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Zhao W, Kepecs B, Mahadevan NR, Segerstolpe A, Weirather JL, Besson NR, Giotti B, Soong BY, Li C, Vigneau S, Slyper M, Wakiro I, Jane-Valbuena J, Ashenberg O, Rotem A, Bueno R, Rozenblatt-Rosen O, Pfaff K, Rodig S, Hata AN, Regev A, Johnson BE, Tsankov AM. A cellular and spatial atlas of TP53 -associated tissue remodeling in lung adenocarcinoma. bioRxiv 2024:2023.06.28.546977. [PMID: 37425718 PMCID: PMC10327017 DOI: 10.1101/2023.06.28.546977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
TP53 is the most frequently mutated gene across many cancers and is associated with shorter survival in lung adenocarcinoma (LUAD). To define how TP53 mutations affect the LUAD tumor microenvironment (TME), we constructed a multi-omic cellular and spatial tumor atlas of 23 treatment-naïve human lung tumors. We found that TP53 -mutant ( TP53 mut ) malignant cells lose alveolar identity and upregulate highly proliferative and entropic gene expression programs consistently across resectable LUAD patient tumors, genetically engineered mouse models, and cell lines harboring a wide spectrum of TP53 mutations. We further identified a multicellular tumor niche composed of SPP1 + macrophages and collagen-expressing fibroblasts that coincides with hypoxic, pro-metastatic expression programs in TP53 mut tumors. Spatially correlated angiostatic and immune checkpoint interactions, including CD274 - PDCD1 and PVR - TIGIT , are also enriched in TP53 mut LUAD tumors, which may influence response to checkpoint blockade therapy. Our methodology can be further applied to investigate mutation-specific TME changes in other cancers.
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2
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Huffman BM, Singh H, Ali LR, Horick N, Wang SJ, Hoffman MT, Metayer KA, Murray S, Bird A, Abrams TA, Biller LH, Chan JA, Meyerhardt JA, McCleary NJ, Goessling W, Patel AK, Wisch JS, Yurgelun MB, Mouw K, Reardon B, Van Allen EM, Zerillo JA, Clark JW, Parikh A, Mayer RJ, Schlechter B, Ng K, Kumar S, Del Vecchio Fitz C, Kuperwasser C, Hanna GJ, Coveler AL, Rubinson DA, Welsh EL, Pfaff K, Rodig S, Dougan SK, Cleary JM. Biomarkers of pembrolizumab efficacy in advanced anal squamous cell carcinoma: analysis of a phase II clinical trial and a cohort of long-term responders. J Immunother Cancer 2024; 12:e008436. [PMID: 38272561 PMCID: PMC10824013 DOI: 10.1136/jitc-2023-008436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Recent trials suggest that programmed cell death 1 (PD-1)-directed immunotherapy may be beneficial for some patients with anal squamous cell carcinoma and biomarkers predictive of response are greatly needed. METHODS This multicenter phase II clinical trial (NCT02919969) enrolled patients with metastatic or locally advanced incurable anal squamous cell carcinoma (n=32). Patients received pembrolizumab 200 mg every 3 weeks. The primary endpoint of the trial was objective response rate (ORR). Exploratory objectives included analysis of potential predictive biomarkers including assessment of tumor-associated immune cell populations with multichannel immunofluorescence and analysis of circulating tumor tissue modified viral-human papillomavirus DNA (TTMV-HPV DNA) using serially collected blood samples. To characterize the clinical features of long-term responders, we combined data from our prospective trial with a retrospective cohort of patients with anal cancer treated with anti-PD-1 immunotherapy (n=18). RESULTS In the phase II study, the ORR to pembrolizumab monotherapy was 9.4% and the median progression-free survival was 2.2 months. Despite the high level of HPV positivity observed with circulating TTMV-HPV DNA testing, the majority of patients had low levels of tumor-associated CD8+PD-1+ T cells on pretreatment biopsy. Patients who benefited from pembrolizumab had decreasing TTMV-HPV DNA scores and a complete responder's TTMV-HPV DNA became undetectable. Long-term pembrolizumab responses were observed in one patient from the trial (5.3 years) and three patients (2.5, 6, and 8 years) from the retrospective cohort. Long-term responders had HPV-positive tumors, lacked liver metastases, and achieved a radiological complete response. CONCLUSIONS Pembrolizumab has durable efficacy in a rare subset of anal cancers. However, despite persistence of HPV infection, indicated by circulating HPV DNA, most advanced anal cancers have low numbers of tumor-associated CD8+PD-1+ T cells and are resistant to pembrolizumab.
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Affiliation(s)
- Brandon M Huffman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Harshabad Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Lestat R Ali
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Nora Horick
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | - S Jennifer Wang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Megan T Hoffman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Katherine A Metayer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Shayla Murray
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Alexandra Bird
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Thomas A Abrams
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Leah H Biller
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Jennifer A Chan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffrey A Meyerhardt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Nadine J McCleary
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Wolfram Goessling
- Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Anuj K Patel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffrey S Wisch
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Matthew B Yurgelun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Kent Mouw
- Harvard Medical School, Boston, Massachusetts, USA
| | | | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jessica A Zerillo
- Harvard Medical School, Boston, Massachusetts, USA
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Jeffrey W Clark
- Department of Medical Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Aparna Parikh
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Robert J Mayer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Benjamin Schlechter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | - Glenn J Hanna
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew L Coveler
- University of Washington School of Medicine, Seattle, Washington, USA
| | - Douglas A Rubinson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Emma L Welsh
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kathleen Pfaff
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Stephanie K Dougan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - James M Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
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Katz MHG, Petroni GR, Bauer T, Reilley MJ, Wolpin BM, Stucky CC, Bekaii-Saab TS, Elias R, Merchant N, Dias Costa A, Lenehan P, Cardot-Ruffino V, Rodig S, Pfaff K, Dougan SK, Nowak JA, Varadhachary GR, Slingluff CL, Rahma O. Multicenter randomized controlled trial of neoadjuvant chemoradiotherapy alone or in combination with pembrolizumab in patients with resectable or borderline resectable pancreatic adenocarcinoma. J Immunother Cancer 2023; 11:e007586. [PMID: 38040420 PMCID: PMC10693876 DOI: 10.1136/jitc-2023-007586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is a challenging target for immunotherapy because it has an immunosuppressive tumor microenvironment. Neoadjuvant chemoradiotherapy can increase tumor-infiltrating lymphocyte (TIL) density, which may predict overall survival (OS). We hypothesized that adding programmed cell death protein 1 (PD-1) blockade to chemoradiotherapy would be well tolerated and increase TILs among patients with localized PDAC. METHODS Patients were randomized 2:1 to Arm A (receiving pembrolizumab plus chemoradiotherapy (capecitabine and external beam radiation)) or Arm B (receiving chemoradiotherapy alone) before anticipated pancreatectomy. Primary endpoints were (1) incidence and severity of adverse events during neoadjuvant therapy and (2) density of TILs in resected tumor specimens. TIL density was assessed using multiplexed immunofluorescence histologic examination. RESULTS Thirty-seven patients were randomized to Arms A (n=24) and B (n=13). Grade ≥3 adverse events related to neoadjuvant treatment were experienced by 9 (38%) and 4 (31%) patients in Arms A and B, respectively, with one patient experiencing dose-limiting toxicity in Arm A. Seventeen (71%) and 7 (54%) patients in Arms A and B, respectively, underwent pancreatectomy. Median CD8+ T-cell densities in Arms A and B were 67.4 (IQR: 39.2-141.8) and 37.9 (IQR: 22.9-173.4) cells/mm2, respectively. Arms showed no noticeable differences in density of CD8+Ki67+, CD4+, or CD4+FOXP3+ regulatory T cells; M1-like and M2-like macrophages; or granulocytes. Median OS durations were 27.8 (95% CI: 17.1 to NR) and 24.3 (95% CI: 12.6 to NR) months for Arms A and B, respectively. CONCLUSIONS Adding pembrolizumab to neoadjuvant chemoradiotherapy was safe. However, no convincing effect on CD8+ TILs was observed.
