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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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.