290 results on '"Rodig SJ"'
Search Results
2. Abstract PD6-09: The immune microenvironment in hormone receptor-positive breast cancer patients and relationship to treatment outcome following preoperative chemotherapy plus bevacizumab
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Waks, AG, primary, Stover, DG, additional, Barry, W, additional, Dillon, D, additional, Gjini, E, additional, Rodig, SJ, additional, Brock, J, additional, Baltay, M, additional, Savoie, J, additional, Winer, EP, additional, Krop, I, additional, and Tolaney, SM, additional
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- 2018
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3. Synergy between PI3K Signaling and MYC in Burkitt Lymphomagenesis
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Sander S, Calado DP, Srinivasan L, Kxf6chert K, Zhang B, Rosolowski M, Rodig SJ, Holzmann K, Stilgenbauer S, Siebert R, Bullinger L, and Rajewsky K.
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- 2012
4. Signatures of murine B-cell development implicate Yy1 as a regulator of the germinal center-specific program
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Green, Mr, Monti, S, Dalla Favera, R, Pasqualucci, Laura, Walsh, Nc, Schmidt Supprian, M, Kutok, Jl, Rodig, Sj, Neuberg, Ds, Rajewsky, K, Golub, Tr, Alt, Fw, Shipp, Ma, and Manis, Jp
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- 2011
5. CARM1 (PMRT4) is required for proper control of proliferation and differentiation of pulmonary epithelial cells
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O'Brien K., Alberich-Jorda' M., Yadav N., Kocher O., Di Ruscio A., Ebralidze A., Levantini E., Sng NJL., Bhasin M., Caron T., Kim D., Steidl U., Huang G., Halmos B., Rodig SJ., Bedfords MT., Tenen DG., and Kobayashi S
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CARM1 ,epithelial proliferation ,knock out mice ,murine models ,lung development - Abstract
Coactivator-associated arginine methyltransferase I (CARM1; PRMT4) regulates gene expression by multiple mechanisms including methylation of histones and coactivation of steroid receptor transcription. Mice lacking CARM1 are small, fail to breathe and die shortly after birth, demonstrating the crucial role of CARM1 in development. In adults, CARM1 is overexpressed in human grade- III breast tumors and prostate adenocarcinomas, and knockdown of CARM1 inhibits proliferation of breast and prostate cancer cell lines. Based on these observations, we hypothesized that loss of CARM1 in mouse embryos would inhibit pulmonary cell proliferation, resulting in respiratory distress. By contrast, we report here that loss of CARM1 results in hyperproliferation of pulmonary epithelial cells during embryonic development. The lungs of newborn mice lacking CARM1 have substantially reduced airspace compared with their wild-type littermates. In the absence of CARM1, alveolar type II cells show increased proliferation. Electron microscopic analyses demonstrate that lungs from mice lacking CARM1 have immature alveolar type II cells and an absence of alveolar type I cells. Gene expression analysis reveals a dysregulation of cell cycle genes and markers of differentiation in the Carm1 knockout lung. Furthermore, there is an overlap in gene expression in the Carm1 knockout and the glucocorticoid receptor knockout lung, suggesting that hyperproliferation and lack of maturation of the alveolar cells are at least in part caused by attenuation of glucocorticoid-mediated signaling. These results demonstrate for the first time that CARM1 inhibits pulmonary cell proliferation and is required for proper differentiation of alveolar cells.
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- 2010
6. OA031-04. Impairment of HIV-1-specific CD8+ T cell function by soluble epithelial adhesion molecules
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Streeck, H, primary, Kwon, D, additional, Jolin, JS, additional, Trocha, K, additional, Chevalier, M, additional, Caron, T, additional, Law, K, additional, Pyo, A, additional, Toth, I, additional, Kaufmann, DE, additional, Rodig, SJ, additional, Walker, BD, additional, and Altfeld, M, additional
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- 2009
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7. B538 In Vivo Imaging Model of Multiple Myeloma and its Cellular Interaction with the Bone Marrow Milieu
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Runnels, J, primary, Carlson, AL, additional, Thompson, B, additional, Piitsillides, C, additional, Joel, J, additional, Wu, J, additional, Azab, A Kareem, additional, Azab, F, additional, Leleu, X, additional, Jia, X, additional, Burwick, N, additional, Roccaro, AM, additional, Ngo, HT, additional, Melhem, MR, additional, Sacco, A, additional, Rodig, SJ, additional, Kung, A, additional, Anderson, KC, additional, Lin, CP, additional, and Ghobrial, IM, additional
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- 2009
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8. The biology and treatment of EML4-ALK non-small cell lung cancer.
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Sasaki T, Rodig SJ, Chirieac LR, and Jänne PA
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The fusion between echinoderm microtubule-associated protein-like 4 (EML4) and anaplastic lymphoma kinase (ALK) has recently been identified in a subset of non-small cell lung cancers (NSCLCs). EML4-ALK is most often detected in never smokers with lung cancer and has unique pathologic features. EML4-ALK is oncogenic both in vitro and in vivo and ALK kinase inhibitors are quite effective in pre-clinical model systems. More recently ALK inhibitors have entered clinical development and remarkably clinical efficacy has been observed in NSCLC patients harbouring EML4-ALK translocations. This review will focus on the biology, clinical characteristics, diagnosis and treatment of EML4-ALK NSCLC. [ABSTRACT FROM AUTHOR]
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- 2010
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9. Epstein-Barr virus infection is not a characteristic feature of multiple sclerosis brain.
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Willis SN, Stadelmann C, Rodig SJ, Caron T, Gattenloehner S, Mallozzi SS, Roughan JE, Almendinger SE, Blewett MM, Brück W, Hafler DA, O'Connor KC, Willis, Simon N, Stadelmann, Christine, Rodig, Scott J, Caron, Tyler, Gattenloehner, Stefan, Mallozzi, Scott S, Roughan, Jill E, and Almendinger, Stefany E
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Multiple sclerosis is an inflammatory demyelinating disease of the central nervous system (CNS) that is thought to be caused by a combination of genetic and environmental factors. To date, considerable evidence has associated Epstein-Barr virus (EBV) infection with disease development. However, it remains controversial whether EBV infects multiple sclerosis brain and contributes directly to CNS immunopathology. To assess whether EBV infection is a characteristic feature of multiple sclerosis brain, a large cohort of multiple sclerosis specimens containing white matter lesions (nine adult and three paediatric cases) with a heterogeneous B cell infiltrate and a second cohort of multiple sclerosis specimens (12 cases) that included B cell infiltration within the meninges and parenchymal B cell aggregates, were examined for EBV infection using multiple methodologies including in situ hybridization, immunohistochemistry and two independent real-time polymerase chain reaction (PCR) methodologies that detect genomic EBV or the abundant EBV encoded RNA (EBER) 1, respectively. We report that EBV could not be detected in any of the multiple sclerosis specimens containing white matter lesions by any of the methods employed, yet EBV was readily detectable in multiple Epstein-Barr virus-positive control tissues including several CNS lymphomas. Furthermore, EBV was not detected in our second cohort of multiple sclerosis specimens by in situ hybridization. However, our real-time PCR methodologies, which were capable of detecting very few EBV infected cells, detected EBV at low levels in only 2 of the 12 multiple sclerosis meningeal specimens examined. Our finding that CNS EBV infection was rare in multiple sclerosis brain indicates that EBV infection is unlikely to contribute directly to multiple sclerosis brain pathology in the vast majority of cases. [ABSTRACT FROM AUTHOR]
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- 2009
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10. Clinical features and outcome of patients with non-small-cell lung cancer who harbor EML4-ALK.
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Shaw AT, Yeap BY, Mino-Kenudson M, Digumarthy SR, Costa DB, Heist RS, Solomon B, Stubbs H, Admane S, McDermott U, Settleman J, Kobayashi S, Mark EJ, Rodig SJ, Chirieac LR, Kwak EL, Lynch TJ, Iafrate AJ, Shaw, Alice T, and Yeap, Beow Y
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- 2009
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11. OA031-04. Impairment of HIV-1-specific CD8+ T cell function by soluble epithelial adhesion molecules
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Trocha, K, Chevalier, M, Caron, T, Pyo, A, Toth, I, Rodig, SJ, Streeck, Hendrik, Kwon, Douglas, Jolin, Julie Ann, Law, Kayee, Kaufmann, Daniel, Walker, Bruce David, and Altfeld, Marcus
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- 2009
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12. A Peripheral Immune Signature of Responsiveness to PD-1 Blockade in Patients with Classical Hodgkin Lymphoma
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Cader, FZ, primary, Hu, X, additional, Goh, WL, additional, Weinand, K, additional, Ouyang, J, additional, Mandato, E, additional, Redd, R, additional, Lawton, LN, additional, Chen, P, additional, Weirather, JL, additional, Schackmann, RCJ, additional, Li, B, additional, Ma, W, additional, Armand, P, additional, Rodig, SJ, additional, Neuberg, D, additional, Liu, XS, additional, and Shipp, MA, additional
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13. The pre-B-cell receptor associated protein VpreB3 is a useful diagnostic marker for identifying c-MYC translocated lymphomas
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Jeffery L. Kutok, Margaret A. Shipp, Jennifer C. Paterson, Scott J. Rodig, Bjoern Chapuy, Stefano Pileri, Miguel A. Piris, Thomas M. Grogan, Claudio Agostinelli, Teresa Marafioti, Pedro Farinha, Santiago Montes-Moreno, Randy D. Gascoyne, Susana Ben-Neriah, Lynette K. Tumwine, Wenjun Zhang, Hiroaki Nitta, Nathalie A. Johnson, Rodig SJ, Kutok JL, Paterson JC, Nitta H, Zhang W, Chapuy B, Tumwine LK, Montes-Moreno S, Agostinelli C, Johnson NA, Ben-Neriah S, Farinha P, Shipp MA, Piris MA, Grogan TM, Pileri SA, Gascoyne RD, and Marafioti T.
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Pathology ,medicine.medical_specialty ,Lymphoma, B-Cell ,B-cell receptor ,Blotting, Western ,Chromosomal translocation ,Biology ,Immunoglobulin light chain ,Proto-Oncogene Proteins c-myc ,Cell Line, Tumor ,medicine ,Biomarkers, Tumor ,Humans ,B-Lymphocytes ,Large cell ,Gene Expression Profiling ,Germinal center ,Hematology ,medicine.disease ,Germinal Center ,Burkitt Lymphoma ,Immunohistochemistry ,Survival Analysis ,Lymphoma ,Pre-B Cell Receptors ,biology.protein ,Cancer research ,Original Article ,Lymphoma, Large B-Cell, Diffuse ,Antibody ,Diffuse large B-cell lymphoma - Abstract
Background During B-cell development, precursor B cells transiently express the pre-B-cell receptor composed of μ heavy chain complexed with VpreB and λ5 surrogate light chain polypeptides. Recent profiling studies unexpectedly revealed abundant transcripts of one member of the VpreB family, VpreB3, in a subset of mature B cells and Burkitt lymphoma. Design and Methods Here we used a novel antibody to investigate the normal expression pattern of VpreB3 protein in human hematopoietic and lymphoid tissues, and to determine whether VpreB3 could serve as a useful diagnostic biomarker for select B-cell lymphomas. Results We found that VpreB3 protein is normally expressed by precursor B cells in bone marrow and by a subset of normal germinal center B cells in secondary lymphoid organs. Among lymphoid malignancies, we found an association between VpreB3 expression and B-cell tumors with c-MYC abnormalities. VpreB3 was highly expressed in all cases of Burkitt lymphoma, whether of endemic or sporadic origin (44/44 cases, 100%), all cases of B-cell lymphoma, unclassifiable, with features intermediate between diffuse large B-cell lymphoma and Burkitt lymphoma (5/5 cases, 100%), and the majority of diffuse large B-cell lymphomas harboring a c-MYC translocation (15/18 cases, 83%). The expression of VpreB3 in diffuse large B-cell lymphomas without a c-MYC translocation was associated with c-MYC polysomy in 25/75 cases (33%) but only rarely observed in diffuse large B-cell lymphomas lacking a c-MYC abnormality (9/98 cases, 9%). Conclusions We conclude that for B-cell tumors with features suggesting a possible c-MYC translocation, such as intermediate to large cell size and high proliferation rate, the presence of VpreB3 should prompt subsequent confirmatory genetic testing, whereas the absence of VpreB3 is virtually always associated with wild-type c-MYC alleles.