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Affiliation(s)
- Matthew H G Katz
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Gina R Petroni
- Division of Translational Research and Applied Statistics, Department of Public Health Sciences, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Todd Bauer
- Department of Surgery, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Matthew J Reilley
- Division of Hematology and Oncology, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Tanios S Bekaii-Saab
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Mayo Clin, Phoenix, Arizona, USA
| | - Rawad Elias
- Hartford HealthCare Cancer Institute, Plainville, Connecticut, USA
| | - Nipun Merchant
- Department of Surgery, University of Miami, Coral Gables, Florida, USA
| | - Andressa Dias Costa
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Patrick Lenehan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Immunology, Harvard Medical School, Boston, Massachusetts, USA
| | - Victoire Cardot-Ruffino
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Immunology, Harvard Medical School, Boston, Massachusetts, USA
| | - Scott Rodig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Immunology, Harvard Medical School, Boston, Massachusetts, USA
| | - Kathleen Pfaff
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Stephanie K Dougan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Immunology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan Andrew Nowak
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Immunology, Harvard Medical School, Boston, Massachusetts, USA
| | - Gauri R Varadhachary
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Craig L Slingluff
- Department of Surgery, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Osama Rahma
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
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4
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Giannikou K, Klonowska K, Tsuji J, Wu S, Zhu Z, Probst CK, Kao KZ, Wu CL, Rodig S, Marino-Enriquez A, Zen Y, Schaefer IM, Kwiatkowski DJ. TSC2 inactivation, low mutation burden and high macrophage infiltration characterise hepatic angiomyolipomas. Histopathology 2023; 83:569-581. [PMID: 37679051 DOI: 10.1111/his.15005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/30/2023] [Accepted: 06/26/2023] [Indexed: 09/09/2023]
Abstract
AIMS Although TSC1 or TSC2 inactivating mutations that lead to mTORC1 hyperactivation have been reported in hepatic angiomyolipomas (hAML), the role of other somatic genetic events that may contribute to hAML development is unknown. There are also limited data regarding the tumour microenvironment (TME) of hAML. The aim of the present study was to identify other somatic events in genomic level and changes in TME that contribute to tumorigenesis in hAML. METHODS AND RESULTS In this study, we performed exome sequencing in nine sporadic hAML tumours and deep-coverage targeted sequencing for TSC2 in three additional hAML. Immunohistochemistry and multiplex immunofluorescence were carried out for 15 proteins to characterise the tumour microenvironment and assess immune cell infiltration. Inactivating somatic variants in TSC2 were identified in 10 of 12 (83%) cases, with a median allele frequency of 13.6%. Five to 18 somatic variants (median number: nine, median allele frequency 21%) not in TSC1 or TSC2 were also identified, mostly of uncertain clinical significance. Copy number changes were rare, but detection was impaired by low tumour purity. Immunohistochemistry demonstrated numerous CD68+ macrophages of distinct appearance from Küpffer cells. Multiplex immunofluorescence revealed low numbers of exhausted PD-1+/PD-L1+, FOXP3+ and CD8+ T cells. CONCLUSION hAML tumours have consistent inactivating mutations in TSC2 and have a low somatic mutation rate, similar to other TSC-associated tumours. Careful histological review, standard IHC and multiplex immunofluorescence demonstrated marked infiltration by non-neoplastic inflammatory cells, mostly macrophages.
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Affiliation(s)
- Krinio Giannikou
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Cancer Genome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology and Oncology, Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Katarzyna Klonowska
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Cancer Genome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Junko Tsuji
- Genomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shulin Wu
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Zachary Zhu
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Clemens K Probst
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Neurological Sciences, Larner College of Medicine, University of Vermont, Burlighton, VT, USA
| | - Katrina Z Kao
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Chin-Lee Wu
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Adrian Marino-Enriquez
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yoh Zen
- Department of Diagnostic Pathology, Kobe University Hospital, Kobe, Japan
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Inga-Marie Schaefer
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - David J Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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5
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Hoffman SE, Dowrey TW, Villacorta Martin C, Bi K, Titchen B, Johri S, DelloStritto L, Patel M, Mackichan C, Inga S, Chen J, Grimaldi G, Napolitano S, Wakiro I, Wu J, Yeung J, Rotem A, Sicinska E, Shannon E, Clancy T, Wang J, Denning S, Brais L, Besson NR, Pfaff KL, Huang Y, Kao KZ, Rodig S, Hornick JL, Vigneau S, Park J, Kulke MH, Chan J, Van Allen EM, Murphy GJ. Intertumoral lineage diversity and immunosuppressive transcriptional programs in well-differentiated gastroenteropancreatic neuroendocrine tumors. Sci Adv 2023; 9:eadd9668. [PMID: 37756410 PMCID: PMC10530100 DOI: 10.1126/sciadv.add9668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/24/2023] [Indexed: 09/29/2023]
Abstract
Neuroendocrine tumors (NETs) are rare cancers that most often arise in the gastrointestinal tract and pancreas. The fundamental mechanisms driving gastroenteropancreatic (GEP)-NET growth remain incompletely elucidated; however, the heterogeneous clinical behavior of GEP-NETs suggests that both cellular lineage dynamics and tumor microenvironment influence tumor pathophysiology. Here, we investigated the single-cell transcriptomes of tumor and immune cells from patients with gastroenteropancreatic NETs. Malignant GEP-NET cells expressed genes and regulons associated with normal, gastrointestinal endocrine cell differentiation, and fate determination stages. Tumor and lymphoid compartments sparsely expressed immunosuppressive targets commonly investigated in clinical trials, such as the programmed cell death protein-1/programmed death ligand-1 axis. However, infiltrating myeloid cell types within both primary and metastatic GEP-NETs were enriched for genes encoding other immune checkpoints, including VSIR (VISTA), HAVCR2 (TIM3), LGALS9 (Gal-9), and SIGLEC10. Our findings highlight the transcriptomic heterogeneity that distinguishes the cellular landscapes of GEP-NET anatomic subtypes and reveal potential avenues for future precision medicine therapeutics.
