. Felsher, Flora Tang, and Pavan Bachireddy
- Subjects
Multidisciplinary ,Oncogene ,Angiogenesis ,Cancer ,Biological Sciences ,Biology ,Oncogene Addiction ,medicine.disease_cause ,medicine.disease ,Proto-Oncogene Proteins c-myc ,Thrombospondin 1 ,Mice ,Tumor Escape ,Cell Line, Tumor ,Neoplasms ,Cancer research ,medicine ,Animals ,Bioluminescence imaging ,Tumor Suppressor Protein p53 ,Carcinogenesis - Abstract
The targeted inactivation of oncogenes offers a rational therapeutic approach for the treatment of cancer. However, the therapeutic inactivation of a single oncogene has been associated with tumor recurrence. Therefore, it is necessary to develop strategies to override mechanisms of tumor escape from oncogene dependence. We report here that the targeted inactivation of MYC is sufficient to induce sustained regression of hematopoietic tumors in transgenic mice, except in tumors that had lost p53 function. p53 negative tumors were unable to be completely eliminated, as demonstrated by the kinetics of tumor cell elimination revealed by bioluminescence imaging. Histological examination revealed that upon MYC inactivation, the loss of p53 led to a deficiency in thrombospondin-1 (TSP-1) expression, a potent antiangiogenic protein, and the subsequent inability to shut off angiogenesis. Restoration of p53 expression in these tumors re-established TSP-1 expression. This permitted the suppression of angiogenesis and subsequent sustained tumor regression upon MYC inactivation. Similarly, the restoration of TSP-1 alone in p53 negative tumors resulted in the shut down of angiogenesis and led to sustained tumor regression upon MYC inactivation. Hence, the complete regression of tumor mass driven by inactivation of the MYC oncogene requires the p53-dependent induction of TSP-1 and the shut down of angiogenesis. Notably, overexpression of TSP-1 alone did not influence tumor growth. Therefore, the combined inactivation of oncogenes and angiogenesis may be a more clinically effective treatment of cancer. We conclude that angiogenesis is an essential component of oncogene addiction.
- Published
- 2006
37. Getting at MYC through RAS
- Author
-
Pavan K. Bendapudi, Pavan Bachireddy, and Dean W. Felsher
- Subjects
Regulation of gene expression ,Cancer Research ,MEDLINE ,Cancer ,Biology ,medicine.disease ,Farnesol ,Models, Biological ,Salicylates ,Cancer treatment ,Gene Expression Regulation, Neoplastic ,Proto-Oncogene Proteins c-myc ,Neuroblastoma ,Oncology ,Cell Line, Tumor ,ras Proteins ,Cancer research ,medicine ,Humans ,Cell Proliferation ,Signal Transduction - Abstract
The discovery of oncogenes provided insight into the molecular underpinnings of cancer and suggested the promise of novel molecular strategies for cancer treatment as highlighted in this issue by Yaari et al. and by Bishop previously ([1][1], [2][2]). However, only recently have effective drugs that
- Published
- 2005
38. Reversal of in situ T-cell exhaustion during effective human antileukemia responses to donor lymphocyte infusion
- Author
-
Wandi Zhang, Edwin P. Alyea, Olga Pozdnyakova, Michael Rooney, Natalie R. Goldstein, Nir Hacohen, Haesook T. Kim, Ursula Hainz, Catherine J. Wu, Julie Aldridge, F. Stephen Hodi, Jerome Ritz, Karyn E. O'Connell, Xiaoyun Liao, Pavan Bachireddy, Christine Canning, Robert J. Soiffer, and W. Nicholas Haining
- Subjects
Lymphocyte Transfusion ,T cell ,medicine.medical_treatment ,T-Lymphocytes ,Immunology ,Blood Donors ,Bone Marrow Cells ,Biochemistry ,Immunotherapy, Adoptive ,Donor lymphocyte infusion ,Lymphocyte Depletion ,Cohort Studies ,Immune system ,Lymphocytes, Tumor-Infiltrating ,Downregulation and upregulation ,Leukemia, Myelogenous, Chronic, BCR-ABL Positive ,medicine ,Humans ,Lymphocyte Count ,Transplantation ,business.industry ,Cell Biology ,Hematology ,Immunotherapy ,medicine.disease ,Tumor Burden ,Leukemia ,medicine.anatomical_structure ,Treatment Outcome ,business ,Transcriptome ,CD8 - Abstract