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- 2010
14. Graph Fourier transform for spatial omics representation and analyses of complex organs.
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Chang Y, Liu J, Jiang Y, Ma A, Yeo YY, Guo Q, McNutt M, Krull JE, Rodig SJ, Barouch DH, Nolan GP, Xu D, Jiang S, Li Z, Liu B, and Ma Q
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- Humans, Mice, Animals, Lymph Nodes metabolism, Transcriptome, Machine Learning, Gene Expression Profiling methods, Palatine Tonsil metabolism, Palatine Tonsil cytology, B-Lymphocytes metabolism, Fourier Analysis, Proteomics methods
- Abstract
Spatial omics technologies decipher functional components of complex organs at cellular and subcellular resolutions. We introduce Spatial Graph Fourier Transform (SpaGFT) and apply graph signal processing to a wide range of spatial omics profiling platforms to generate their interpretable representations. This representation supports spatially variable gene identification and improves gene expression imputation, outperforming existing tools in analyzing human and mouse spatial transcriptomics data. SpaGFT can identify immunological regions for B cell maturation in human lymph nodes Visium data and characterize variations in secondary follicles using in-house human tonsil CODEX data. Furthermore, it can be integrated seamlessly into other machine learning frameworks, enhancing accuracy in spatial domain identification, cell type annotation, and subcellular feature inference by up to 40%. Notably, SpaGFT detects rare subcellular organelles, such as Cajal bodies and Set1/COMPASS complexes, in high-resolution spatial proteomics data. This approach provides an explainable graph representation method for exploring tissue biology and function., (© 2024. The Author(s).)
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- 2024
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15. A multidimensional analysis reveals distinct immune phenotypes and the composition of immune aggregates in pediatric acute myeloid leukemia.
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Koedijk JB, van der Werf I, Penter L, Vermeulen MA, Barneh F, Perzolli A, Meesters-Ensing JI, Metselaar DS, Margaritis T, Fiocco M, de Groot-Kruseman HA, Moeniralam R, Bang Christensen K, Porter B, Pfaff K, Garcia JS, Rodig SJ, Wu CJ, Hasle H, Nierkens S, Belderbos ME, Zwaan CM, and Heidenreich O
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Because of the low mutational burden and consequently, fewer potential neoantigens, children with acute myeloid leukemia (AML) are thought to have a T cell-depleted or 'cold' tumor microenvironment and may have a low likelihood of response to T cell-directed immunotherapies. Understanding the composition, phenotype, and spatial organization of T cells and other microenvironmental populations in the pediatric AML bone marrow (BM) is essential for informing future immunotherapeutic trials about targetable immune-evasion mechanisms specific to pediatric AML. Here, we conducted a multidimensional analysis of the tumor immune microenvironment in pediatric AML and non-leukemic controls. We demonstrated that nearly one-third of pediatric AML cases has an immune-infiltrated BM, which is characterized by a decreased ratio of M2- to M1-like macrophages. Furthermore, we detected the presence of large T cell networks, both with and without colocalizing B cells, in the BM and dissected the cellular composition of T- and B cell-rich aggregates using spatial transcriptomics. These analyses revealed that these aggregates are hotspots of CD8
+ T cells, memory B cells, plasma cells and/or plasmablasts, and M1-like macrophages. Collectively, our study provides a multidimensional characterization of the BM immune microenvironment in pediatric AML and indicates starting points for further investigations into immunomodulatory mechanisms in this devastating disease., (© 2024. The Author(s).)- Published
- 2024
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16. Intrapatient variation in PD-L1 expression and tumor mutational burden and the impact on outcomes to immune checkpoint inhibitor therapy in patients with non-small-cell lung cancer.
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Di Federico A, Alden SL, Smithy JW, Ricciuti B, Alessi JV, Wang X, Pecci F, Lamberti G, Gandhi MM, Vaz VR, Spurr LF, Sholl LM, Pfaff KL, Rodig SJ, Li YY, Cherniack AD, Nishino M, Johnson BE, and Awad MM
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- Humans, Male, Female, Aged, Middle Aged, Aged, 80 and over, Adult, Progression-Free Survival, Prognosis, Carcinoma, Non-Small-Cell Lung drug therapy, Carcinoma, Non-Small-Cell Lung genetics, Carcinoma, Non-Small-Cell Lung pathology, Carcinoma, Non-Small-Cell Lung mortality, Carcinoma, Non-Small-Cell Lung immunology, B7-H1 Antigen genetics, B7-H1 Antigen antagonists & inhibitors, Immune Checkpoint Inhibitors therapeutic use, Lung Neoplasms drug therapy, Lung Neoplasms genetics, Lung Neoplasms pathology, Lung Neoplasms mortality, Lung Neoplasms immunology, Mutation, Biomarkers, Tumor genetics, Biomarkers, Tumor metabolism
- Abstract
Background: Programmed death receptor ligand 1 (PD-L1) tumor proportion score (TPS) and tumor mutational burden (TMB) are key predictive biomarkers for immune checkpoint inhibitor (ICI) efficacy in non-small-cell lung cancer (NSCLC). Data on their variation across multiple samples are limited., Patients and Methods: Patients with NSCLC and multiple PD-L1 TPS and/or TMB assessments were included. Clinicopathologic and genomic data were analyzed according to PD-L1 and TMB variation., Results: In total, 402 PD-L1 sample pairs and 413 TMB sample pairs were included. Concordance between pairs was moderate for PD-L1 (ρ = 0.53, P < 0.0001) and high for TMB (ρ = 0.80, P < 0.0001). Shorter time between biopsies correlated with higher concordance in PD-L1, but not in TMB. Major increases (ΔTPS ≥ +50%) and decreases (ΔTPS ≤ -50%) in PD-L1 were observed in 9.7% and 8.0% of cases, respectively. PD-L1, but not TMB, decreased with intervening ICI (P = 0.02). Acquired copy number loss of CD274, PDCD1LG2, and JAK2 were associated with major decrease in PD-L1 (q < 0.05). Among patients with multiple PD-L1 assessments before ICI, cases where all samples had a PD-L1 ≥1%, compared to cases with at least one sample with PD-L1 <1% and another with PD-L1 ≥1%, achieved improved objective response rate and progression-free survival (PFS). Among patients with at least one PD-L1 <1% and one ≥1% before ICI, cases where the most proximal sample was PD-L1 ≥1% had longer median PFS compared to cases where the most proximal PD-L1 was <1%. Among patients with multiple TMB assessments before ICI, patients with a TMB ≥10 mut/Mb based on the most recent assessment, as compared to those with a TMB <10 mut/Mb, achieved improved PFS and overall survival to ICI; instead, no differences were observed when patients were categorized using the oldest TMB assessment., Conclusions: Despite intrapatient concordance in PD-L1 and TMB, variation in these biomarkers can influence ICI outcomes, warranting consideration for reassessment before ICI initiation when feasible., (Copyright © 2024 European Society for Medical Oncology. Published by Elsevier Ltd. All rights reserved.)
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- 2024
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17. Cross-domain information fusion for enhanced cell population delineation in single-cell spatial-omics data.
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Zhu B, Gao S, Chen S, Yeung J, Bai Y, Huang AY, Yeo YY, Liao G, Mao S, Jiang ZG, Rodig SJ, Shalek AK, Nolan GP, Jiang S, and Ma Z
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Cell population delineation and identification is an essential step in single-cell and spatial-omics studies. Spatial-omics technologies can simultaneously measure information from three complementary domains related to this task: expression levels of a panel of molecular biomarkers at single-cell resolution, relative positions of cells, and images of tissue sections, but existing computational methods for performing this task on single-cell spatial-omics datasets often relinquish information from one or more domains. The additional reliance on the availability of "atlas" training or reference datasets limits cell type discovery to well-defined but limited cell population labels, thus posing major challenges for using these methods in practice. Successful integration of all three domains presents an opportunity for uncovering cell populations that are functionally stratified by their spatial contexts at cellular and tissue levels: the key motivation for employing spatial-omics technologies in the first place. In this work, we introduce Cell Spatio- and Neighborhood-informed Annotation and Patterning (CellSNAP), a self-supervised computational method that learns a representation vector for each cell in tissue samples measured by spatial-omics technologies at the single-cell or finer resolution. The learned representation vector fuses information about the corresponding cell across all three aforementioned domains. By applying CellSNAP to datasets spanning both spatial proteomic and spatial transcriptomic modalities, and across different tissue types and disease settings, we show that CellSNAP markedly enhances de novo discovery of biologically relevant cell populations at fine granularity, beyond current approaches, by fully integrating cells' molecular profiles with cellular neighborhood and tissue image information., Competing Interests: CONFLICT OF INTERESTS S.J. is a co-founder of Elucidate Bio Inc, has received speaking honorariums from Cell Signaling Technology, and has received research support from Roche unrelated to this work. G.P.N. received research grants from Pfizer, Inc.; Vaxart, Inc.; Celgene, Inc.; and Juno Therapeutics, Inc. during the time of and unrelated to this work. G.P.N. is a co-founder of Akoya Biosciences, Inc. and of Ionpath Inc., inventor on patent US9909167, and is a Scientific Advisory Board member for Akoya Biosciences, Inc. A.K.S. reports compensation for consulting and/or scientific advisory board membership from Honeycomb Biotechnologies, Cellarity, Ochre Bio, Relation Therapeutics, IntrECate Biotherapeutics, Bio-Rad Laboratories, Fog pharma, Passkey Therapeutics, and Dahlia Biosciences unrelated to this work. S.J.R. receives research support from Bristol-Myers-Squibb and KITE/Gilead. S.J.R. is a member of the SAB of Immunitas Therapeutics. The other authors declare no competing interests.
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- 2024
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18. Genomic and Immunophenotypic Landscape of Acquired Resistance to PD-(L)1 Blockade in Non-Small-Cell Lung Cancer.
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Ricciuti B, Lamberti G, Puchala SR, Mahadevan NR, Lin JR, Alessi JV, Chowdhury A, Li YY, Wang X, Spurr L, Pecci F, Di Federico A, Venkatraman D, Barrichello AP, Gandhi M, Vaz VR, Pangilinan AJ, Haradon D, Lee E, Gupta H, Pfaff KL, Welsh EL, Nishino M, Cherniack AD, Johnson BE, Weirather JL, Dryg ID, Rodig SJ, Sholl LM, Sorger P, Santagata S, Umeton R, and Awad MM
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- Humans, Genomics, Immunophenotyping, Kelch-Like ECH-Associated Protein 1 metabolism, NF-E2-Related Factor 2 metabolism, NF-E2-Related Factor 2 therapeutic use, Antineoplastic Agents, Immunological therapeutic use, Carcinoma, Non-Small-Cell Lung drug therapy, Carcinoma, Non-Small-Cell Lung genetics, Carcinoma, Non-Small-Cell Lung pathology, Lung Neoplasms drug therapy, Lung Neoplasms genetics, Lung Neoplasms pathology
- Abstract
Purpose: Although immune checkpoint inhibitors (ICI) have extended survival in patients with non-small-cell lung cancer (NSCLC), acquired resistance (AR) to ICI frequently develops after an initial benefit. However, the mechanisms of AR to ICI in NSCLC are largely unknown., Methods: Comprehensive tumor genomic profiling, machine learning-based assessment of tumor-infiltrating lymphocytes, multiplexed immunofluorescence, and/or HLA-I immunohistochemistry (IHC) were performed on matched pre- and post-ICI tumor biopsies from patients with NSCLC treated with ICI at the Dana-Farber Cancer Institute who developed AR to ICI. Two additional cohorts of patients with intervening chemotherapy or targeted therapies between biopsies were included as controls., Results: We performed comprehensive genomic profiling and immunophenotypic characterization on samples from 82 patients with NSCLC and matched pre- and post-ICI biopsies and compared findings with a control cohort of patients with non-ICI intervening therapies between biopsies (chemotherapy, N = 32; targeted therapies, N = 89; both, N = 17). Putative resistance mutations were identified in 27.8% of immunotherapy-treated cases and included acquired loss-of-function mutations in STK11 , B2M , APC , MTOR , KEAP1 , and JAK1 / 2 ; these acquired alterations were not observed in the control groups. Immunophenotyping of matched pre- and post-ICI samples demonstrated significant decreases in intratumoral lymphocytes, CD3e
+ and CD8a+ T cells, and PD-L1-PD1 engagement, as well as increased distance between tumor cells and CD8+ PD-1+ T cells. There was a significant decrease in HLA class I expression in the immunotherapy cohort at the time of AR compared with the chemotherapy ( P = .005) and the targeted therapy ( P = .01) cohorts., Conclusion: These findings highlight the genomic and immunophenotypic heterogeneity of ICI resistance in NSCLC, which will need to be considered when developing novel therapeutic strategies aimed at overcoming resistance.- Published
- 2024
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19. Epstein-Barr Virus Orchestrates Spatial Reorganization and Immunomodulation within the Classic Hodgkin Lymphoma Tumor Microenvironment.