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Affiliation(s)
- Samantha E. Hoffman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Harvard-MIT MD-PhD Program, Harvard Medical School, Boston, MA 02115, USA
- PhD Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Todd W. Dowrey
- Section of Hematology and Medical Oncology, Boston University School of Medicine and Boston Medical Center, Boston, MA 02118, USA
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Carlos Villacorta Martin
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Kevin Bi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Breanna Titchen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- PhD Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Shreya Johri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- PhD Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | | | - Miraj Patel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Colin Mackichan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Stephanie Inga
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Judy Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Grace Grimaldi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Sara Napolitano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Isaac Wakiro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jingyi Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jason Yeung
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Asaf Rotem
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Ewa Sicinska
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Erin Shannon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Thomas Clancy
- Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jiping Wang
- Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah Denning
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Lauren Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Naomi R. Besson
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Kathleen L. Pfaff
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Ying Huang
- Molecular Pathology Core Laboratory, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Katrina Z. Kao
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jason L. Hornick
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sebastien Vigneau
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jihye Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Matthew H. Kulke
- Section of Hematology and Medical Oncology, Boston University School of Medicine and Boston Medical Center, Boston, MA 02118, USA
| | - Jennifer Chan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Eliezer M. Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - George J. Murphy
- Section of Hematology and Medical Oncology, Boston University School of Medicine and Boston Medical Center, Boston, MA 02118, USA
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
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6
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Nyman J, Denize T, Bakouny Z, Labaki C, Titchen BM, Bi K, Hari SN, Rosenthal J, Mehta N, Jiang B, Sharma B, Felt K, Umeton R, Braun DA, Rodig S, Choueiri TK, Signoretti S, Van Allen EM. Spatially aware deep learning reveals tumor heterogeneity patterns that encode distinct kidney cancer states. Cell Rep Med 2023; 4:101189. [PMID: 37729872 PMCID: PMC10518628 DOI: 10.1016/j.xcrm.2023.101189] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 06/20/2023] [Accepted: 08/16/2023] [Indexed: 09/22/2023]
Abstract
Clear cell renal cell carcinoma (ccRCC) is molecularly heterogeneous, immune infiltrated, and selectively sensitive to immune checkpoint inhibition (ICI). However, the joint tumor-immune states that mediate ICI response remain elusive. We develop spatially aware deep-learning models of tumor and immune features to learn representations of ccRCC tumors using diagnostic whole-slide images (WSIs) in untreated and treated contexts (n = 1,102 patients). We identify patterns of grade heterogeneity in WSIs not achievable through human pathologist analysis, and these graph-based "microheterogeneity" structures associate with PBRM1 loss of function and with patient outcomes. Joint analysis of tumor phenotypes and immune infiltration identifies a subpopulation of highly infiltrated, microheterogeneous tumors responsive to ICI. In paired multiplex immunofluorescence images of ccRCC, microheterogeneity associates with greater PD1 activation in CD8+ lymphocytes and increased tumor-immune interactions. Our work reveals spatially interacting tumor-immune structures underlying ccRCC biology that may also inform selective response to ICI.
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Affiliation(s)
- Jackson Nyman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Graduate Program in Systems Biology, Cambridge, MA, USA; Broad Institute, Cambridge, MA, USA
| | - Thomas Denize
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Ziad Bakouny
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chris Labaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Breanna M Titchen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA; Harvard Graduate Program in Biological and Biomedical Sciences, Boston, MA, USA
| | - Kevin Bi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA
| | - Surya Narayanan Hari
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA
| | - Jacob Rosenthal
- Department of Informatics & Analytics, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Nicita Mehta
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Bowen Jiang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA; Stanford University, Stanford, CA, USA
| | - Bijaya Sharma
- ImmunoProfile, Department of Pathology, Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kristen Felt
- ImmunoProfile, Department of Pathology, Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, MA, USA
| | - Renato Umeton
- Department of Informatics & Analytics, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - David A Braun
- Center of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Brigham and Women's Hospital, Boston, MA, USA
| | - Sabina Signoretti
- Broad Institute, Cambridge, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
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7
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Ricciuti B, Elkrief A, Alessi J, Wang X, Li Y, Gupta H, Muldoon DM, Bertram AA, Pecci F, Lamberti G, Federico AD, Barrichello A, Vaz VR, Gandhi M, Lee E, Shapiro GI, Park H, Nishino M, Lindsay J, Felt KD, Sharma B, Cherniack AD, Rodig S, Gomez DR, Shaverdian N, Rakaee M, Bandlamudi C, Ladanyi M, Janne PA, Schoenfeld AJ, Sholl LM, Awad MM, Cheng ML. Clinicopathologic, Genomic, and Immunophenotypic Landscape of ATM Mutations in Non-Small Cell Lung Cancer. Clin Cancer Res 2023; 29:2540-2550. [PMID: 37097610 PMCID: PMC11031845 DOI: 10.1158/1078-0432.ccr-22-3413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/09/2023] [Accepted: 04/20/2023] [Indexed: 04/26/2023]
Abstract
PURPOSE ATM is the most commonly mutated DNA damage and repair gene in non-small cell lung cancer (NSCLC); however, limited characterization has been pursued. EXPERIMENTAL DESIGN Clinicopathologic, genomic, and treatment data were collected for 5,172 patients with NSCLC tumors which underwent genomic profiling. ATM IHC was performed on 182 NSCLCs with ATM mutations. Multiplexed immunofluorescence was performed on a subset of 535 samples to examine tumor-infiltrating immune cell subsets. RESULTS A total of 562 deleterious ATM mutations were identified in 9.7% of NSCLC samples. ATM-mutant (ATMMUT) NSCLC was significantly associated with female sex (P = 0.02), ever smoking status (P < 0.001), non-squamous histology (P = 0.004), and higher tumor mutational burden (DFCI, P < 0.0001; MSK, P < 0.0001) compared with ATM-wild-type (ATMWT) cases. Among 3,687 NSCLCs with comprehensive genomic profiling, co-occurring KRAS, STK11, and ARID2 oncogenic mutations were significantly enriched among ATMMUT NSCLCs (Q < 0.05), while TP53 and EGFR mutations were enriched in ATMWT NSCLCs. Among 182 ATMMUT samples with ATM IHC, tumors with nonsense, insertions/deletions, or splice site mutations were significantly more likely to display ATM loss by IHC (71.4% vs. 28.6%; P < 0.0001) compared with tumors with only predicted pathogenic missense mutations. Clinical outcomes to PD-(L)1 monotherapy (N = 1,522) and chemo-immunotherapy (N = 951) were similar between ATMMUT and ATMWT NSCLCs. Patients with concurrent ATM/TP53 mutations had significantly improved response rate and progression-free survival with PD-(L)1 monotherapy. CONCLUSIONS Deleterious ATM mutations defined a subset of NSCLC with unique clinicopathologic, genomic, and immunophenotypic features. Our data may serve as resource to guide interpretation of specific ATM mutations in NSCLC.