Increasing evidence across malignancies suggests that infiltrating T cells at the site of disease are crucial to tumor control. We hypothesized that marrow-infiltrating immune populations play a critical role in response to donor lymphocyte infusion (DLI), an established and potentially curative immune therapy whose precise mechanism remains unknown. We therefore analyzed marrow-infiltrating immune populations in 29 patients (22 responders, 7 nonresponders) with relapsed chronic myelogenous leukemia who received CD4(+) DLI in the pre-tyrosine kinase inhibitor era. Immunohistochemical analysis of pretreatment marrow revealed that the presence of >4% marrow-infiltrating CD8(+) (but not CD4(+)) T cells predicted DLI response, even in the setting of high leukemia burden. Furthermore, mRNA expression profiling of marrow-infiltrating T cells of a subset of responders compared with nonresponders revealed enrichment of T-cell exhaustion-specific genes in pretreatment T cells of DLI responders and significant downregulation of gene components in the same pathway in responders in conjunction with clinical response. Our data demonstrate that response to DLI is associated with quantity of preexisting marrow CD8(+) T cells and local reversal of T-cell exhaustion. Our studies implicate T-cell exhaustion as a therapeutic target of DLI and support the potential use of novel anti-PD1/PDL1 agents in lieu of DLI.
- Published
- 2014
39. Understanding anti-leukemia responses to donor lymphocyte infusion
- Author
-
Pavan Bachireddy and Catherine J. Wu
- Subjects
T cell exhaustion ,business.industry ,Tumor-infiltrating lymphocytes ,Immunology ,Hematopoietic stem cell ,Model system ,chemical and pharmacologic phenomena ,donor lymphocyte infusion ,medicine.disease ,stem cell transplantation ,Donor lymphocyte infusion ,Immune therapy ,Leukemia ,medicine.anatomical_structure ,Oncology ,Immunity ,hemic and lymphatic diseases ,tumor-infiltrating lymphocytes ,Immunology and Allergy ,Medicine ,business ,Author's View ,CML - Abstract
Donor lymphocyte infusion (DLI) is an established and potentially curative immune therapy for relapsed leukemia after hematopoietic stem cell transplant (HSCT). Herein, we describe the utility of DLI as a tractable model system to glean fresh insights into understanding and predicting effective anti-leukemia immunity.
- Published
- 2014
40. Immunology in the clinic review series; focus on cancer: multiple roles for the immune system in oncogene addiction
- Author
-
Pavan Bachireddy, Kavya Rakhra, and Dean W. Felsher
- Subjects
Senescence ,CD4-Positive T-Lymphocytes ,Angiogenesis ,Immunology ,Cell ,Antineoplastic Agents ,Mice, Transgenic ,Biology ,medicine.disease_cause ,Mice ,Immune system ,Neoplasms ,medicine ,Immunology and Allergy ,Animals ,Humans ,Epigenetics ,Molecular Targeted Therapy ,Review Articles ,Cellular Senescence ,Oncogene Proteins ,Neovascularization, Pathologic ,Tumor Suppressor Proteins ,Cancer ,Oncogenes ,Oncogene Addiction ,medicine.disease ,Combined Modality Therapy ,medicine.anatomical_structure ,Cell Transformation, Neoplastic ,Gene Knockdown Techniques ,Cytokines ,Immunotherapy ,Carcinogenesis - Abstract
Summary OTHER THEMES PUBLISHED IN THIS IMMUNOLOGY IN THE CLINIC REVIEW SERIES Metabolic Diseases, Host Responses, Allergies, Autoinflammatory Diseases, Type 1 diabetes and viruses. Despite complex genomic and epigenetic abnormalities, many cancers are irrevocably dependent on an initiating oncogenic lesion whose restoration to a normal physiological activation can elicit a dramatic and sudden reversal of their neoplastic properties. This phenomenon of the reversal of tumorigenesis has been described as oncogene addiction. Oncogene addiction had been thought to occur largely through tumour cell-autonomous mechanisms such as proliferative arrest, apoptosis, differentiation and cellular senescence. However, the immune system plays an integral role in almost every aspect of tumorigenesis, including tumour initiation, prevention and progression as well as the response to therapeutics. Here we highlight more recent evidence suggesting that oncogene addiction may be integrally dependent upon host immune-mediated mechanisms, including specific immune effectors and cytokines that regulate tumour cell senescence and tumour-associated angiogenesis. Hence, the host immune system is essential to oncogene addiction.