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Yeo YY, Qiu H, Bai Y, Zhu B, Chang Y, Yeung J, Michel HA, Wright K, Shaban M, Sadigh S, Nkosi D, Shanmugam V, Rock P, Tung Yiu SP, Cramer P, Paczkowska J, Stephan P, Liao G, Huang AY, Wang H, Chen H, Frauenfeld L, Mitra B, Gewurz BE, Schürch CM, Zhao B, Nolan GP, Zhang B, Shalek AK, Angelo M, Mahmood F, Ma Q, Burack WR, Shipp MA, Rodig SJ, and Jiang S
- Abstract
Classic Hodgkin Lymphoma (cHL) is a tumor composed of rare malignant Hodgkin and Reed-Sternberg (HRS) cells nested within a T-cell rich inflammatory immune infiltrate. cHL is associated with Epstein-Barr Virus (EBV) in 25% of cases. The specific contributions of EBV to the pathogenesis of cHL remain largely unknown, in part due to technical barriers in dissecting the tumor microenvironment (TME) in high detail. Herein, we applied multiplexed ion beam imaging (MIBI) spatial pro-teomics on 6 EBV-positive and 14 EBV-negative cHL samples. We identify key TME features that distinguish between EBV-positive and EBV-negative cHL, including the relative predominance of memory CD8 T cells and increased T-cell dysfunction as a function of spatial proximity to HRS cells. Building upon a larger multi-institutional cohort of 22 EBV-positive and 24 EBV-negative cHL samples, we orthogonally validated our findings through a spatial multi-omics approach, coupling whole transcriptome capture with antibody-defined cell types for tu-mor and T-cell populations within the cHL TME. We delineate contrasting transcriptomic immunological signatures between EBV-positive and EBV-negative cases that differently impact HRS cell proliferation, tumor-immune interactions, and mecha-nisms of T-cell dysregulation and dysfunction. Our multi-modal framework enabled a comprehensive dissection of EBV-linked reorganization and immune evasion within the cHL TME, and highlighted the need to elucidate the cellular and molecular fac-tors of virus-associated tumors, with potential for targeted therapeutic strategies.
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- 2024
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20. Association of Baseline Tumor-Specific Neoantigens and CD8 + T-Cell Infiltration With Immune-Related Adverse Events Secondary to Immune Checkpoint Inhibitors.
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Kerepesi C, Abushukair HM, Ricciuti B, Nassar AH, Adib E, Alessi JV, Pecci F, Rakaee M, Fadlullah MZH, Tőkés AM, Rodig SJ, Awad MM, Tan AC, Bakacs T, and Naqash AR
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- Humans, Immune Checkpoint Inhibitors adverse effects, CD8-Positive T-Lymphocytes pathology, Retrospective Studies, Tumor Microenvironment, Carcinoma, Non-Small-Cell Lung drug therapy, Carcinoma, Non-Small-Cell Lung pathology, Lung Neoplasms drug therapy, Lung Neoplasms pathology
- Abstract
Purpose: Recent evidence has shown that higher tumor mutational burden strongly correlates with an increased risk of immune-related adverse events (irAEs). By using an integrated multiomics approach, we further studied the association between relevant tumor immune microenvironment (TIME) features and irAEs., Methods: Leveraging the US Food and Drug Administration Adverse Event Reporting System, we extracted cases of suspected irAEs to calculate the reporting odds ratios (RORs) of irAEs for cancers treated with immune checkpoint inhibitors (ICIs). TIME features for 32 cancer types were calculated on the basis of the cancer genomic atlas cohorts and indirectly correlated with each cancer's ROR for irAEs. A separate ICI-treated cohort of non-small-cell lung cancer (NSCLC) was used to evaluate the correlation between tissue-based immune markers (CD8
+ , PD-1/L1+, FOXP3+, tumor-infiltrating lymphocytes [TILs]) and irAE occurrence., Results: The analysis of 32 cancers and 33 TIME features demonstrated a significant association between irAE RORs and the median number of base insertions and deletions (INDEL), neoantigens (r = 0.72), single-nucleotide variant neoantigens (r = 0.67), and CD8+ T-cell fraction (r = 0.51). A bivariate model using the median number of INDEL neoantigens and CD8 T-cell fraction had the highest accuracy in predicting RORs (adjusted r2 = 0.52, P = .002). Immunoprofile assessment of 156 patients with NSCLC revealed a strong trend for higher baseline median CD8+ T cells within patients' tumors who experienced any grade irAEs. Using machine learning, an expanded ICI-treated NSCLC cohort (n = 378) further showed a treatment duration-independent association of an increased proportion of high TIL (>median) in patients with irAEs (59.7% v 44%, P = .005). This was confirmed by using the Fine-Gray competing risk approach, demonstrating higher baseline TIL density (>median) associated with a higher cumulative incidence of irAEs ( P = .028)., Conclusion: Our findings highlight a potential role for TIME features, specifically INDEL neoantigens and baseline-immune infiltration, in enabling optimal irAE risk stratification of patients.- Published
- 2024
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21. A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity.
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Patel AG, Ashenberg O, Collins NB, Segerstolpe Å, Jiang S, Slyper M, Huang X, Caraccio C, Jin H, Sheppard H, Xu K, Chang TC, Orr BA, Shirinifard A, Chapple RH, Shen A, Clay MR, Tatevossian RG, Reilly C, Patel J, Lupo M, Cline C, Dionne D, Porter CBM, Waldman J, Bai Y, Zhu B, Barrera I, Murray E, Vigneau S, Napolitano S, Wakiro I, Wu J, Grimaldi G, Dellostritto L, Helvie K, Rotem A, Lako A, Cullen N, Pfaff KL, Karlström Å, Jané-Valbuena J, Todres E, Thorner A, Geeleher P, Rodig SJ, Zhou X, Stewart E, Johnson BE, Wu G, Chen F, Yu J, Goltsev Y, Nolan GP, Rozenblatt-Rosen O, Regev A, and Dyer MA
- Abstract
Neuroblastoma is a pediatric cancer arising from the developing sympathoadrenal lineage with complex inter- and intra-tumoral heterogeneity. To chart this complexity, we generated a comprehensive cell atlas of 55 neuroblastoma patient tumors, collected from two pediatric cancer institutions, spanning a range of clinical, genetic, and histologic features. Our atlas combines single-cell/nucleus RNA-seq (sc/scRNA-seq), bulk RNA-seq, whole exome sequencing, DNA methylation profiling, spatial transcriptomics, and two spatial proteomic methods. Sc/snRNA-seq revealed three malignant cell states with features of sympathoadrenal lineage development. All of the neuroblastomas had malignant cells that resembled sympathoblasts and the more differentiated adrenergic cells. A subset of tumors had malignant cells in a mesenchymal cell state with molecular features of Schwann cell precursors. DNA methylation profiles defined four groupings of patients, which differ in the degree of malignant cell heterogeneity and clinical outcomes. Using spatial proteomics, we found that neuroblastomas are spatially compartmentalized, with malignant tumor cells sequestered away from immune cells. Finally, we identify spatially restricted signaling patterns in immune cells from spatial transcriptomics. To facilitate the visualization and analysis of our atlas as a resource for further research in neuroblastoma, single cell, and spatial-omics, all data are shared through the Human Tumor Atlas Network Data Commons at www.humantumoratlas.org.
- Published
- 2024
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22. MAPS: pathologist-level cell type annotation from tissue images through machine learning.
- Author
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Shaban M, Bai Y, Qiu H, Mao S, Yeung J, Yeo YY, Shanmugam V, Chen H, Zhu B, Weirather JL, Nolan GP, Shipp MA, Rodig SJ, Jiang S, and Mahmood F
- Subjects
- Humans, Diagnostic Imaging, Proteomics methods, Pathologists, Machine Learning
- Abstract
Highly multiplexed protein imaging is emerging as a potent technique for analyzing protein distribution within cells and tissues in their native context. However, existing cell annotation methods utilizing high-plex spatial proteomics data are resource intensive and necessitate iterative expert input, thereby constraining their scalability and practicality for extensive datasets. We introduce MAPS (Machine learning for Analysis of Proteomics in Spatial biology), a machine learning approach facilitating rapid and precise cell type identification with human-level accuracy from spatial proteomics data. Validated on multiple in-house and publicly available MIBI and CODEX datasets, MAPS outperforms current annotation techniques in terms of speed and accuracy, achieving pathologist-level precision even for typically challenging cell types, including tumor cells of immune origin. By democratizing rapidly deployable and scalable machine learning annotation, MAPS holds significant potential to expedite advances in tissue biology and disease comprehension., (© 2024. The Author(s).)
- Published
- 2024
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23. A Hitchhiker's guide to high-dimensional tissue imaging with multiplexed ion beam imaging.
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Yeo YY, Cramer P, Deisher A, Bai Y, Zhu B, Yeo WJ, Shipp MA, Rodig SJ, and Jiang S
- Subjects
- Humans, Spectrometry, Mass, Secondary Ion methods, Tissue Fixation methods, Image Processing, Computer-Assisted methods, Formaldehyde chemistry, Paraffin Embedding methods
- Abstract
Advancements in multiplexed tissue imaging technologies are vital in shaping our understanding of tissue microenvironmental influences in disease contexts. These technologies now allow us to relate the phenotype of individual cells to their higher-order roles in tissue organization and function. Multiplexed Ion Beam Imaging (MIBI) is one of such technologies, which uses metal isotope-labeled antibodies and secondary ion mass spectrometry (SIMS) to image more than 40 protein markers simultaneously within a single tissue section. Here, we describe an optimized MIBI workflow for high-plex analysis of Formalin-Fixed Paraffin-Embedded (FFPE) tissues following antigen retrieval, metal isotope-conjugated antibody staining, imaging using the MIBI instrument, and subsequent data processing and analysis. While this workflow is focused on imaging human FFPE samples using the MIBI, this workflow can be easily extended to model systems, biological questions, and multiplexed imaging modalities., (Copyright © 2024 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.)
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- 2024
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24. Cutaneous Manifestations of Myeloid Neoplasms Exhibit Broad and Divergent Morphologic and Immunophenotypic Features but Share Ancestral Clonal Mutations With Bone Marrow.
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Sadigh S, DeAngelo DJ, Garcia JS, Hasserjian RP, Hergott CB, Lane AA, Lovitch SB, Lucas F, Luskin MR, Morgan EA, Pinkus GS, Pozdnyakova O, Rodig SJ, Shanmugam V, Tsai HK, Winer ES, Zemmour D, and Kim AS
- Subjects
- Humans, Bone Marrow pathology, Dendritic Cells metabolism, Mutation, Nuclear Proteins genetics, Leukemia, Myeloid, Acute pathology, Hematologic Neoplasms pathology, Skin Neoplasms pathology, Myeloproliferative Disorders pathology
- Abstract
In this study, we performed a comprehensive molecular analysis of paired skin and peripheral blood/bone marrow (BM) samples from 17 patients with cutaneous myeloid or cutaneous histiocytic-dendritic neoplasms. The cutaneous manifestations included 10 patients with cutaneous acute myeloid leukemia (c-AML), 2 patients with full or partial Langerhans cell differentiation, 2 patients with blastic plasmacytoid dendritic cell neoplasms (BPDCN), 1 patient with both Langerhans cell differentiation and BPDCN, and 2 patients with full or partial indeterminate dendritic cell differentiation. Seven of the 10 c-AML patients (70%) exhibited concurrent or subsequent marrow involvement by acute myeloid leukemia, with all 7 cases (100%) demonstrating shared clonal mutations in both the skin and BM. However, clonal relatedness was documented in one additional case that never had any BM involvement. Nevertheless, NPM1 mutations were identified in 7 of the 10 (70%) of these c-AML cases while one had KMT2A rearrangement and one showed inv(16). All 3 patients (100%) with Langerhans cell neoplasms, 2 patients with BPDCN (100%), and one of the 2 patients (50%) with other cutaneous dendritic cell neoplasms also demonstrated shared mutations between the skin and concurrent or subsequent myeloid neoplasms. Both BM and c-AML shared identical founding drivers, with a predominance of NPM1, DNMT3A, and translocations associated with monocytic differentiation, with common cutaneous-only mutations involving genes in the signal transduction and epigenetic pathways. Cutaneous histiocytic-dendritic neoplasms shared founding drivers in ASXL1, TET2, and/or SRSF2. However, in the Langerhans cell histiocytosis or histiocytic sarcoma cases, there exist recurrent secondary RAS pathway hits, whereas cutaneous BPDCN cases exhibit copy number or structural variants. These results enrich and broaden our understanding of clonally related cutaneous manifestations of myeloid neoplasms and further illuminate the highly diverse spectrum of morphologic and immunophenotypic features they exhibit., (Copyright © 2023 United States & Canadian Academy of Pathology. Published by Elsevier Inc. All rights reserved.)