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Affiliation(s)
- Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Arielle Elkrief
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joao Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Xinan Wang
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Yvonne Li
- Department of Analytics and Informatics, Dana-Farber Cancer Institute, Boston, Massachusetts; Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts
| | - Hersh Gupta
- Department of Analytics and Informatics, Dana-Farber Cancer Institute, Boston, Massachusetts; Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts
| | - Daniel M. Muldoon
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Arrien A. Bertram
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Federica Pecci
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Giuseppe Lamberti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alessandro Di Federico
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Adriana Barrichello
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Victor R. Vaz
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Malini Gandhi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Elinton Lee
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Geoffrey I. Shapiro
- Center for DNA Damage and Repair (CDDR), Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Hyesun Park
- Department of Radiology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Mizuki Nishino
- Department of Radiology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - James Lindsay
- ImmunoProfile, Brigham & Women’s Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kristen D. Felt
- ImmunoProfile, Brigham & Women’s Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Bijaya Sharma
- ImmunoProfile, Brigham & Women’s Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Andrew D. Cherniack
- Department of Analytics and Informatics, Dana-Farber Cancer Institute, Boston, Massachusetts; Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts
| | - Scott Rodig
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Daniel R. Gomez
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Narek Shaverdian
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mehrdad Rakaee
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Chaitanya Bandlamudi
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pasi A. Janne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Adam J. Schoenfeld
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lynette M. Sholl
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Mark M. Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Michael L. Cheng
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
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8
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Nyman J, Denize T, Bakouny Z, Labaki C, Titchen BM, Bi K, Hari SN, Rosenthal J, Mehta N, Jiang B, Sharma B, Felt K, Umeton R, Braun DA, Rodig S, Choueiri TK, Signoretti S, Van Allen EM. Spatially aware deep learning reveals tumor heterogeneity patterns that encode distinct kidney cancer states. bioRxiv 2023:2023.01.18.524545. [PMID: 36712053 PMCID: PMC9882334 DOI: 10.1101/2023.01.18.524545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Clear cell renal cell carcinoma (ccRCC) is molecularly heterogeneous, immune infiltrated, and selectively sensitive to immune checkpoint inhibition (ICI). Established histopathology paradigms like nuclear grade have baseline prognostic relevance for ccRCC, although whether existing or novel histologic features encode additional heterogeneous biological and clinical states in ccRCC is uncertain. Here, we developed spatially aware deep learning models of tumor- and immune-related features to learn representations of ccRCC tumors using diagnostic whole-slide images (WSI) in untreated and treated contexts (n = 1102 patients). We discovered patterns of nuclear grade heterogeneity in WSI not achievable through human pathologist analysis, and these graph-based "microheterogeneity" structures associated with PBRM1 loss of function, adverse clinical factors, and selective patient response to ICI. Joint computer vision analysis of tumor phenotypes with inferred tumor infiltrating lymphocyte density identified a further subpopulation of highly infiltrated, microheterogeneous tumors responsive to ICI. In paired multiplex immunofluorescence images of ccRCC, microheterogeneity associated with greater PD1 activation in CD8+ lymphocytes and increased tumor-immune interactions. Thus, our work reveals novel spatially interacting tumor-immune structures underlying ccRCC biology that can also inform selective response to ICI.
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Affiliation(s)
- Jackson Nyman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Graduate Program in Systems Biology, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Thomas Denize
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Ziad Bakouny
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Chris Labaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Breanna M Titchen
- Harvard Graduate Program in Biological and Biomedical Sciences, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Kevin Bi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Surya Narayanan Hari
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Jacob Rosenthal
- Department of Informatics & Analytics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Nicita Mehta
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Bowen Jiang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- Stanford University, Stanford, CA, USA
| | - Bijaya Sharma
- ImmunoProfile, Department of Pathology, Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, MA
| | - Kristen Felt
- ImmunoProfile, Department of Pathology, Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, MA
| | - Renato Umeton
- Department of Informatics & Analytics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - David A Braun
- Center of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Sabina Signoretti
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
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9
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Gadi D, Martindale SP, Chiu PY, Khalsa J, Chen PH, Fernandes SM, Wang Z, Tyekucheva S, Machado JH, Fisher DC, Armand P, Davids MS, Rodig S, Sherry B, Brown JR. Circulating Th17 T cells at treatment onset predict autoimmune toxicity of PI3Kδ inhibitors. Blood Cancer J 2023; 13:22. [PMID: 36732326 PMCID: PMC9895075 DOI: 10.1038/s41408-023-00788-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 12/29/2022] [Accepted: 01/09/2023] [Indexed: 02/04/2023] Open
Abstract
PI3Kδ inhibitors are approved for the therapy of B cell malignancies, but their clinical use has been limited by unpredictable autoimmune toxicity, despite promising efficacy and evidence that toxicity is associated with improved clinical outcomes. Prior phenotypic evaluation by CyTOF has identified increases in activated CD8 T cells with activation of Th17 T cells, as well as decreases in Tregs, particularly in patients with toxicity. Here we sought to further understand the effects of idelalisib and duvelisib in vitro, and demonstrate that both idelalisib and duvelisib can inhibit T cell proliferation as well as Th1 and Treg differentiation in vitro, while promoting Th2 and Th17 differentiation. We further demonstrate directly using intracellular flow cytometry that autoimmune toxicity in patients is associated with higher absolute numbers of CD4 and CD8 T cells with Th17 differentiation in peripheral blood prior to therapy, and that gastrointestinal tissues from patients with active autoimmune complications of PI3Kδ inhibitors show infiltration with Th17+ T cells. These same tissues show depletion of Tregs as compared to CLL patients without toxicity, suggesting that loss of Tregs may be permissive for Th17 activation to lead to autoimmune toxicity. Clinical trials to restore this balance are warranted.