- Published
- 2012
41. Lymphomas that recur after MYC suppression continue to exhibit oncogene addiction
- Author
-
Andrew J. Gentles, Pavan Bachireddy, Dean W. Felsher, Stacey J. Adam, Kavya Rakhra, Peter S. Choi, Sylvia K. Plevritis, and Jan van Riggelen
- Subjects
Genetically modified mouse ,Transgene ,Genes, myc ,Gene Expression ,Mice, Transgenic ,Biology ,Lymphoma, T-Cell ,Precursor T-Cell Lymphoblastic Leukemia-Lymphoma ,Transactivation ,Mice ,Gene expression ,medicine ,Animals ,Humans ,RNA, Small Interfering ,Multidisciplinary ,Oncogene ,Tetracycline Resistance ,Biological Sciences ,medicine.disease ,Oncogene Addiction ,Lymphoma ,Gene expression profiling ,Phenotype ,Gene Knockdown Techniques ,Mutation ,Cancer research ,Trans-Activators ,Neoplasm Recurrence, Local - Abstract
The suppression of oncogenic levels of MYC is sufficient to induce sustained tumor regression associated with proliferative arrest, differentiation, cellular senescence, and/or apoptosis, a phenomenon known as oncogene addiction. However, after prolonged inactivation of MYC in a conditional transgenic mouse model of Eμ-tTA/tetO-MYC T-cell acute lymphoblastic leukemia, some of the tumors recur, recapitulating what is frequently observed in human tumors in response to targeted therapies. Here we report that these recurring lymphomas express either transgenic or endogenous Myc, albeit in many cases at levels below those in the original tumor, suggesting that tumors continue to be addicted to MYC. Many of the recurring lymphomas (76%) harbored mutations in the tetracycline transactivator, resulting in expression of the MYC transgene even in the presence of doxycycline. Some of the remaining recurring tumors expressed high levels of endogenous Myc, which was associated with a genomic rearrangement of the endogenous Myc locus or activation of Notch1. By gene expression profiling, we confirmed that the primary and recurring tumors have highly similar transcriptomes. Importantly, shRNA-mediated suppression of the high levels of MYC in recurring tumors elicited both suppression of proliferation and increased apoptosis, confirming that these tumors remain oncogene addicted. These results suggest that tumors induced by MYC remain addicted to overexpression of this oncogene.