- Published
- 2024
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25. A multi-cohort phase 1b trial of rituximab in combination with immunotherapy doublets in relapsed/refractory follicular lymphoma.
- Author
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Merryman RW, Redd RA, Freedman AS, Ahn IE, Brown JR, Crombie JL, Davids MS, Fisher DC, Jacobsen ED, Kim AI, LaCasce AS, Ng S, Odejide OO, Parry EM, Isufi I, Kline J, Cohen JB, Mehta-Shah N, Bartlett NL, Mei M, Kuntz TM, Wolff J, Rodig SJ, Armand P, and Jacobson CA
- Subjects
- Humans, Rituximab, Programmed Cell Death 1 Receptor, Antineoplastic Combined Chemotherapy Protocols therapeutic use, Neoplasm Recurrence, Local drug therapy, Antibodies, Monoclonal adverse effects, Immunotherapy, Tumor Microenvironment, Lymphoma, Follicular drug therapy, Antineoplastic Agents therapeutic use
- Abstract
Antibodies targeting PD-1 or 4-1BB achieve objective responses in follicular lymphoma (FL), but only in a minority of patients. We hypothesized that targeting multiple immune receptors could overcome immune resistance and increase response rates in patients with relapsed/refractory FL. We therefore conducted a phase 1b trial testing time-limited therapy with different immunotherapy doublets targeting 4-1BB (utomilumab), OX-40 (ivuxolimab), and PD-L1 (avelumab) in combination with rituximab among patients with relapsed/refractory grade 1-3A FL. Patients were enrolled onto 2 of 3 planned cohorts (cohort 1 - rituximab/utomilumab/avelumab; cohort 2 - rituximab/ivuxolimab/utomilumab). 3+3 dose escalation was followed by dose expansion at the recommended phase 2 dose (RP2D). Twenty-four patients were enrolled (16 in cohort 1 and 9 in cohort 2, with one treated in both cohorts). No patients discontinued treatment due to adverse events and the RP2D was the highest dose level tested in both cohorts. In cohort 1, the objective and complete response rates were 44% and 19%, respectively (50% and 30%, respectively, at RP2D). In cohort 2, no responses were observed. The median progression-free survivals in cohorts 1 and 2 were 6.9 and 3.2 months, respectively. In cohort 1, higher density of PD-1+ tumor-infiltrating T-cells on baseline biopsies and lower density of 4-1BB+ and TIGIT+ T-cells in on-treatment biopsies were associated with response. Abundance of Akkermansia in stool samples was also associated with response. Our results support a possible role for 4-1BB agonist therapy in FL and suggest that features of the tumor microenvironment and stool microbiome may be associated with clinical outcomes (NCT03636503)., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
- Published
- 2024
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26. Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues.
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Wang H, Huang R, Nelson J, Gao C, Tran M, Yeaton A, Felt K, Pfaff KL, Bowman T, Rodig SJ, Wei K, Goods BA, and Farhi SL
- Abstract
Emerging imaging spatial transcriptomics (iST) platforms and coupled analytical methods can recover cell-to-cell interactions, groups of spatially covarying genes, and gene signatures associated with pathological features, and are thus particularly well-suited for applications in formalin fixed paraffin embedded (FFPE) tissues. Here, we benchmarked the performance of three commercial iST platforms on serial sections from tissue microarrays (TMAs) containing 23 tumor and normal tissue types for both relative technical and biological performance. On matched genes, we found that 10x Xenium shows higher transcript counts per gene without sacrificing specificity, but that all three platforms concord to orthogonal RNA-seq datasets and can perform spatially resolved cell typing, albeit with different false discovery rates, cell segmentation error frequencies, and with varying degrees of sub-clustering for downstream biological analyses. Taken together, our analyses provide a comprehensive benchmark to guide the choice of iST method as researchers design studies with precious samples in this rapidly evolving field., Competing Interests: Declaration of interests All authors declare that they have no conflicts of interest.
- Published
- 2023
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27. Impact of Aneuploidy and Chromosome 9p Loss on Tumor Immune Microenvironment and Immune Checkpoint Inhibitor Efficacy in NSCLC.
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Alessi JV, Wang X, Elkrief A, Ricciuti B, Li YY, Gupta H, Spurr LF, Rizvi H, Luo J, Pecci F, Lamberti G, Recondo G, Venkatraman D, Di Federico A, Gandhi MM, Vaz VR, Nishino M, Sholl LM, Cherniack AD, Ladanyi M, Price A, Richards AL, Donoghue M, Lindsay J, Sharma B, Turner MM, Pfaff KL, Felt KD, Rodig SJ, Lin X, Meyerson ML, Johnson BE, Christiani DC, Schoenfeld AJ, and Awad MM
- Subjects
- Humans, Immune Checkpoint Inhibitors therapeutic use, B7-H1 Antigen, Retrospective Studies, Aneuploidy, Chromosome Aberrations, Chromosomes metabolism, Tumor Microenvironment, Lung Neoplasms drug therapy, Lung Neoplasms genetics, Lung Neoplasms pathology, Carcinoma, Non-Small-Cell Lung drug therapy, Carcinoma, Non-Small-Cell Lung genetics, Carcinoma, Non-Small-Cell Lung pathology
- Abstract
Introduction: Although gene-level copy number alterations have been studied as a potential biomarker of immunotherapy efficacy in NSCLC, the impact of aneuploidy burden and chromosomal arm-level events on immune checkpoint inhibitor (ICI) efficacy in NSCLC is uncertain., Methods: Patients who received programmed cell death protein 1 or programmed death-ligand 1 (PD-L1) inhibitor at two academic centers were included. Across all 22 chromosomes analyzed, an arm was considered altered if at least 70% of its territory was either gained or deleted. Among nonsquamous NSCLCs which underwent targeted next-generation sequencing, we retrospectively quantified aneuploidy using the adjusted fraction of chromosomal arm alterations (FAA), defined as the number of altered chromosome arms divided by the number of chromosome arms assessed, adjusted for tumor purity., Results: Among 2293 nonsquamous NSCLCs identified, the median FAA increased with more advanced cancer stage and decreased with higher PD-L1 tumor proportion score (TPS) levels (median FAA in TPS < 1%: 0.09, TPS 1%-49%: 0.08, TPS ≥ 50%: 0.05, p < 0.0001). There was a very weak correlation between FAA and tumor mutational burden when taken as continuous variables (R: 0.07, p = 0.0005). A total of 765 advanced nonsquamous NSCLCs with available FAA values were treated with ICIs. With decreasing FAA tertiles, there was a progressive improvement in objective response rate (ORR 15.1% in upper tertile versus 23.2% in middle tertile versus 28.4% in lowest tertile, p = 0.001), median progression-free survival (mPFS 2.5 versus 3.3 versus 4.1 mo, p < 0.0001), and median overall survival (mOS 12.5 versus 13.9 versus 16.4 mo, p = 0.006), respectively. In the arm-level enrichment analysis, chromosome 9p loss (OR = 0.22, Q = 0.0002) and chromosome 1q gain (OR = 0.43, Q = 0.002) were significantly enriched in ICI nonresponders after false discovery rate adjustment. Compared with NSCLCs without chromosome 9p loss (n = 452), those with 9p loss (n = 154) had a lower ORR (28.1% versus 7.8%, p < 0.0001), a shorter mPFS (4.1 versus 2.3 mo, p < 0.0001), and a shorter mOS (18.0 versus 9.6 mo, p < 0.0001) to immunotherapy. In addition, among NSCLCs with high PD-L1 expression (TPS ≥ 50%), chromosome 9p loss was associated with lower ORR (43% versus 6%, p < 0.0001), shorter mPFS (6.4 versus 2.6 mo, p = 0.0006), and shorter mOS (30.2 versus 14.3 mo, p = 0.0008) to immunotherapy compared with NSCLCs without 9p loss. In multivariable analysis, adjusting for key variables including FAA, chromosome 9p loss, but not 1q gain, retained a significant impact on ORR (hazard ratio [HR] = 0.25, p < 0.001), mPFS (HR = 1.49, p = 0.001), and mOS (HR = 1.47, p = 0.003). Multiplexed immunofluorescence and computational deconvolution of RNA sequencing data revealed that tumors with either high FAA levels or chromosome 9p loss had significantly fewer tumor-associated cytotoxic immune cells., Conclusions: Nonsquamous NSCLCs with high aneuploidy and chromosome 9p loss have a distinct tumor immune microenvironment and less favorable outcomes to ICIs., (Copyright © 2023 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.)
- Published
- 2023
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28. Clinical trial links oncolytic immunoactivation to survival in glioblastoma.
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Ling AL, Solomon IH, Landivar AM, Nakashima H, Woods JK, Santos A, Masud N, Fell G, Mo X, Yilmaz AS, Grant J, Zhang A, Bernstock JD, Torio E, Ito H, Liu J, Shono N, Nowicki MO, Triggs D, Halloran P, Piranlioglu R, Soni H, Stopa B, Bi WL, Peruzzi P, Chen E, Malinowski SW, Prabhu MC, Zeng Y, Carlisle A, Rodig SJ, Wen PY, Lee EQ, Nayak L, Chukwueke U, Gonzalez Castro LN, Dumont SD, Batchelor T, Kittelberger K, Tikhonova E, Miheecheva N, Tabakov D, Shin N, Gorbacheva A, Shumskiy A, Frenkel F, Aguilar-Cordova E, Aguilar LK, Krisky D, Wechuck J, Manzanera A, Matheny C, Tak PP, Barone F, Kovarsky D, Tirosh I, Suvà ML, Wucherpfennig KW, Ligon K, Reardon DA, and Chiocca EA
- Subjects
- Humans, Nestin genetics, Reproducibility of Results, Survival Analysis, T-Lymphocytes cytology, T-Lymphocytes immunology, Treatment Outcome, Tumor Microenvironment immunology, Brain Neoplasms immunology, Brain Neoplasms pathology, Glioblastoma immunology, Glioblastoma pathology, Oncolytic Virotherapy adverse effects, Oncolytic Viruses genetics, Oncolytic Viruses immunology, Oncolytic Viruses physiology, Herpesvirus 1, Human genetics, Herpesvirus 1, Human immunology, Herpesvirus 1, Human physiology
- Abstract
Immunotherapy failures can result from the highly suppressive tumour microenvironment that characterizes aggressive forms of cancer such as recurrent glioblastoma (rGBM)
1,2 . Here we report the results of a first-in-human phase I trial in 41 patients with rGBM who were injected with CAN-3110-an oncolytic herpes virus (oHSV)3 . In contrast to other clinical oHSVs, CAN-3110 retains the viral neurovirulence ICP34.5 gene transcribed by a nestin promoter; nestin is overexpressed in GBM and other invasive tumours, but not in the adult brain or healthy differentiated tissue4 . These modifications confer CAN-3110 with preferential tumour replication. No dose-limiting toxicities were encountered. Positive HSV1 serology was significantly associated with both improved survival and clearance of CAN-3110 from injected tumours. Survival after treatment, particularly in individuals seropositive for HSV1, was significantly associated with (1) changes in tumour/PBMC T cell counts and clonal diversity, (2) peripheral expansion/contraction of specific T cell clonotypes; and (3) tumour transcriptomic signatures of immune activation. These results provide human validation that intralesional oHSV treatment enhances anticancer immune responses even in immunosuppressive tumour microenvironments, particularly in individuals with cognate serology to the injected virus. This provides a biological rationale for use of this oncolytic modality in cancers that are otherwise unresponsive to immunotherapy (ClinicalTrials.gov: NCT03152318 )., (© 2023. The Author(s).)- Published
- 2023
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29. MYD88L265P augments proximal B-cell receptor signaling in large B-cell lymphomas via an interaction with DOCK8.