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Affiliation(s)
- Deepti Gadi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Stephen P Martindale
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Pui Yan Chiu
- Center for Immunology & Inflammation, Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Jasneet Khalsa
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Pei-Hsuan Chen
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Stacey M Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Zixu Wang
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - John-Hanson Machado
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - David C Fisher
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Philippe Armand
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Matthew S Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Scott Rodig
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Barbara Sherry
- Center for Immunology & Inflammation, Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
- Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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10
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Le Y, Gao H, Zhu A, Felt K, Rodig S, Bleday R, Zhu Z. NF-κB-regulated VentX expression mediates tumoricidal effects of chemotherapeutics at noncytotoxic concentrations. iScience 2022; 25:105426. [DOI: 10.1016/j.isci.2022.105426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 08/09/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
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11
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Mandato E, Calabretta E, Bai G, Song L, Sun Y, Shanmugam V, Paczkowska J, Choi IK, Redd R, Tang M, Lawton LN, Neuberg D, Rodig S, Michor F, Zhang B, Shipp MA. Abstract A38: Cd70 genetic perturbation limits the development of an effective CD8+ T-cell immune response to Bcl6-driven diffuse large B-cell lymphoma. Blood Cancer Discov 2022. [DOI: 10.1158/2643-3249.lymphoma22-a38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Multiple immunomodulatory pathways shape the development of anti-tumor immune responses to lymphoid malignancies. We previously defined the recurrent genetic alterations in diffuse large B-cell lymphoma (DLBCL) and identified associated substructure and additional potential genetic bases for immune escape. CD70 was the most commonly perturbed immune response pathway component in our cohort of primary DLBCLs; alterations included inactivating mutations and copy loss. CD70 co-stimulation of CD27+ T cells induces antigen-dependent T-cell expansion and immune surveillance of normal and malignant B cells. Given the frequent co-association of CD70 alterations and BCL6 translocations in our DLBCL patient series, we assessed the consequences of Cd70 deficiency on Bcl6-driven lymphomagenesis in a murine model. We crossed previously generated Cd70 −/- and Bcl6 tg/+ mice to obtain Cd70 −/−; Bcl6 tg/+ animals. In our aging cohorts, Cd70− / −; Bcl6tg/+ mice developed significantly increased numbers of histopathologically confirmed DLBCLs at earlier timepoints, compared to Bcl6 tg/+ animals. Both the Cd70 −/−; Bcl6 tg/+ and Bcl6 tg/+ mice that were euthanized for symptoms exhibited massive splenomegaly and lymphomatous splenic infiltration. None of the wild-type (WT) and Cd70 −/- animals developed lymphoma. To characterize potential differences in anti-tumor responses in Cd70 −/−; Bcl6 tg/+ versus Bcl6 tg/+ mice, we harvested spleens from asymptomatic animals in each cohort at 6, 14 and 18 months (mo). Cd70 −/−; Bcl6 tg/+ mice exhibited significantly earlier onset splenomegaly than Bcl6 tg/+ animals (both in comparison with WT mice). We performed single cell RNA sequencing of splenic cell suspensions from each murine cohort at the above-mentioned predetermined timepoints (6, 14 and 18 mo) and describe genotype-related changes in splenic CD8+ T-cell infiltration in this abstract. Our study revealed an age-related decline in the percentages of naive CD8+ T cells in all genotypes, with more striking and earlier changes in Cd70 −/−; Bcl6 tg/+ animals. Cd70 −/−; Bcl6 tg/+ and Bcl6 tg/+ mice exhibited a selective and significant expansion of CD8+ cytotoxic T cells (CTLs), which expressed Gzmb and Prf1 and the exhaustion markers, Pdcd1, Lag3, Tigit, Tox and Tim3, and exhibited clonal expansion. At 6 mo, prior to splenic enlargement and the development of symptoms, CD8+ CTLs in Cd70 −/−; Bcl6 tg/+ animals expressed significantly higher levels of exhaustion markers than those in Bcl6 tg/+ mice. Consistent with this finding, there was a more limited expansion and a subsequent contraction of these splenic CD8+ CTLs in Cd70 −/−; Bcl6 tg/+ mice, in comparison to Bcl6 tg/+ animals. Taken together, these findings suggest that initial anti-tumor immune responses are less effective in Cd70 −/−; Bcl6 tg/+ mice than in Bcl6 tg/+ animals and highlight the likely importance of CD70/CD27 co-stimulation in CD8+ T-cell response to Bcl6-driven DLBCL.
Citation Format: Elisa Mandato, Eleonora Calabretta, Gali Bai, Li Song, Yanbo Sun, Vignesh Shanmugam, Julia Paczkowska, Il-Kyu Choi, Robert Redd, Ming Tang, Lee N Lawton, Donna Neuberg, Scott Rodig, Franziska Michor, Baochun Zhang, Margaret A Shipp. Cd70 genetic perturbation limits the development of an effective CD8+ T-cell immune response to Bcl6-driven diffuse large B-cell lymphoma [abstract]. In: Proceedings of the Third AACR International Meeting: Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2022 Jun 23-26; Boston, MA. Philadelphia (PA): AACR; Blood Cancer Discov 2022;3(5_Suppl):Abstract nr A38.
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Affiliation(s)
| | | | - Gali Bai
- 1Dana-Farber Cancer Institute, Boston, MA,
| | - Li Song
- 1Dana-Farber Cancer Institute, Boston, MA,
| | - Yanbo Sun
- 1Dana-Farber Cancer Institute, Boston, MA,
| | | | | | | | | | - Ming Tang
- 1Dana-Farber Cancer Institute, Boston, MA,
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12
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Campisi M, Chen M, Schol P, Tarannum M, Wolff J, Romee R, Rodig S, Barbie D, Mahadevan N. P2.10-04 Immunologic Subtype of Small Cell Lung Carcinoma Dictates Susceptibility to NK Cell-Mediated Cytotoxicity. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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13
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Yao S, Campbell PT, Ugai T, Gierach G, Abubakar M, Adalsteinsson V, Almeida J, Brennan P, Chanock S, Golub T, Hanash S, Harris C, Hathaway CA, Kelsey K, Landi MT, Mahmood F, Newton C, Quackenbush J, Rodig S, Schultz N, Tearney G, Tworoger SS, Wang M, Zhang X, Garcia-Closas M, Rebbeck TR, Ambrosone CB, Ogino S. Proceedings of the fifth international Molecular Pathological Epidemiology (MPE) meeting. Cancer Causes Control 2022; 33:1107-1120. [PMID: 35759080 PMCID: PMC9244289 DOI: 10.1007/s10552-022-01594-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 05/20/2022] [Indexed: 01/19/2023]
Abstract
Cancer heterogeneities hold the key to a deeper understanding of cancer etiology and progression and the discovery of more precise cancer therapy. Modern pathological and molecular technologies offer a powerful set of tools to profile tumor heterogeneities at multiple levels in large patient populations, from DNA to RNA, protein and epigenetics, and from tumor tissues to tumor microenvironment and liquid biopsy. When coupled with well-validated epidemiologic methodology and well-characterized epidemiologic resources, the rich tumor pathological and molecular tumor information provide new research opportunities at an unprecedented breadth and depth. This is the research space where Molecular Pathological Epidemiology (MPE) emerged over a decade ago and has been thriving since then. As a truly multidisciplinary field, MPE embraces collaborations from diverse fields including epidemiology, pathology, immunology, genetics, biostatistics, bioinformatics, and data science. Since first convened in 2013, the International MPE Meeting series has grown into a dynamic and dedicated platform for experts from these disciplines to communicate novel findings, discuss new research opportunities and challenges, build professional networks, and educate the next-generation scientists. Herein, we share the proceedings of the Fifth International MPE meeting, held virtually online, on May 24 and 25, 2021. The meeting consisted of 21 presentations organized into the three main themes, which were recent integrative MPE studies, novel cancer profiling technologies, and new statistical and data science approaches. Looking forward to the near future, the meeting attendees anticipated continuous expansion and fruition of MPE research in many research fronts, particularly immune-epidemiology, mutational signatures, liquid biopsy, and health disparities.