- Published
- 2011
42. Orthovoltage intraoperative radiation therapy for pancreatic adenocarcinoma
- Author
-
Daniel S. Kapp, Melissa Horoschak, Albert C. Koong, Daniel T. Chang, Diane Tseng, Pavan Bachireddy, and Phuoc T. Tran
- Subjects
Adult ,Male ,lcsh:Medical physics. Medical radiology. Nuclear medicine ,medicine.medical_specialty ,medicine.medical_treatment ,lcsh:R895-920 ,Kaplan-Meier Estimate ,Adenocarcinoma ,lcsh:RC254-282 ,Intraoperative Period ,Pancreatic cancer ,medicine ,Humans ,Radiology, Nuclear Medicine and imaging ,Intraoperative radiation therapy ,Aged ,Retrospective Studies ,Aged, 80 and over ,Chemotherapy ,Radiotherapy ,business.industry ,Research ,Retrospective cohort study ,Middle Aged ,medicine.disease ,lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,Surgery ,Pancreatic Neoplasms ,Radiation therapy ,Treatment Outcome ,medicine.anatomical_structure ,Oncology ,Radiology Nuclear Medicine and imaging ,Female ,Radiology ,business ,Pancreas - Abstract
Purpose To analyze the outcomes of patients from a single institution treated with surgery and orthovoltage intraoperative radiotherapy (IORT) for pancreatic adenocarcinoma. Methods We retrospectively reviewed 23 consecutive patients from 1990-2001 treated with IORT to 23 discrete sites with median and mean follow up of 6.5 and 21 months, respectively. Most tumors were located in the head of the pancreas (83%) and sites irradiated included: tumor bed (57%), vessels (26%), both the tumor bed/vessels (13%) and other (4%). The majority of patients (83%) had IORT at the time of their definitive surgery. Three patients had preoperative chemoradiation (13%). Orthovoltage X-rays (200-250 kVp) were employed via individually sized and beveled cone applicators. Additional mean clinical characteristics include: age 64 (range 41-81); tumor size 4 cm (range 1.4-11); and IORT dose 1106 cGy (range 600-1500). Post-operative external beam radiation (EBRT) or chemotherapy was given to 65% and 76% of the assessable patients, respectively. Outcomes measured were infield control (IFC), loco-regional control (LRC), distant metastasis free survival (DMFS), overall survival (OS) and treatment-related complications. Results Kaplan-Meier (KM) 2-year IFC, LRC, DMFS and OS probabilities for the whole group were 83%, 61%, 26%, and 27%, respectively. Our cohort had three grade 3-5 complications associated with treatment (surgery and IORT). Conclusions Orthovoltage IORT following tumor reductive surgery is reasonably well tolerated and seems to confer in-field control in carefully selected patients. However, distant metastases remain the major problem for patients with pancreatic adenocarcinoma.
- Published
- 2010
43. CD4+ T-cells Contribute to the Remodeling of the Microenvironment Required for Sustained Tumor Regression upon Oncogene Inactivation
- Author
-
Kavya Rakhra, Alice C. Fan, Andrew M. Kopelman, Liwen Xu, Qiwei Yang, Lior Z. Braunstein, Sandra Ryeom, Erika J. Crosby, Dean W. Felsher, Tahera Zabuawala, Robert Zeiser, and Pavan Bachireddy
- Subjects
CD4-Positive T-Lymphocytes ,Cancer Research ,T cell ,Fusion Proteins, bcr-abl ,Apoptosis ,Mice, Transgenic ,Biology ,medicine.disease_cause ,Article ,Proto-Oncogene Proteins c-myc ,Thrombospondin 1 ,Mice ,Immune system ,Neoplasms ,hemic and lymphatic diseases ,medicine ,Tumor Microenvironment ,Animals ,Gene Silencing ,Thrombospondins ,Cellular Senescence ,Cell Proliferation ,Tumor microenvironment ,Leukemia, Experimental ,Oncogene ,Neovascularization, Pathologic ,Remission Induction ,Oncogenes ,Cell Biology ,Oncogene Addiction ,Gene Expression Regulation, Neoplastic ,medicine.anatomical_structure ,Oncology ,Cancer research ,Cyclosporine ,Chemokines ,Carcinogenesis ,Cell aging ,Immunosuppressive Agents - Abstract
SummaryOncogene addiction is thought to occur cell autonomously. Immune effectors are implicated in the initiation and restraint of tumorigenesis, but their role in oncogene inactivation-mediated tumor regression is unclear. Here, we show that an intact immune system, specifically CD4+ T cells, is required for the induction of cellular senescence, shutdown of angiogenesis, and chemokine expression resulting in sustained tumor regression upon inactivation of the MYC or BCR-ABL oncogenes in mouse models of T cell acute lymphoblastic lymphoma and pro-B cell leukemia, respectively. Moreover, immune effectors knocked out for thrombospondins failed to induce sustained tumor regression. Hence, CD4+ T cells are required for the remodeling of the tumor microenvironment through the expression of chemokines, such as thrombospondins, in order to elicit oncogene addiction.