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Mandato E, Yan Q, Ouyang J, Paczkowska J, Qin Y, Hao Y, Bojarczuk K, Hansen J, Chapuy B, Rodig SJ, Khan SJ, Redd RA, and Shipp MA
- Subjects
- Animals, Humans, Mice, Focal Adhesion Kinase 2 metabolism, Guanine Nucleotide Exchange Factors metabolism, Receptors, Antigen, B-Cell metabolism, Signal Transduction, Toll-Like Receptors, Lymphoma, Large B-Cell, Diffuse pathology, Myeloid Differentiation Factor 88 genetics, Myeloid Differentiation Factor 88 metabolism
- Abstract
Diffuse large B-cell lymphoma (DLBCL) is a clinically and genetically heterogeneous disease with at least 5 recognized molecular subtypes. Cluster 5 (C5)/MCD tumors frequently exhibit concurrent alterations in the toll-like receptor (TLR) and B-cell receptor (BCR) pathway members, MYD88L265P and CD79B, and have a less favorable prognosis. In healthy B cells, the synergy between TLR and BCR signaling pathways integrates innate and adaptive immune responses and augments downstream NF-κB activation. In addition, physiologic TLR9 pathway engagement via MYD88, protein tyrosine kinase 2 (PYK2), and dedicator of cytokinesis 8 (DOCK8) increases proximal BCR signaling in healthy murine B cells. Although C5/MCD DLBCLs are selectively sensitive to Bruton tyrosine kinase (BTK) inhibition in in vitro studies and certain clinical trials, the role of mutated MYD88 in proximal BCR signaling remains undefined. Using engineered DLBCL cell line models, we found that concurrent MYD88L265P and CD79B alterations significantly increased the magnitude and duration of proximal BCR signaling, at the level of spleen tyrosine kinase and BTK, and augmented PYK2-dependent DOCK8 phosphorylation. MYD88L265P DLBCLs have significantly increased colocalization of DOCK8 with both MYD88 and the proximal BCR-associated Src kinase, LYN, in comparison with MYD88WT DLBCLs, implicating DOCK8 in MYD88L265P/proximal BCR cross talk. Additionally, DOCK8 depletion selectively decreased proximal BCR signaling, cellular proliferation, and viability of DLBCLs with endogenous MYD88L265P/CD79BY196F alterations and increased the efficacy of BTK blockade in these lymphomas. Therefore, MYD88L265P/DOCK8-enhanced proximal BCR signaling is a likely mechanism for the increased sensitivity of C5/MCD DLBCLs to BTK blockade., (© 2023 by The American Society of Hematology.)
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- 2023
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30. Preexisting tumor-resident T cells with cytotoxic potential associate with response to neoadjuvant anti-PD-1 in head and neck cancer.
- Author
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Oliveira G, Egloff AM, Afeyan AB, Wolff JO, Zeng Z, Chernock RD, Zhou L, Messier C, Lizotte P, Pfaff KL, Stromhaug K, Penter L, Haddad RI, Hanna GJ, Schoenfeld JD, Goguen LA, Annino DJ, Jo V, Oppelt P, Pipkorn P, Jackson R, Puram SV, Paniello RC, Rich JT, Webb J, Zevallos JP, Mansour M, Fu J, Dunn GP, Rodig SJ, Ley J, Morris LGT, Dunn L, Paweletz CP, Kallogjeri D, Piccirillo JF, Adkins DR, Wu CJ, and Uppaluri R
- Subjects
- Humans, Neoadjuvant Therapy, CD8-Positive T-Lymphocytes, Squamous Cell Carcinoma of Head and Neck, Tumor Microenvironment, Head and Neck Neoplasms drug therapy, Antineoplastic Agents
- Abstract
About 50% of patients with locally advanced head and neck squamous cell carcinoma (HNSCC) experience recurrences after definitive therapy. The presurgical administration of anti-programmed cell death protein 1 (PD-1) immunotherapy results in substantial pathologic tumor responses (pTR) within the tumor microenvironment (TME). However, the mechanisms underlying the dynamics of antitumor T cells upon neoadjuvant PD-1 blockade remain unresolved, and approaches to increase pathologic responses are lacking. In a phase 2 trial (NCT02296684), we observed that 45% of patients treated with two doses of neoadjuvant pembrolizumab experienced marked pTRs (≥50%). Single-cell analysis of 17,158 CD8
+ T cells from 14 tumor biopsies, including 6 matched pre-post neoadjuvant treatment, revealed that responding tumors had clonally expanded putative tumor-specific exhausted CD8+ tumor-infiltrating lymphocytes (TILs) with a tissue-resident memory program, characterized by high cytotoxic potential (CTX+ ) and ZNF683 expression, within the baseline TME. Pathologic responses after 5 weeks of PD-1 blockade were consistent with activation of preexisting CTX+ ZNF683+ CD8+ TILs, paralleling loss of viable tumor and associated tumor antigens. Response was associated with high numbers of CD103+ PD-1+ CD8+ T cells infiltrating pretreatment lesions, whereas revival of nonexhausted persisting clones and clonal replacement were modest. By contrast, nonresponder baseline TME exhibited a relative absence of ZNF683+ CTX+ TILs and subsequent accumulation of highly exhausted clones. In HNSCC, revival of preexisting ZNF683+ CTX+ TILs is a major mechanism of response in the immediate postneoadjuvant setting.- Published
- 2023
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31. Diffuse large B-cell lymphomas have spatially defined, tumor immune microenvironments revealed by high-parameter imaging.
- Author
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Wright KT, Weirather JL, Jiang S, Kao KZ, Sigal Y, Giobbie-Hurder A, Shipp MA, and Rodig SJ
- Subjects
- Humans, Diagnostic Imaging, CD8-Positive T-Lymphocytes, Indoleamine-Pyrrole 2,3,-Dioxygenase, Tumor Microenvironment, Lymphoma, Large B-Cell, Diffuse, Lymphoma, Non-Hodgkin
- Abstract
Diffuse large B-cell lymphoma (DLBCL) not otherwise specified is the most common aggressive non-Hodgkin lymphoma and a biologically heterogeneous disease. Despite the development of effective immunotherapies, the organization of the DLBCL tumor-immune microenvironment (TIME) remains poorly understood.We interrogated the intact TIME of 51 de novo DLBCLs with triplicate sampling to characterize 337 995 tumor and immune cells using a 27-plex antibody panel that captured cell lineage, architectural, and functional markers. We spatially assigned individual cells, identified local cell neighborhoods, and established their topographical organization in situ. We found that the organization of local tumor and immune cells can be modeled by 6 composite cell neighborhood types (CNTs). Differential CNT representation divided cases into 3 aggregate TIME categories: immune-deficient, dendritic cell-enriched (DC-enriched), and macrophage-enriched (Mac-enriched). Cases with immune-deficient TIMEs have tumor cell-rich CNTs, in which the few infiltrating immune cells are enriched near CD31+ vessels, in keeping with limited immune activity. Cases with DC-enriched TIMEs selectively include tumor cell-poor/immune cell-rich CNTs with high numbers of CD11c+ DCs and antigen-experienced T cells also enriched near CD31+ vessels, in keeping with increased immune activity. Cases with Mac-enriched TIMEs selectively include tumor cell-poor/immune cell-rich CNTs with high numbers of CD163+ macrophages and CD8 T cells throughout the microenvironment, accompanied by increased IDO-1 and LAG-3 and decreased HLA-DR expression and genetic signatures in keeping with immune evasion. Our findings reveal that the heterogenous cellular components of DLBCL are not randomly distributed but organized into CNTs that define aggregate TIMEs with distinct cellular, spatial, and functional features., (© 2023 by The American Society of Hematology. Licensed under Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0), permitting only noncommercial, nonderivative use with attribution. All other rights reserved.)
- Published
- 2023
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32. Targeting KDM2A Enhances T-cell Infiltration in NSD1-Deficient Head and Neck Squamous Cell Carcinoma.
- Author
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Chen C, Shin JH, Fang Z, Brennan K, Horowitz NB, Pfaff KL, Welsh EL, Rodig SJ, Gevaert O, Gozani O, Uppaluri R, and Sunwoo JB
- Subjects
- Animals, Mice, Chemokines, Squamous Cell Carcinoma of Head and Neck genetics, T-Lymphocytes, Tumor Microenvironment, Humans, Head and Neck Neoplasms genetics, Histones genetics
- Abstract
In head and neck squamous cell carcinoma (HNSCC), a significant proportion of tumors have inactivating mutations in the histone methyltransferase NSD1. In these tumors, NSD1 inactivation is a driver of T-cell exclusion from the tumor microenvironment (TME). A better understanding of the NSD1-mediated mechanism regulating infiltration of T cells into the TME could help identify approaches to overcome immunosuppression. Here, we demonstrated that NSD1 inactivation results in lower levels of H3K36 dimethylation and higher levels of H3K27 trimethylation, the latter being a known repressive histone mark enriched on the promoters of key T-cell chemokines CXCL9 and CXCL10. HNSCC with NSD1 mutations had lower levels of these chemokines and lacked responses to PD-1 immune checkpoint blockade. Inhibition of KDM2A, the primary lysine demethylase that is selective for H3K36, reversed the altered histone marks induced by NSD1 loss and restored T-cell infiltration into the TME. Importantly, KDM2A suppression decreased growth of NSD1-deficient tumors in immunocompetent, but not in immunodeficient, mice. Together, these data indicate that KDM2A is an immunotherapeutic target for overcoming immune exclusion in HNSCC., Significance: The altered epigenetic landscape of NSD1-deficient tumors confers sensitivity to inhibition of the histone-modifying enzyme KDM2A as an immunotherapeutic strategy to stimulate T-cell infiltration and suppress tumor growth., (©2023 American Association for Cancer Research.)
- Published
- 2023
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33. Impact of TMB/PD-L1 expression and pneumonitis on chemoradiation and durvalumab response in stage III NSCLC.
- Author
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Alessi JV, Ricciuti B, Wang X, Pecci F, Di Federico A, Lamberti G, Elkrief A, Rodig SJ, Lebow ES, Eicholz JE, Thor M, Rimner A, Schoenfeld AJ, Chaft JE, Johnson BE, Gomez DR, Awad MM, and Shaverdian N
- Subjects
- Humans, B7-H1 Antigen genetics, Retrospective Studies, Carcinoma, Non-Small-Cell Lung genetics, Carcinoma, Non-Small-Cell Lung therapy, Lung Neoplasms genetics, Lung Neoplasms therapy, Pneumonia
- Abstract
Although concurrent chemoradiation (CRT) and durvalumab consolidation has become a standard treatment for stage III non-small cell lung cancer (NSCLC), clinicopathologic and genomic factors associated with its efficacy remain poorly characterized. Here, in a multi-institutional retrospective cohort study of 328 patients treated with CRT and durvalumab, we identify that very high PD-L1 tumor proportion score (TPS) expression ( ≥ 90%) and increased tumor mutational burden (TMB) are independently associated with prolonged disease control. Additionally, we identify the impact of pneumonitis and its timing on disease outcomes among patients who discontinue durvalumab: compared to patients who experienced early-onset pneumonitis ( < 3 months) leading to durvalumab discontinuation, patients with late-onset pneumonitis had a significantly longer PFS (12.7 months vs not reached; HR 0.24 [95% CI, 0.10 to 0.58]; P = 0.001) and overall survival (37.2 months vs not reached; HR 0.26 [95% CI, 0.09 to 0.79]; P = 0.017). These findings suggest that opportunities exist to improve outcomes in patients with lower PD-L1 and TMB levels, and those at highest risk for pneumonitis., (© 2023. The Author(s).)
- Published
- 2023
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34. Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology.