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Affiliation(s)
- Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA.
| | - Peter T Campbell
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tomotaka Ugai
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Gretchen Gierach
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Mustapha Abubakar
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | - Jonas Almeida
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Paul Brennan
- International Agency for Research On Cancer (IARC/WHO), Genomic Epidemiology Branch, Lyon, France
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Todd Golub
- Broad Institute of MIT and Harvard, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Samir Hanash
- Department of Clinical Cancer Prevention, MD Anderson Cancer Institute, Houston, TX, USA
| | - Curtis Harris
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Cassandra A Hathaway
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Karl Kelsey
- Department of Epidemiology, Brown School of Public Health, Brown University, Providence, RI, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Faisal Mahmood
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Christina Newton
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - John Quackenbush
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Nikolaus Schultz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Guillermo Tearney
- Department of Pathology and Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
| | - Shelley S Tworoger
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Molin Wang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Xuehong Zhang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Timothy R Rebbeck
- Zhu Family Center for Global Cancer Prevention, Harvard T.H. Chan School of Public Health and Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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14
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Barroso-Sousa R, Forman J, Collier K, Weber ZT, Jammihal TR, Kao KZ, Richardson ET, Keenan T, Cohen O, Manos MP, Brennick RC, Ott PA, Hodi FS, Dillon DA, Attaya V, O'Meara T, Lin NU, Van Allen EM, Rodig S, Winer EP, Mittendorf EA, Wu CJ, Wagle N, Stover DG, Shukla SA, Tolaney SM. Multidimensional Molecular Profiling of Metastatic Triple-Negative Breast Cancer and Immune Checkpoint Inhibitor Benefit. JCO Precis Oncol 2022; 6:e2100413. [PMID: 35797509 PMCID: PMC9848556 DOI: 10.1200/po.21.00413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
PURPOSE In metastatic triple-negative breast cancer (mTNBC), consistent biomarkers of immune checkpoint inhibitor (ICI) therapy benefit remain elusive. We evaluated the immune, genomic, and transcriptomic landscape of mTNBC in patients treated with ICIs. METHODS We identified 29 patients with mTNBC treated with pembrolizumab or atezolizumab, either alone (n = 9) or in combination with chemotherapy (n = 14) or targeted therapy (n = 6), who had tumor tissue and/or blood available before ICI therapy for whole-exome sequencing. RNA sequencing and CIBERSORTx-inferred immune population analyses were performed (n = 20). Immune cell populations and programmed death-ligand 1 expression were assessed using multiplexed immunofluorescence (n = 18). Clonal trajectories were evaluated via serial tumor/circulating tumor DNA whole-exome sequencing (n = 4). Association of biomarkers with progression-free survival and overall survival (OS) was assessed. RESULTS Progression-free survival and OS were longer in patients with high programmed death-ligand 1 expression and tumor mutational burden. Patients with longer survival also had a higher relative inferred fraction of CD8+ T cells, activated CD4+ memory T cells, M1 macrophages, and follicular helper T cells and enrichment of inflammatory gene expression pathways. A mutational signature of defective repair of DNA damage by homologous recombination was enriched in patients with both shorter OS and primary resistance. Exploratory analysis of clonal evolution among four patients treated with programmed cell death protein 1 blockade and a tyrosine kinase inhibitor suggested that clonal stability post-treatment was associated with short time to progression. CONCLUSION This study identified potential biomarkers of response to ICIs among patients with mTNBC: high tumor mutational burden; presence of CD8+, CD4 memory T cells, follicular helper T cells, and M1 macrophages; and inflammatory gene expression pathways. Pretreatment deficiencies in the homologous recombination DNA damage repair pathway and the absence of or minimal clonal evolution post-treatment may be associated with worse outcomes.
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Affiliation(s)
| | - Juliet Forman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Broad Institute of MIT and Harvard, Cambridge, MA.,Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Tejas R Jammihal
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Katrina Z Kao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Tanya Keenan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Ofir Cohen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Michael P Manos
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Ryan C Brennick
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Patrick A Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Deborah A Dillon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Victoria Attaya
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Tess O'Meara
- Internal Medicine, Brigham and Women's Hospital, Boston, MA
| | - Nancy U Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
| | | | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Eric P Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
| | - Elizabeth A Mittendorf
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA.,Divison of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
| | | | - Sachet A Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Broad Institute of MIT and Harvard, Cambridge, MA.,Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA
| | - Sara M Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
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15
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Chou J, Arihara Y, Budka J, Huang L, Tiwari G, Falk A, Jacobson CA, Rodig S, Armand P, Miklos DB, Neelapu SS, Locke FL, Lekakis LJ, Ghobadi A, Lin Y, Dong J, Milletti F, Mattie M, Bot A, Ritz J. Pre and Post-Treatment CD27+ T Cells Track with Clinical Efficacy of Axi-Cel in DLBCL Patients. Transplant Cell Ther 2022. [DOI: 10.1016/s2666-6367(22)00368-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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Rahma OE, Tyan K, Giobbie-Hurder A, Brohl AS, Bedard PL, Renouf DJ, Sharon E, Streicher H, Hathaway E, Cunningham R, Manos M, Severgnini M, Rodig S, Stephen Hodi F. Phase IB study of ziv-aflibercept plus pembrolizumab in patients with advanced solid tumors. J Immunother Cancer 2022; 10:e003569. [PMID: 35264434 PMCID: PMC8915279 DOI: 10.1136/jitc-2021-003569] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The combination of antiangiogenic agents with immune checkpoint inhibitors could potentially overcome immune suppression driven by tumor angiogenesis. We report results from a phase IB study of ziv-aflibercept plus pembrolizumab in patients with advanced solid tumors. METHODS This is a multicenter phase IB dose-escalation study of the combination of ziv-aflibercept (at 2-4 mg/kg) plus pembrolizumab (at 2 mg/kg) administered intravenously every 2 weeks with expansion cohorts in programmed cell death protein 1 (PD-1)/programmed death-ligand 1(PD-L1)-naïve melanoma, renal cell carcinoma (RCC), microsatellite stable colorectal cancer (CRC), and ovarian cancer. The primary objective was to determine maximum tolerated dose (MTD) and recommended dose of the combination. Secondary endpoints included overall response rate (ORR) and overall survival (OS). Exploratory objectives included correlation of clinical efficacy with tumor and peripheral immune population densities. RESULTS Overall, 33 patients were enrolled during dose escalation (n=3) and dose expansion (n=30). No dose-limiting toxicities were reported in the initial dose level. Ziv-aflibercept 4 mg/kg plus pembrolizumab 2 mg/kg every 2 weeks was established as the MTD. Grade ≥3 adverse events occurred in 19/33 patients (58%), the most common being hypertension (36%) and proteinuria (18%). ORR in the dose-expansion cohort was 16.7% (5/30, 90% CI 7% to 32%). Complete responses occurred in melanoma (n=2); partial responses occurred in RCC (n=1), mesothelioma (n=1), and melanoma (n=1). Median OS was as follows: melanoma, not reached (NR); RCC, 15.7 months (90% CI 2.5 to 15.7); CRC, 3.3 months (90% CI 0.6 to 3.4); ovarian, 12.5 months (90% CI 3.8 to 13.6); other solid tumors, NR. Activated tumor-infiltrating CD8 T cells at baseline (CD8+PD1+), high CD40L expression, and increased peripheral memory CD8 T cells correlated with clinical response. CONCLUSION The combination of ziv-aflibercept and pembrolizumab demonstrated an acceptable safety profile with antitumor activity in solid tumors. The combination is currently being studied in sarcoma and anti-PD-1-resistant melanoma. TRIAL REGISTRATION NUMBER NCT02298959.