- Published
- 2010
44. Definition of an enhanced immune cell therapy in mice that can target stem-like lymphoma cells
- Author
-
Tobi L. Schmidt, Steve H. Thorne, Alice C. Fan, Robert S. Negrin, Pavan Bachireddy, Dean W. Felsher, Rachel P. Sikorski, and Christopher H. Contag
- Subjects
Cancer Research ,Neoplasm, Residual ,Lymphoma ,medicine.medical_treatment ,Cell- and Tissue-Based Therapy ,Mice, Transgenic ,Mice, SCID ,Biology ,Article ,Cell therapy ,Proto-Oncogene Proteins c-myc ,Mice ,Immune system ,Mice, Inbred NOD ,medicine ,Tumor Cells, Cultured ,Animals ,Humans ,Oncolytic Virotherapy ,Mice, Inbred BALB C ,Cancer ,Immunotherapy ,medicine.disease ,Acquired immune system ,Oncolytic virus ,Oncolytic Viruses ,Treatment Outcome ,Oncology ,Immunology ,Cancer cell ,Natural Killer T-Cells ,Stem cell - Abstract
Current treatments of high-grade lymphoma often have curative potential, but unfortunately many patients relapse and develop therapeutic resistance. Thus, there remains a need for novel therapeutics that can target the residual cancer cells whose phenotypes are distinct from the bulk tumor and that are capable of reforming tumors from very few cells. Oncolytic viruses offer an approach to destroy tumors by multiple mechanisms, but they cannot effectively reach residual disease or micrometastases, especially within the lymphatic system. To address these limitations, we have generated immune cells infected with oncolytic viruses as a therapeutic strategy that can combine effective cellular delivery with synergistic tumor killing. In this study, we tested this approach against minimal disease states of lymphomas characterized by the persistence of cancer cells that display stem cell–like properties and resistance to conventional therapies. We found that the immune cells were capable of trafficking to and targeting residual cancer cells. The combination biotherapy used prevented relapse by creating a long-term, disease-free state, with acquired immunity to the tumor functioning as an essential mediator of this effect. Immune components necessary for this acquired immunity were identified. We further demonstrated that the dual biotherapy could be applied before or after conventional therapy. Our approach offers a potentially powerful new way to clear residual cancer cells, showing how restoring immune surveillance is critical for maintenance of a disease-free state. Cancer Res; 70(23); 9837–45. ©2010 AACR.
- Published
- 2010
45. A quantitative PCR method to detect blood microRNAs associated with tumorigenesis in transgenic mice
- Author
-
Marianna Goldrick, Yu Liang, Alice C. Fan, Dean W. Felsher, Pavan Bachireddy, and Jennifer Ho
- Subjects
Pathology ,medicine.medical_specialty ,Cancer Research ,Short Communication ,Mice, Transgenic ,Biology ,medicine.disease_cause ,Malignancy ,lcsh:RC254-282 ,Polymerase Chain Reaction ,03 medical and health sciences ,Mice ,0302 clinical medicine ,microRNA ,medicine ,Animals ,030304 developmental biology ,Whole blood ,0303 health sciences ,Gene Expression Profiling ,Cancer ,Neoplasms, Experimental ,medicine.disease ,lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,3. Good health ,Lymphoma ,MicroRNAs ,Real-time polymerase chain reaction ,Oncology ,030220 oncology & carcinogenesis ,Osteosarcoma ,Molecular Medicine ,Carcinogenesis - Abstract
MicroRNA (miRNA) dysregulation frequently occurs in cancer. Analysis of whole blood miRNA in tumor models has not been widely reported, but could potentially lead to novel assays for early detection and monitoring of cancer. To determine whether miRNAs associated with malignancy could be detected in the peripheral blood, we used real-time reverse transcriptase-PCR to determine miRNA profiles in whole blood obtained from transgenic mice with c-MYC-induced lymphoma, hepatocellular carcinoma and osteosarcoma. The PCR-based assays used in our studies require only 10 nanograms of total RNA, allowing serial mini-profiles (20 – 30 miRNAs) to be carried out on individual animals over time. Blood miRNAs were measured from mice at different stages of MYC-induced lymphomagenesis and regression. Unsupervised hierarchical clustering of the data identified specific miRNA expression profiles that correlated with tumor type and stage. The miRNAs found to be altered in the blood of mice with tumors frequently reverted to normal levels upon tumor regression. Our results suggest that specific changes in blood miRNA can be detected during tumorigenesis and tumor regression.