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Bai Y, Zhu B, Oliveria JP, Cannon BJ, Feyaerts D, Bosse M, Vijayaragavan K, Greenwald NF, Phillips D, Schürch CM, Naik SM, Ganio EA, Gaudilliere B, Rodig SJ, Miller MB, Angelo M, Bendall SC, Rovira-Clavé X, Nolan GP, and Jiang S
- Subjects
- Humans, Vacuum, Hydrogels chemistry, Microscopy methods, Proteins
- Abstract
Cellular organization and functions encompass multiple scales in vivo. Emerging high-plex imaging technologies are limited in resolving subcellular biomolecular features. Expansion Microscopy (ExM) and related techniques physically expand samples for enhanced spatial resolution, but are challenging to be combined with high-plex imaging technologies to enable integrative multiscaled tissue biology insights. Here, we introduce Expand and comPRESS hydrOgels (ExPRESSO), an ExM framework that allows high-plex protein staining, physical expansion, and removal of water, while retaining the lateral tissue expansion. We demonstrate ExPRESSO imaging of archival clinical tissue samples on Multiplexed Ion Beam Imaging and Imaging Mass Cytometry platforms, with detection capabilities of > 40 markers. Application of ExPRESSO on archival human lymphoid and brain tissues resolved tissue architecture at the subcellular level, particularly that of the blood-brain barrier. ExPRESSO hence provides a platform for extending the analysis compatibility of hydrogel-expanded biospecimens to mass spectrometry, with minimal modifications to protocols and instrumentation., (© 2023. The Author(s).)
- Published
- 2023
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35. High-plex immunofluorescence imaging and traditional histology of the same tissue section for discovering image-based biomarkers.
- Author
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Lin JR, Chen YA, Campton D, Cooper J, Coy S, Yapp C, Tefft JB, McCarty E, Ligon KL, Rodig SJ, Reese S, George T, Santagata S, and Sorger PK
- Subjects
- Humans, Retrospective Studies, Diagnostic Imaging, Biomarkers, Tumor, Fluorescent Antibody Technique, Neoplasms
- Abstract
Precision medicine is critically dependent on better methods for diagnosing and staging disease and predicting drug response. Histopathology using hematoxylin and eosin (H&E)-stained tissue (not genomics) remains the primary diagnostic method in cancer. Recently developed highly multiplexed tissue imaging methods promise to enhance research studies and clinical practice with precise, spatially resolved single-cell data. Here, we describe the 'Orion' platform for collecting H&E and high-plex immunofluorescence images from the same cells in a whole-slide format suitable for diagnosis. Using a retrospective cohort of 74 colorectal cancer resections, we show that immunofluorescence and H&E images provide human experts and machine learning algorithms with complementary information that can be used to generate interpretable, multiplexed image-based models predictive of progression-free survival. Combining models of immune infiltration and tumor-intrinsic features achieves a 10- to 20-fold discrimination between rapid and slow (or no) progression, demonstrating the ability of multimodal tissue imaging to generate high-performance biomarkers., (© 2023. The Author(s).)
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- 2023
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36. MAPS: Pathologist-level cell type annotation from tissue images through machine learning.
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Shaban M, Bai Y, Qiu H, Mao S, Yeung J, Yeo YY, Shanmugam V, Chen H, Zhu B, Nolan GP, Shipp MA, Rodig SJ, Jiang S, and Mahmood F
- Abstract
Highly multiplexed protein imaging is emerging as a potent technique for analyzing protein distribution within cells and tissues in their native context. However, existing cell annotation methods utilizing high-plex spatial proteomics data are resource intensive and necessitate iterative expert input, thereby constraining their scalability and practicality for extensive datasets. We introduce MAPS (Machine learning for Analysis of Proteomics in Spatial biology), a machine learning approach facilitating rapid and precise cell type identification with human-level accuracy from spatial proteomics data. Validated on multiple in-house and publicly available MIBI and CODEX datasets, MAPS outperforms current annotation techniques in terms of speed and accuracy, achieving pathologist-level precision even for challenging cell types, including tumor cells of immune origin. By democratizing rapidly deployable and scalable machine learning annotation, MAPS holds significant potential to expedite advances in tissue biology and disease comprehension., Competing Interests: CONFLICT OF INTERESTS S.J.R. has received research support from Affimed, Merck, and Bristol-Myers Squibb (BMS), he is on the Scientific Advisory Board for Immunitas Therapeutics and part of Bristol Myers Squibb International Immuno-Oncology Network (II-ON). M.A.S. has research funding from BMS, Bayer, Abbvie, and AstraZeneca, and is on advisory boards for AstraZeneca and BMS. G.P.N., is co-founder and stockholder of IonPath Inc, which manufactures the instrument used in this manuscript, is a co-founder and stockholder of Akoya Biosciences, Inc. and inventor on patent US9909167, and is a Scientific Advisory Board member for Akoya Biosciences, Inc. The other authors declare no competing interests.
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- 2023
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37. Brief Communication on Pathologic Assessment of Persistent Stable Metastatic Lesions in Patients Treated With Anti-CTLA-4 or Anti-CTLA-4 + Anti-PD-1 Therapy.
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Buchbinder EI, Pfaff KL, Turner MM, Manos M, Ouyang O, Ott PA, Giobbie-Hurder A, Rodig SJ, and Hodi FS
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- Humans, Ipilimumab adverse effects, Positron Emission Tomography Computed Tomography, Inflammation chemically induced, Nivolumab adverse effects, Melanoma pathology
- Abstract
Despite the wide use of immune checkpoint inhibition for the treatment of melanoma, the mechanisms leading to long-term stable disease are incompletely understood. Patients with metastatic melanoma who had received ipilimumab alone or ipilimumab plus nivolumab 2+years prior and attained at least 6 months of stable disease were identified. Positron emission tomography/computed tomography (PET/CT) was performed. Pretreatment and posttreatment biopsies of areas of stable disease were assessed for tumor, fibrosis, and inflammation. Seven patients underwent PET/CT and tissue biopsy. Fluorodeoxyglucose avid lesions on PET/CT ranged from no activity to an SUV of 22. In 6 patients, the residual stable lesions were composed of necrosis and fibrosis with a prominent pigment containing macrophages and no residual melanoma. In 1 patient, a nodal lesion demonstrated melanoma with active inflammation. In most patients with durable stable disease after treatment with ipilimumab or ipilimumab/nivolumab, residual lesions demonstrated predominantly necrosis and fibrosis consistent with resolving lesions. The presence of melanophages in these samples may suggest ongoing immune surveillance. One patient did demonstrate residual melanoma, indicating the need for ongoing monitoring of this patient population., (Copyright © 2023 The Author(s). Published by Wolters Kluwer Health, Inc.)
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- 2023
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38. Mechanisms of response and resistance to combined decitabine and ipilimumab for advanced myeloid disease.
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Penter L, Liu Y, Wolff JO, Yang L, Taing L, Jhaveri A, Southard J, Patel M, Cullen NM, Pfaff KL, Cieri N, Oliveira G, Kim-Schulze S, Ranasinghe S, Leonard R, Robertson T, Morgan EA, Chen HX, Song MH, Thurin M, Li S, Rodig SJ, Cibulskis C, Gabriel S, Bachireddy P, Ritz J, Streicher H, Neuberg DS, Hodi FS, Davids MS, Gnjatic S, Livak KJ, Altreuter J, Michor F, Soiffer RJ, Garcia JS, and Wu CJ
- Subjects
- Humans, Ipilimumab therapeutic use, Decitabine therapeutic use, Recurrence, Myelodysplastic Syndromes genetics, Leukemia, Myeloid, Acute drug therapy, Leukemia, Myeloid, Acute genetics, Leukemia, Myeloid, Acute pathology, Hematopoietic Stem Cell Transplantation
- 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., (© 2023 by The American Society of Hematology.)
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- 2023
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39. Ipilimumab plus decitabine for patients with MDS or AML in posttransplant or transplant-naïve settings.
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Garcia JS, Flamand Y, Penter L, Keng M, Tomlinson BK, Mendez LM, Koller P, Cullen N, Arihara Y, Pfaff K, Wolff JO, Brunner AM, Galinsky I, Bashey A, Antin JH, Cutler C, Ho V, Jonas BA, Luskin MR, Wadleigh M, Winer ES, Savell A, Leonard R, Robertson T, Davids MS, Streicher H, Rodig SJ, Ritz J, Wu CJ, DeAngelo DJ, Neuberg D, Stone RM, and Soiffer RJ
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- Humans, Decitabine therapeutic use, Ipilimumab adverse effects, Azacitidine therapeutic use, Myelodysplastic Syndromes drug therapy, Leukemia, Myeloid, Acute drug therapy
- Published
- 2023
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40. Inference of single cell profiles from histology stains with the Single-Cell omics from Histology Analysis Framework (SCHAF).
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Comiter C, Vaishnav ED, Ciampricotti M, Li B, Yang Y, Rodig SJ, Turner M, Pfaff KL, Jané-Valbuena J, Slyper M, Waldman J, Vigneau S, Wu J, Blosser TR, Segerstolpe Å, Abravanel D, Wagle N, Zhuang X, Rudin CM, Klughammer J, Rozenblatt-Rosen O, Kobayash-Kirschvink KJ, Shu J, and Regev A
- Abstract
Tissue biology involves an intricate balance between cell-intrinsic processes and interactions between cells organized in specific spatial patterns, which can be respectively captured by single-cell profiling methods, such as single-cell RNA-seq (scRNA-seq), and histology imaging data, such as Hematoxylin-and-Eosin (H&E) stains. While single-cell profiles provide rich molecular information, they can be challenging to collect routinely and do not have spatial resolution. Conversely, histological H&E assays have been a cornerstone of tissue pathology for decades, but do not directly report on molecular details, although the observed structure they capture arises from molecules and cells. Here, we leverage adversarial machine learning to develop SCHAF (Single-Cell omics from Histology Analysis Framework), to generate a tissue sample's spatially-resolved single-cell omics dataset from its H&E histology image. We demonstrate SCHAF on two types of human tumors-from lung and metastatic breast cancer-training with matched samples analyzed by both sc/snRNA-seq and by H&E staining. SCHAF generated appropriate single-cell profiles from histology images in test data, related them spatially, and compared well to ground-truth scRNA-Seq, expert pathologist annotations, or direct MERFISH measurements. SCHAF opens the way to next-generation H&E2.0 analyses and an integrated understanding of cell and tissue biology in health and disease.
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- 2023
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41. Clonal KEAP1 mutations with loss of heterozygosity share reduced immunotherapy efficacy and low immune cell infiltration in lung adenocarcinoma.
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Scalera S, Ricciuti B, Mazzotta M, Calonaci N, Alessi JV, Cipriani L, Bon G, Messina B, Lamberti G, Di Federico A, Pecci F, Milite S, Krasniqi E, Barba M, Vici P, Vecchione A, De Nicola F, Ciuffreda L, Goeman F, Fanciulli M, Buglioni S, Pescarmona E, Sharma B, Felt KD, Lindsay J, Rodig SJ, De Maria R, Caravagna G, Cappuzzo F, Ciliberto G, Awad MM, and Maugeri-Saccà M
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- Humans, Kelch-Like ECH-Associated Protein 1 genetics, NF-E2-Related Factor 2 genetics, Mutation, Loss of Heterozygosity, Immunotherapy, Lung Neoplasms pathology, Adenocarcinoma of Lung
- Abstract
Background: KEAP1 mutations have been associated with reduced survival in lung adenocarcinoma (LUAD) patients treated with immune checkpoint inhibitors (ICIs), particularly in the presence of STK11/KRAS alterations. We hypothesized that, beyond co-occurring genomic events, clonality prediction may help identify deleterious KEAP1 mutations and their counterparts with retained sensitivity to ICIs., Patients and Methods: Beta-binomial modelling of sequencing read counts was used to infer KEAP1 clonal inactivation by combined somatic mutation and loss of heterozygosity (KEAP1 C-LOH) versus partial inactivation [KEAP1 clonal diploid-subclonal (KEAP1 CD-SC)] in the Memorial Sloan Kettering Cancer Center (MSK) MetTropism cohort (N = 2550). Clonality/LOH prediction was compared to a streamlined clinical classifier that relies on variant allele frequencies (VAFs) and tumor purity (TP) (VAF/TP ratio). The impact of this classification on survival outcomes was tested in two independent cohorts of LUAD patients treated with immunotherapy (MSK/Rome N = 237; DFCI N = 461). Immune-related features were studied by exploiting RNA-sequencing data (TCGA) and multiplexed immunofluorescence (DFCI mIF cohort)., Results: Clonality/LOH inference in the MSK MetTropism cohort overlapped with a clinical classification model defined by the VAF/TP ratio. In the ICI-treated MSK/Rome discovery cohort, predicted KEAP1 C-LOH mutations were associated with shorter progression-free survival (PFS) and overall survival (OS) compared to KEAP1 wild-type cases (PFS log-rank P = 0.001; OS log-rank P < 0.001). Similar results were obtained in the DFCI validation cohort (PFS log-rank P = 0.006; OS log-rank P = 0.014). In both cohorts, we did not observe any significant difference in survival outcomes when comparing KEAP1 CD-SC and wild-type tumors. Immune deconvolution and multiplexed immunofluorescence revealed that KEAP1 C-LOH and KEAP1 CD-SC differed for immune-related features., Conclusions: KEAP1 C-LOH mutations are associated with an immune-excluded phenotype and worse clinical outcomes among advanced LUAD patients treated with ICIs. By contrast, survival outcomes of patients whose tumors harbored KEAP1 CD-SC mutations were similar to those with KEAP1 wild-type LUADs., Competing Interests: Disclosure PV reports travel grants from Eisai, Roche, Pfizer, Novartis; speaker fees/advisory boards from Roche, Pfizer, Novartis, Gentili. RDM reports serving as a scientific advisory board member at Exosomics SpA (Siena IT), HiberCell Inc. (New York, NY), Kiromic Inc. (Houston, TX) and Exiris Inc. (Rome, IT). FC reports personal fees from Roche/Genentech, AstraZeneca, Takeda, Pfizer, Bristol-Myers Squibb, Merck Sharp & Dohme, Lilly, and Bayer. MMA reported serving as a consultant for Achilles, AbbVie, Neon, Maverick, Nektar, and Hegrui; receiving grants and personal fees from Genentech, Bristol-Myers Squibb, Merck, AstraZeneca, and Lilly; and receiving personal fees from Maverick, Blueprint Medicine, Syndax, Ariad, Nektar, Gritstone, ArcherDx, Mirati, NextCure, Novartis, EMD Serono, and NovaRx. All other authors have declared no conflicts of interest. Data sharing Data concerning the Rome cohort are disclosed in our previous work.(8) MSK studies are available at www.cbioportal.org. The DFCI cohort is available from the authors upon reasonable request (B. Ricciuti and M.M. Awad)., (Copyright © 2022 European Society for Medical Oncology. Published by Elsevier Ltd. All rights reserved.)