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Affiliation(s)
- Osama E Rahma
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Kevin Tyan
- Harvard Medical School, Boston, Massachusetts, USA
| | - Anita Giobbie-Hurder
- Division of Biostatistics, Department of Data Sciences, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Andrew S Brohl
- Sarcoma Department and Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Philippe L Bedard
- Division of Medical Oncology and Hematology, University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Daniel J Renouf
- Cancer and Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elad Sharon
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland, USA
| | - Howard Streicher
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland, USA
| | - Emma Hathaway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Center for Immuno-Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Rachel Cunningham
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Center for Immuno-Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Michael Manos
- Center for Immuno-Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Mariano Severgnini
- Center for Immuno-Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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17
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Shah H, Wang Y, Cheng SC, Gunasti L, Chen YH, Lako A, Guenette J, Rodig S, Jo VY, Uppaluri R, Haddad R, Schoenfeld JD, Jacene HA. Use of Fluoro-[18F]-Deoxy-2-D-Glucose Positron Emission Tomography/Computed Tomography to Predict Immunotherapy Treatment Response in Patients With Squamous Cell Oral Cavity Cancers. JAMA Otolaryngol Head Neck Surg 2022; 148:268-276. [PMID: 35050348 PMCID: PMC8778607 DOI: 10.1001/jamaoto.2021.4052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
IMPORTANCE Neoadjuvant immunotherapy is a novel approach with the potential to improve outcomes for patients with oral cavity squamous cell cancer (OCSCC). Adverse events of varying severity are reported with immunotherapy, and a biomarker to predict response would be clinically useful to avoid toxic effects in those unlikely to benefit. OBJECTIVE To correlate changes on fluoro-[18F]-deoxy-2-D-glucose positron emission tomography/computed tomography (FDG-PET/CT) scans with primary tumor pathologic response and immunologic biomarkers in patients with OCSCC receiving neoadjuvant immunotherapy. DESIGN, SETTING, AND PARTICIPANTS This was a retrospective analysis of serial FDG-PET/CT scans obtained prospectively as part of a phase 2 open-label randomized clinical trial investigating neoadjuvant immunotherapy in patients with untreated OCSCC between 2016 and 2019. Included were a total of 29 patients from a single academic medical center with untreated OCSCC (≥T2, or clinically node positive) randomized 1:1 to receive neoadjuvant therapy with single agent nivolumab or combination nivolumab and ipilimumab followed by surgery and standard of care adjuvant therapy. INTERVENTIONS The interventions in this study were FDG-PET/CT scans before (T0) and after (T1) preoperative immunotherapy. MAIN OUTCOMES AND MEASURES Data collected from FDG-PET/CT scans included maximum standardized uptake value (SUVmax) of primary OCSCC and cervical lymph nodes (LNs) at T0 and T1 and new LN uptake and uptake consistent with radiologic immune-related adverse events (irAEs) at T1. Primary OCSCC pathologic response reported as percentages of viable vs nonviable tumor. The number of CD8+ cells/mm2 was determined in the primary tumor biopsy specimen and at surgery. RESULTS There was no correlation between pathologic response and change in SUVmax in the primary OCSCC between T0 and T1. Out of 27 total participants, 13 had newly FDG-avid ipsilateral LNs at T1, most negative on pathology. A total of 9 had radiologic irAEs, most commonly sarcoid-like LN (7 of 27). No correlations were found between primary OCSCC SUVmax at T0 and CD8+ T-cell number in the primary tumor biopsy, and no correlations were found between primary OCSCC SUVmax at T1 and CD8+ T-cell number in the primary tumor at surgery. CONCLUSIONS AND RELEVANCE There were no correlations between changes in FDG uptake after neoadjuvant immunotherapy and pathologic primary tumor response. Importantly, newly FDG-avid ipsilateral LNs following neoadjuvant immunotherapy were commonly observed but did not represent progressive disease or indicate pathologically disease positive nodes in most cases. These findings argue against altering surgical plans in this setting and suggest that the role of FDG-PET/CT may be limited as an early imaging biomarker for predicting pathologic response to preoperative immunotherapy for OCSCC. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT02919683.