- Published
- 2008
46. Identifying critical signaling molecules for the treatment of cancer
- Author
-
Constadina, Arvanitis, Pavan K, Bendapudi, Pavan, Bachireddy, and Dean W, Felsher
- Subjects
Disease Models, Animal ,Mice ,Neoplasms ,Animals ,Mice, Transgenic ,Oncogenes ,Neoplasm Proteins ,Signal Transduction - Published
- 2007
47. Angiotensin II Blockade Reverses Myocardial Fibrosis in a Transgenic Mouse Model of Human Hypertrophic Cardiomyopathy
- Author
-
Ali J. Marian, Keith A. Youker, Pavan Bachireddy, Silvia Lutucuta, Robert Roberts, Do Sun Lim, Mark L. Entman, and Alida J. Evans
- Subjects
medicine.medical_specialty ,Cardiomyopathy ,Mice, Transgenic ,Article ,Losartan ,Muscle hypertrophy ,Transforming Growth Factor beta1 ,Angiotensin Receptor Antagonists ,Mice ,Troponin T ,Fibrosis ,Transforming Growth Factor beta ,Physiology (medical) ,Internal medicine ,medicine ,Animals ,Humans ,Antihypertensive Agents ,business.industry ,Myocardium ,Hypertrophic cardiomyopathy ,Cardiomyopathy, Hypertrophic ,medicine.disease ,Angiotensin II ,Disease Models, Animal ,Endocrinology ,cardiovascular system ,Myocardial fibrosis ,Collagen ,Cardiology and Cardiovascular Medicine ,business ,medicine.drug - Abstract
Background —Hypertrophic cardiomyopathy (HCM), the most common cause of sudden cardiac death in the young, is characterized by cardiac hypertrophy, myocyte disarray, and interstitial fibrosis. We propose that hypertrophy and fibrosis are secondary to the activation of trophic and mitotic factors and, thus, potentially reversible. We determined whether the blockade of angiotensin II, a known cardiotrophic factor, could reverse or attenuate interstitial fibrosis in a transgenic mouse model of human HCM. Methods and Results —We randomized 24 adult cardiac troponin T (cTnT-Q 92 ) mice, which exhibit myocyte disarray and interstitial fibrosis, to treatment with losartan or placebo and included 12 nontransgenic mice as controls. The mean dose of losartan and the mean duration of therapy were 14.2±5.3 mg · kg –1 · d –1 and 42±9.6 days, respectively. Mean age, number of males and females, and heart/body weight ratio were similar in the groups. Collagen volume fraction and extent of myocyte disarray were increased in the cTnT-Q 92 mice (placebo group) compared with nontransgenic mice (9.9±6.8% versus 4.5±2.2%, P =0.01, and 27.6±10.6% versus 3.9±2.3%, P Conclusions —Treatment with losartan reversed interstitial fibrosis and the expression of collagen 1α (I) and transforming growth factor-β1 in the hearts of cTnT-Q 92 mice. These findings suggest that losartan has the potential to reverse or attenuate interstitial fibrosis, a major predictor of sudden cardiac death, in human patients with HCM.