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- 2023
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42. A randomized phase 2 study of neoadjuvant carboplatin and paclitaxel with or without atezolizumab in triple negative breast cancer (TNBC) - NCI 10013.
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Ademuyiwa FO, Gao F, Street CR, Chen I, Northfelt DW, Wesolowski R, Arora M, Brufsky A, Dees EC, Santa-Maria CA, Connolly RM, Force J, Moreno-Aspitia A, Herndon JM, Carmody M, Davies SR, Larson S, Pfaff KL, Jones SM, Weirather JL, Giobbie-Hurder A, Rodig SJ, Liu Z, Hagemann IS, Sharon E, and Gillanders WE
- Abstract
Atezolizumab with chemotherapy has shown improved progression-free and overall survival in patients with metastatic PD-L1 positive triple negative breast cancer (TNBC). Atezolizumab with anthracycline- and taxane-based neoadjuvant chemotherapy has also shown increased pathological complete response (pCR) rates in early TNBC. This trial evaluated neoadjuvant carboplatin and paclitaxel with or without atezolizumab in patients with clinical stages II-III TNBC. The co-primary objectives were to evaluate if chemotherapy and atezolizumab increase pCR rate and tumor infiltrating lymphocyte (TIL) percentage compared to chemotherapy alone in the mITT population. Sixty-seven patients (ages 25-78 years; median, 52 years) were randomly assigned - 22 patients to Arm A, and 45 to Arm B. Median follow up was 6.6 months. In the modified intent to treat population (all patients evaluable for the primary endpoints who received at least one dose of combination therapy), the pCR rate was 18.8% (95% CI 4.0-45.6%) in Arm A, and 55.6% (95% CI 40.0-70.4%) in Arm B (estimated treatment difference: 36.8%, 95% CI 8.5-56.6%; p = 0.018). Grade 3 or higher treatment-related adverse events occurred in 62.5% of patients in Arm A, and 57.8% of patients in Arm B. One patient in Arm B died from recurrent disease during the follow-up period. TIL percentage increased slightly from baseline to cycle 1 in both Arm A (mean ± SD: 0.6% ± 21.0%) and Arm B (5.7% ± 15.8%) (p = 0.36). Patients with pCR had higher median TIL percentages (24.8%) than those with non-pCR (14.2%) (p = 0.02). Although subgroup analyses were limited by the small sample size, PD-L1-positive patients treated with chemotherapy and atezolizumab had a pCR rate of 75% (12/16). The addition of atezolizumab to neoadjuvant carboplatin and paclitaxel resulted in a statistically significant and clinically relevant increased pCR rate in patients with clinical stages II and III TNBC. (Funded by National Cancer Institute)., (© 2022. The Author(s).)
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- 2022
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43. Hippo Signaling Pathway Regulates Cancer Cell-Intrinsic MHC-II Expression.
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Zeng Z, Gu SS, Ouardaoui N, Tymm C, Yang L, Wong CJ, Li D, Zhang W, Wang X, Weirather JL, Rodig SJ, Hodi FS, Brown M, and Liu XS
- Subjects
- Humans, Immunotherapy, Antigen-Presenting Cells metabolism, Hippo Signaling Pathway, Melanoma drug therapy
- Abstract
MHC-II is known to be mainly expressed on the surface of antigen-presenting cells. Evidence suggests MHC-II is also expressed by cancer cells and may be associated with better immunotherapy responses. However, the role and regulation of MHC-II in cancer cells remain unclear. In this study, we leveraged data mining and experimental validation to elucidate the regulation of MHC-II in cancer cells and its role in modulating the response to immunotherapy. We collated an extensive collection of omics data to examine cancer cell-intrinsic MHC-II expression and its association with immunotherapy outcomes. We then tested the functional relevance of cancer cell-intrinsic MHC-II expression using a syngeneic transplantation model. Finally, we performed data mining to identify pathways potentially involved in the regulation of MHC-II expression, and experimentally validated candidate regulators. Analyses of preimmunotherapy clinical samples in the CheckMate 064 trial revealed that cancer cell-intrinsic MHC-II protein was positively correlated with more favorable immunotherapy outcomes. Comprehensive meta-analyses of multiomics data from an exhaustive collection of data revealed that MHC-II is heterogeneously expressed in various solid tumors, and its expression is particularly high in melanoma. Using a syngeneic transplantation model, we further established that melanoma cells with high MHC-II responded better to anti-PD-1 treatment. Data mining followed by experimental validation revealed the Hippo signaling pathway as a potential regulator of melanoma MHC-II expression. In summary, we identified the Hippo signaling pathway as a novel regulator of cancer cell-intrinsic MHC-II expression. These findings suggest modulation of MHC-II in melanoma could potentially improve immunotherapy response., (©2022 American Association for Cancer Research.)
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- 2022
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44. Genomic profiling for clinical decision making in lymphoid neoplasms.
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de Leval L, Alizadeh AA, Bergsagel PL, Campo E, Davies A, Dogan A, Fitzgibbon J, Horwitz SM, Melnick AM, Morice WG, Morin RD, Nadel B, Pileri SA, Rosenquist R, Rossi D, Salaverria I, Steidl C, Treon SP, Zelenetz AD, Advani RH, Allen CE, Ansell SM, Chan WC, Cook JR, Cook LB, d'Amore F, Dirnhofer S, Dreyling M, Dunleavy K, Feldman AL, Fend F, Gaulard P, Ghia P, Gribben JG, Hermine O, Hodson DJ, Hsi ED, Inghirami G, Jaffe ES, Karube K, Kataoka K, Klapper W, Kim WS, King RL, Ko YH, LaCasce AS, Lenz G, Martin-Subero JI, Piris MA, Pittaluga S, Pasqualucci L, Quintanilla-Martinez L, Rodig SJ, Rosenwald A, Salles GA, San-Miguel J, Savage KJ, Sehn LH, Semenzato G, Staudt LM, Swerdlow SH, Tam CS, Trotman J, Vose JM, Weigert O, Wilson WH, Winter JN, Wu CJ, Zinzani PL, Zucca E, Bagg A, and Scott DW
- Subjects
- Humans, Genomics methods, Precision Medicine, High-Throughput Nucleotide Sequencing, Clinical Decision-Making, Lymphoma diagnosis, Lymphoma genetics, Lymphoma therapy, Neoplasms
- Abstract
With the introduction of large-scale molecular profiling methods and high-throughput sequencing technologies, the genomic features of most lymphoid neoplasms have been characterized at an unprecedented scale. Although the principles for the classification and diagnosis of these disorders, founded on a multidimensional definition of disease entities, have been consolidated over the past 25 years, novel genomic data have markedly enhanced our understanding of lymphomagenesis and enriched the description of disease entities at the molecular level. Yet, the current diagnosis of lymphoid tumors is largely based on morphological assessment and immunophenotyping, with only few entities being defined by genomic criteria. This paper, which accompanies the International Consensus Classification of mature lymphoid neoplasms, will address how established assays and newly developed technologies for molecular testing already complement clinical diagnoses and provide a novel lens on disease classification. More specifically, their contributions to diagnosis refinement, risk stratification, and therapy prediction will be considered for the main categories of lymphoid neoplasms. The potential of whole-genome sequencing, circulating tumor DNA analyses, single-cell analyses, and epigenetic profiling will be discussed because these will likely become important future tools for implementing precision medicine approaches in clinical decision making for patients with lymphoid malignancies., (© 2022 by The American Society of Hematology.)
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- 2022
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45. Dissecting the clinicopathologic, genomic, and immunophenotypic correlates of KRAS G12D -mutated non-small-cell lung cancer.
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Ricciuti B, Alessi JV, Elkrief A, Wang X, Cortellini A, Li YY, Vaz VR, Gupta H, Pecci F, Barrichello A, Lamberti G, Nguyen T, Lindsay J, Sharma B, Felt K, Rodig SJ, Nishino M, Sholl LM, Barbie DA, Negrao MV, Zhang J, Cherniack AD, Heymach JV, Meyerson M, Ambrogio C, Jänne PA, Arbour KC, Pinato DJ, Skoulidis F, Schoenfeld AJ, Awad MM, and Luo J
- Subjects
- B7-H1 Antigen, Forkhead Transcription Factors, Genomics, Humans, Mutation, Programmed Cell Death 1 Receptor, Proto-Oncogene Proteins p21(ras) genetics, Carcinoma, Non-Small-Cell Lung drug therapy, Carcinoma, Non-Small-Cell Lung genetics, Carcinoma, Non-Small-Cell Lung pathology, Lung Neoplasms drug therapy, Lung Neoplasms genetics, Lung Neoplasms pathology
- Abstract
Background: Allele-specific KRAS inhibitors are an emerging class of cancer therapies. KRAS-mutant (KRAS
MUT ) non-small-cell lung cancers (NSCLCs) exhibit heterogeneous outcomes, driven by differences in underlying biology shaped by co-mutations. In contrast to KRASG12C NSCLC, KRASG12D NSCLC is associated with low/never-smoking status and is largely uncharacterized., Patients and Methods: Clinicopathologic and genomic information were collected from patients with NSCLCs harboring a KRAS mutation at the Dana-Farber Cancer Institute (DFCI), Memorial Sloan Kettering Cancer Center, MD Anderson Cancer Center, and Imperial College of London. Multiplexed immunofluorescence for CK7, programmed cell death protein 1 (PD-1), programmed death-ligand 1 (PD-L1), Foxp3, and CD8 was carried out on a subset of samples with available tissue at the DFCI. Clinical outcomes to PD-(L)1 inhibition ± chemotherapy were analyzed according to KRAS mutation subtype., Results: Of 2327 patients with KRAS-mutated (KRASMUT ) NSCLC, 15% (n = 354) harbored KRASG12D . Compared to KRASnon-G12D NSCLC, KRASG12D NSCLC had a lower pack-year (py) smoking history (median 22.5 py versus 30.0 py, P < 0.0001) and was enriched in never smokers (22% versus 5%, P < 0.0001). KRASG12D had lower PD-L1 tumor proportion score (TPS) (median 1% versus 5%, P < 0.01) and lower tumor mutation burden (TMB) compared to KRASnon-G12D (median 8.4 versus 9.9 mt/Mb, P < 0.0001). Of the samples which underwent multiplexed immunofluorescence, KRASG12D had lower intratumoral and total CD8+ PD1+ T cells (P < 0.05). Among 850 patients with advanced KRASMUT NSCLC who received PD-(L)1-based therapies, KRASG12D was associated with a worse objective response rate (ORR) (15.8% versus 28.4%, P = 0.03), progression-free survival (PFS) [hazard ratio (HR) 1.51, 95% confidence interval (CI) 1.45-2.00, P = 0.003], and overall survival (OS; HR 1.45, 1.05-1.99, P = 0.02) to PD-(L)1 inhibition alone but not to chemo-immunotherapy combinations [ORR 30.6% versus 35.7%, P = 0.51; PFS HR 1.28 (95%CI 0.92-1.77), P = 0.13; OS HR 1.36 (95%CI 0.95-1.96), P = 0.09] compared to KRASnon-G12D ., Conclusions: KRASG12D lung cancers harbor distinct clinical, genomic, and immunologic features compared to other KRAS-mutated lung cancers and worse outcomes to PD-(L)1 blockade. Drug development for KRASG12D lung cancers will have to take these differences into account., (Copyright © 2022 European Society for Medical Oncology. Published by Elsevier Ltd. All rights reserved.)- Published
- 2022
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46. The identification of TCF1+ progenitor exhausted T cells in THRLBCL may predict a better response to PD-1/PD-L1 blockade.
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Tabanelli V, Melle F, Motta G, Mazzara S, Fabbri M, Agostinelli C, Calleri A, Del Corvo M, Fiori S, Lorenzini D, Cesano A, Chiappella A, Vitolo U, Derenzini E, Griffin GK, Rodig SJ, Vanazzi A, Sabattini E, Tarella C, Sapienza MR, and Pileri SA
- Subjects
- Apoptosis, Hepatocyte Nuclear Factor 1-alpha, Histiocytes metabolism, Histiocytes pathology, Humans, Ligands, Programmed Cell Death 1 Receptor, Tumor Microenvironment, B7-H1 Antigen genetics, Lymphoma, Large B-Cell, Diffuse drug therapy, Lymphoma, Large B-Cell, Diffuse genetics
- Abstract
T-cell/histiocyte-rich large B-cell lymphoma (THRLBCL) is a rare and aggressive variant of diffuse large B-cell lymphoma (DLBCL) that usually affects young to middle-aged patients, with disseminated disease at presentation. The tumor microenvironment (TME) plays a key role in THRLBCL due to its peculiar cellular composition (<10% neoplastic B cells interspersed in a cytotoxic T-cell/histiocyte-rich background). A significant percentage of THRLBCL is refractory to rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (RCHOP)-based regimens and to chimeric antigen receptor T-cell therapy; thus, the development of a specific therapeutic approach for these patients represents an unmet clinical need. To better understand the interaction of immune cells in THRLBCL TME and identify more promising therapeutic strategies, we compared the immune gene expression profiles of 12 THRLBCL and 10 DLBCL samples, and further corroborated our findings in an extended in silico set. Gene coexpression network analysis identified the predominant role of the programmed cell death protein 1 (PD-1)/programmed cell death ligand 1 (PD-L1) axis in the modulation of the immune response. Furthermore, the PD-1/PD-L1 activation was flanked by the overexpression of 48 genes related to the functional exhaustion of T cells. Globally, THRLBCL TME was highly interferon-inflamed and severely exhausted. The immune gene profiling findings strongly suggest that THRLBCL may be responsive to anti-PD-1 therapy but also allowed us to take a step forward in understanding THRLBCL TME. Of therapeutic relevance, we validated our results by immunohistochemistry, identifying a subset of TCF1+ (T cell-specific transcription factor 1, encoded by the TCF7 gene) progenitor exhausted T cells enriched in patients with THRLBCL. This subset of TCF1+ exhausted T cells correlates with good clinical response to immune checkpoint therapy and may improve prediction of anti-PD-1 response in patients with THRLBCL., (© 2022 by The American Society of Hematology. Licensed under Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0), permitting only noncommercial, nonderivative use with attribution. All other rights reserved.)
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- 2022
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47. Association of High Tumor Mutation Burden in Non-Small Cell Lung Cancers With Increased Immune Infiltration and Improved Clinical Outcomes of PD-L1 Blockade Across PD-L1 Expression Levels.
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Ricciuti B, Wang X, Alessi JV, Rizvi H, Mahadevan NR, Li YY, Polio A, Lindsay J, Umeton R, Sinha R, Vokes NI, Recondo G, Lamberti G, Lawrence M, Vaz VR, Leonardi GC, Plodkowski AJ, Gupta H, Cherniack AD, Tolstorukov MY, Sharma B, Felt KD, Gainor JF, Ravi A, Getz G, Schalper KA, Henick B, Forde P, Anagnostou V, Jänne PA, Van Allen EM, Nishino M, Sholl LM, Christiani DC, Lin X, Rodig SJ, Hellmann MD, and Awad MM
- Subjects
- Adult, Aged, Aged, 80 and over, B7-H1 Antigen, Biomarkers, Tumor genetics, Cohort Studies, Female, Humans, Male, Middle Aged, Mutation, Programmed Cell Death 1 Receptor, Young Adult, Carcinoma, Non-Small-Cell Lung drug therapy, Carcinoma, Non-Small-Cell Lung genetics, Carcinoma, Non-Small-Cell Lung pathology, Lung Neoplasms drug therapy, Lung Neoplasms genetics, Lung Neoplasms pathology
- Abstract
Importance: Although tumor mutation burden (TMB) has been explored as a potential biomarker of immunotherapy efficacy in solid tumors, there still is a lack of consensus about the optimal TMB threshold that best discriminates improved outcomes of immune checkpoint inhibitor therapy among patients with non-small cell lung cancer (NSCLC)., Objectives: To determine the association between increasing TMB levels and immunotherapy efficacy across clinically relevant programmed death ligand-1 (PD-L1) levels in patients with NSCLC., Design, Setting, and Participants: This multicenter cohort study included patients with advanced NSCLC treated with immunotherapy who received programmed cell death-1 (PD-1) or PD-L1 inhibition in the Dana-Farber Cancer Institute (DFCI), Memorial Sloan Kettering Cancer Center (MSKCC), and in the Stand Up To Cancer (SU2C)/Mark Foundation data sets. Clinicopathological and genomic data were collected from patients between September 2013 and September 2020. Data analysis was performed from November 2021 to February 2022., Exposures: Treatment with PD-1/PD-L1 inhibition without chemotherapy., Main Outcomes and Measures: Association of TMB levels with objective response rate (ORR), progression-free survival (PFS), and overall survival (OS)., Results: In the entire cohort of 1552 patients with advanced NSCLC who received PD-1/PD-L1 blockade, the median (range) age was 66 (22-92) years, 830 (53.5%) were women, and 1347 (86.8%) had cancer with nonsquamous histologic profile. A regression tree modeling ORR as a function of TMB identified 2 TMB groupings in the discovery cohort (MSKCC), defined as low TMB (≤19.0 mutations per megabase) and high TMB (>19.0 mutations per megabase), which were associated with increasing improvements in ORR, PFS, and OS in the discovery cohort and in 2 independent cohorts (DFCI and SU2C/Mark Foundation). These TMB levels also were associated with significant improvements in outcomes of immunotherapy in each PD-L1 tumor proportion score subgroup of less than 1%, 1% to 49%, and 50% or higher. The ORR to PD-1/PD-L1 inhibition was as high as 57% in patients with high TMB and PD-L1 expression 50% or higher and as low as 8.7% in patients with low TMB and PD-L1 expression less than 1%. Multiplexed immunofluorescence and transcriptomic profiling revealed that high TMB levels were associated with increased CD8-positive, PD-L1-positive T-cell infiltration, increased PD-L1 expression on tumor and immune cells, and upregulation of innate and adaptive immune response signatures., Conclusions and Relevance: These findings suggest that increasing TMB levels are associated with immune cell infiltration and an inflammatory T-cell-mediated response, resulting in increased sensitivity to PD-1/PD-L1 blockade in NSCLC across PD-L1 expression subgroups.
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- 2022
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48. Reversal of viral and epigenetic HLA class I repression in Merkel cell carcinoma.
- Author
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Lee PC, Klaeger S, Le PM, Korthauer K, Cheng J, Ananthapadmanabhan V, Frost TC, Stevens JD, Wong AY, Iorgulescu JB, Tarren AY, Chea VA, Carulli IP, Lemvigh CK, Pedersen CB, Gartin AK, Sarkizova S, Wright KT, Li LW, Nomburg J, Li S, Huang T, Liu X, Pomerance L, Doherty LM, Apffel AM, Wallace LJ, Rachimi S, Felt KD, Wolff JO, Witten E, Zhang W, Neuberg D, Lane WJ, Zhang G, Olsen LR, Thakuria M, Rodig SJ, Clauser KR, Starrett GJ, Doench JG, Buhrlage SJ, Carr SA, DeCaprio JA, Wu CJ, and Keskin DB
- Subjects
- Antigens, Viral, Tumor genetics, Antigens, Viral, Tumor metabolism, Epigenesis, Genetic, Humans, Ubiquitin-Specific Peptidase 7 metabolism, Carcinoma, Merkel Cell genetics, Carcinoma, Merkel Cell pathology, Merkel cell polyomavirus genetics, Merkel cell polyomavirus metabolism, Polyomavirus Infections genetics, Skin Neoplasms pathology
- Abstract
Cancers avoid immune surveillance through an array of mechanisms, including perturbation of HLA class I antigen presentation. Merkel cell carcinoma (MCC) is an aggressive, HLA-I-low, neuroendocrine carcinoma of the skin often caused by the Merkel cell polyomavirus (MCPyV). Through the characterization of 11 newly generated MCC patient-derived cell lines, we identified transcriptional suppression of several class I antigen presentation genes. To systematically identify regulators of HLA-I loss in MCC, we performed parallel, genome-scale, gain- and loss-of-function screens in a patient-derived MCPyV-positive cell line and identified MYCL and the non-canonical Polycomb repressive complex 1.1 (PRC1.1) as HLA-I repressors. We observed physical interaction of MYCL with the MCPyV small T viral antigen, supporting a mechanism of virally mediated HLA-I suppression. We further identify the PRC1.1 component USP7 as a pharmacologic target to restore HLA-I expression in MCC.
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- 2022
- Full Text
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49. Preparation of Yeast Cells for Staining.
- Author
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Rodig SJ
- Subjects
- Antibodies, Spheroplasts, Staining and Labeling, Antigens, Saccharomyces cerevisiae
- Abstract
Staining yeast cells for the presence and location of antigens is particularly challenging. They are small, making the resolution of any antigen difficult; they have a thick cell wall that antibodies cannot penetrate and that is difficult to remove; and they grow in suspension, making handling difficult. In addition, background problems can be especially severe, particularly with polyclonal antibodies, because many antisera contain antibodies to yeast cell wall components. In this protocol, yeast cells are treated with paraformaldehyde, the cell wall is removed by enzymic digestion, and the spheroplasts are attached to poly-l-lysine-coated slides. After cell lysis, the cells are ready to be stained as per normal. Except in unusual circumstances, the detection reagent should be fluorochrome-labeled., (© 2022 Cold Spring Harbor Laboratory Press.)
- Published
- 2022
- Full Text
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50. Cell Staining.
- Author
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Rodig SJ
- Subjects
- Staining and Labeling, Antibodies, Antigens
- Abstract
When labeled antibodies are used to detect antigens in cells or tissues, several characteristics of an antigen can be readily determined. Most importantly, cell staining will show both the presence and subcellular localization of an antigen. Double-labeling techniques permit the simultaneous detection of two antigens, allowing comparisons of the relative distribution of different antigens. Many cell-staining methods can also be used in conjunction with conventional histological stains and autoradiographic methods to compare the localization of the antigen with other markers. Cell staining can also be used in pathology studies for determining such variables as the type of infectious organism, the progenitor of a neoplastic cell, or the presence of an inflammatory response. With certain modifications, the procedure can be used to purify cells on the basis of the antigenic composition of their cell surface. Cell staining is a versatile technique and, if the antigen is highly localized, can detect as few as a thousand antigen molecules in a cell or tissue. In some circumstances, cell staining may also be used to determine the approximate concentration of an antigen. Improvements in antibody labeling methods, microscopes, cameras, and image analyzers are rapidly extending the sensitivity of cell-staining procedures and are making these techniques more quantitative. Even without these improvements, cell staining can yield important qualitative and semiquantitative data. This introduction describes protocols for cell staining techniques and includes a discussion of major constraints, antibody selection, and troubleshooting., (© 2022 Cold Spring Harbor Laboratory Press.)
- Published
- 2022
- Full Text
- View/download PDF
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