- Published
- 2001
48. Reversal of T Cell Exhaustion in Pre-Treatment Marrow T Cells Is Associated with Effective Graft-Versus-Leukemia Responses to Donor Lymphocyte Infusion
- Author
-
Jerome Ritz, Michael Rooney, Olga Pozdnyakova, Edwin P. Alyea, Robert J. Soiffer, Natalie R. Goldstein, Ursula Hainz, Catherine J. Wu, Julie Aldridge, Christine Canning, Nir Hacohen, W. Nicholas Haining, Pavan Bachireddy, and Haesook T. Kim
- Subjects
Predictive marker ,biology ,business.industry ,CD3 ,T cell ,Immunology ,Cell Biology ,Hematology ,medicine.disease ,Biochemistry ,Donor lymphocyte infusion ,Leukemia ,medicine.anatomical_structure ,Immune system ,Antigen ,medicine ,biology.protein ,business ,CD8 - Abstract
Abstract 1903 Donor lymphocyte infusion (DLI) can provide curative treatment for relapsed hematologic malignancies following allogeneic hematopoietic stem cell transplant (HSCT). However, the precise mechanism by which DLI eliminates leukemia cells in vivo has not been established. We hypothesized that marrow-infiltrating immune populations play a critical role in DLI responses since marrow is the primary site of disease and a reservoir of high-avidity antigen-specific memory T cells that can recognize tumor antigens, therefore potentially mediating graft-versus-leukemia (GvL) responses. We performed immunohistochemical staining of immune cells in serial marrow biopsies collected before and after DLI from 29 patients with relapsed CML. Twenty-two patients achieved cytogenetic remission within twelve months (‘responders’) while 7 patients demonstrated persistent disease (‘non-responders’). While no significant changes in the numbers of circulating T cells were seen between patient groups following DLI, the median number of marrow-infiltrating CD8+ T cells increased 2-fold in responders but remained unchanged in non-responders (P=0.02), demonstrating that clinical response to DLI is associated with T cell responses at the site of disease that may not be apparent in the peripheral blood. To investigate whether immune cell infiltration of the marrow could predict DLI response, we compared pre-treatment samples from both patient groups. Responders exhibited significantly higher proportions of CD8+ T cells in pre-DLI marrow compared to non-responders (5% vs 2.5%; P=0.01). Because disease burden is a known risk factor for ineffectual DLI response, we evaluated the interaction between disease burden and pre-existing CD8+ T cell infiltrate through the clinical course of 8 patients with high (≥70%) pre-treatment marrow cellularity. Three of 8 had ≥5% CD8+ T cell marrow infiltrates, and all 3 subsequently achieved cytogenetic remission. In contrast, 5 of 8 patients had To identify candidate mechanisms underlying T cell responses to DLI, we performed mRNA expression profiling of CD3+ T cells isolated from matched pre- and post-treatment marrows of 4 responders and 2 non-responders (U133+ Affymetrix cDNA microarrays). We first compared global gene expression patterns between pre-treatment marrow-infiltrating T cells of both groups. Notably, 28% of significantly upregulated genes in responders play critical roles in T cell exhaustion. This finding was strengthened by unbiased gene set enrichment analysis (GSEA) using 880 sets from the Molecular Signatures Database spiked with 17 additional specifically curated T cell exhaustion sets. Four of 15 positively enriched sets were T cell exhaustion-specific. We next compared differential gene expression in marrow-infiltrating T cells before and after therapy in responders compared to non-responders and found 21% of significantly down-regulated genes to be components within T cell exhaustion pathways along with repression of multiple, distinct T cell exhaustion gene sets. The robust reversibility of T cell exhaustion signatures after DLI therapy underscores this gene module as a likely therapeutic target of DLI. In conclusion, CD8+ T cell marrow infiltration may serve as a novel predictive marker of response to DLI, including patients with high disease burden. In addition, these data implicate T cell exhaustion in distinguishing responders from non-responders and, provocatively, propose reversal of T cell exhaustion as a potential marker of DLI responsiveness in patients with relapsed CML after HSCT. These studies illustrate the importance of local immune responses at the site of disease and suggest a potential tool to predict DLI response in other hematologic malignancies. The clinical debut of newer agents that reverse T cell exhaustion suggests their use in lieu of DLI to promote GvL responses after allogeneic HSCT. Disclosures: No relevant conflicts of interest to declare.
- Published
- 2012
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.