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Affiliation(s)
- Hina Shah
- Department of Imaging, Dana-Farber Cancer Institute, Boston, Massachusetts,Department of Radiology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Yating Wang
- Division of Biostatistics, Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Su-Chun Cheng
- Division of Biostatistics, Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lauren Gunasti
- Department of Radiation Oncology, Brigham and Women’s Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts,Head and Neck Cancer Treatment Center, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Yu-Hui Chen
- Division of Biostatistics, Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ana Lako
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Bristol Myers Squibb
| | - Jeffrey Guenette
- Department of Imaging, Dana-Farber Cancer Institute, Boston, Massachusetts,Department of Radiology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Scott Rodig
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Vickie Y. Jo
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Ravindra Uppaluri
- Head and Neck Cancer Treatment Center, Dana-Farber Cancer Institute, Boston, Massachusetts,Department of Surgery, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Robert Haddad
- Head and Neck Cancer Treatment Center, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jonathan D. Schoenfeld
- Department of Radiation Oncology, Brigham and Women’s Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts,Head and Neck Cancer Treatment Center, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Heather A. Jacene
- Department of Imaging, Dana-Farber Cancer Institute, Boston, Massachusetts,Department of Radiology, Brigham and Women’s Hospital, Boston, Massachusetts
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18
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Abravanel DL, Klughammer J, Blosser T, Goltsev Y, Jiang S, Bai Y, Murray E, Alon S, Cui Y, Goodwin DR, Sinha A, Cohen O, Slyper M, Ashenberg O, Dionne D, Jané-Valbuena J, Porter CBM, Segerstolpe A, Waldman J, Vigneau S, Helvie K, Frangieh A, DelloStritto L, Patel M, We J, Pfaff K, Cullen N, Lako A, Turner M, Wakiro I, Napolitano S, Kanodia A, Ortiz R, MacKichan C, Inga S, Chen J, Thorner AR, Rotem A, Rodig S, Chen F, Boyden ES, Nolan GP, Zhuang X, Rozenblatt-Rosen O, Johnson BE, Regev A, Wagle N. Abstract PD6-03: Spatio-molecular dissection of the breast cancer metastatic microenvironment. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-pd6-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Metastatic breast cancer (MBC) remains incurable due to inevitable development of therapeutic resistance. Although tumor cell intrinsic mechanisms of resistance in MBC are beginning to be elucidated by bulk sequencing studies, the roles of the tumor microenvironment and intratumor heterogeneity in therapeutic resistance remain underexplored due to both technological barriers and limited availability of samples. To comprehensively capture these characteristics we have adapted a research biopsy protocol to collect tissue for an array of single-cell and spatio-molecular assays whose performance we have optimized for MBC, including single-cell and single-nucleus RNA sequencing, Slide-Seq, Multiplexed Error-Robust FISH (MERFISH), Expansion Sequencing (ExSEQ), Co-detection by Indexing (CODEX) and Multiplexed Ion Beam Imaging (MIBI). To date, we have successfully performed single-cell or single-nucleus RNAseq in 67 MBC biopsies and generated detailed accompanying clinical annotations for each. These samples provide a representation of the clinicopathological diversity of MBC including different breast cancer subtypes (44 HR+/HER2-, 3 HR-/HER2+, 3 HR+/HER2+, 16 TNBC, 1 unknown), common anatomic sites of metastasis (37 liver, 9 axilla, 7 breast, 5 bone, 3 chest wall, 3 neck, 1 brain, 1 lung, 1 skin), metastatic presentations (53 recurrent, 14 de novo) and histologic subtypes in the breast (45 IDC, 7 ILC, 6 mixed, 3 DCIS, 1 mucinous, 5 unknown/NA). Following optimization, both single-cell and single-nucleus RNA seq perform well in these MBC biopsies recovering all expected cell types including the malignant, stromal (e.g. fibroblasts, endothelial cells), myeloid (e.g. monocytes, macrophages) and lymphoid compartments (e.g. T cells, B cells, NK cells) as well as relevant oncogenic programs (e.g. cell cycle programs in all compartments; EMT-like and ER signaling programs in the malignant compartment, immune checkpoint programs in the lymphoid compartment; and fibroblast activation and vascular homeostasis programs in the stromal compartment). In addition to differences between the two techniques, these data demonstrate substantial intratumor heterogeneity in cell type composition. For example in liver biopsies the average number of cells per sample compartment by single nucleus RNA-seq was 6745 malignant (56%, SD 4216), 4637 stromal (41%, SD 3727), 1196 lymphoid (8%, SD 1617) and 874 myeloid (6%, SD 852); in breast biopsies the average number of cells per compartment by single nucleus RNA-seq was 6421 malignant (70%, SD 3497), 1628 stromal (24%, SD 117), 333 lymphoid (4%, SD 170) and 213 myeloid (3%, SD 117). Additionally, we find both inter- and intra-tumor heterogeneity in expression patterns and programs including, for example, expression of ER, PR and HER2 within clinical receptor subtypes (log normalized counts for ER expression in tumor cells by single cell RNA-seq: HR+/HER2- 0.921 (SD 0.714); HR+/HER2+ 0.768 (SD 0.624); HR-/HER2+ 0.018 (SD 0.122); and HR-/HER2- 0.005 (SD 0.066). For a subset of 13 biopsies we are also completing the spatiomolecular characterization methods on serial sections of a single adjacent biopsy. This unique experimental setup was designed to enable efficient comparison and integration of these assays. In spite of differences between experimental techniques and readouts, cell typing can be approached by annotation transfer from matching single cell or single nucleus RNAseq data, enabling exploratory analyses including evaluation of spatial phenotypes and cell type colocalization. Overall, these single cell and spatial data afford a comprehensive atlas including cell types, cell states/programs, cell interactions and spatial organization in MBC lesions. Future analyses will include serial biopsies over time and integration of clinicopathologic data including therapeutic response and resistance.
Citation Format: Daniel L Abravanel, Johanna Klughammer, Timothy Blosser, Yury Goltsev, Sizun Jiang, Yunjao Bai, Evan Murray, Shahar Alon, Yi Cui, Daniel R Goodwin, Anubhav Sinha, Ofir Cohen, Michal Slyper, Orr Ashenberg, Danielle Dionne, Judit Jané-Valbuena, Caroline BM Porter, Asa Segerstolpe, Julia Waldman, Sébastien Vigneau, Karla Helvie, Allison Frangieh, Laura DelloStritto, Miraj Patel, Jingyi We, Kathleen Pfaff, Nicole Cullen, Ana Lako, Madison Turner, Isaac Wakiro, Sara Napolitano, Abhay Kanodia, Rebecca Ortiz, Colin MacKichan, Stephanie Inga, Judy Chen, Aaron R Thorner, Asaf Rotem, Scott Rodig, Fei Chen, Edward S Boyden, Garry P Nolan, Xiaowei Zhuang, Orit Rozenblatt-Rosen, Bruce E Johnson, Aviv Regev, Nikhil Wagle. Spatio-molecular dissection of the breast cancer metastatic microenvironment [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD6-03.
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Affiliation(s)
| | | | | | | | | | | | - Evan Murray
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Shahar Alon
- Massachusetts Institute of Technology, Cambridge, MA
| | - Yi Cui
- Massachusetts Institute of Technology, Cambridge, MA
| | | | - Anubhav Sinha
- Massachusetts Institute of Technology, Cambridge, MA
| | - Ofir Cohen
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Jingyi We
- Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Ana Lako
- Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | | | | | - Judy Chen
- Dana-Farber Cancer Institute, Boston, MA
| | | | - Asaf Rotem
- Dana-Farber Cancer Institute, Boston, MA
| | | | - Fei Chen
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Edward S Boyden
- Massachusetts Institute of Technology, Howard Hughes Medical Institute, Cambridge, MA
| | | | - Xiaowei Zhuang
- Harvard University, Howard Hughes Medical Institute, Cambridge, MA
| | | | | | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA
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19
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Oliveira G, Stromhaug K, Klaeger S, Cieri N, Iorgulescu B, Li S, Braun D, Neuberg D, Carr S, Livak K, Tompers D, Fritsch E, Wind-Rotolo M, Hacohen N, Sade-Feldman M, Keskin D, Ott P, Rodig S, Boland G, Wu C. 655 Landscape of helper and regulatory CD4+ T cells in melanoma. J Immunother Cancer 2021. [DOI: 10.1136/jitc-2021-sitc2021.655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BackgroundWithin the tumor microenvironment, distinct CD4+ T cell subsets can play different and even opposite roles either promoting or suppressing anti-tumor responses through the recognition of antigens presented by human leukocyte antigen (HLA) class II molecules. However, how cancers co-opt these processes to shape the intratumoral CD4+ landscape and achieve immune evasion remains incompletely understood.MethodsWe performed single-cell characterization of CD4+ tumor infiltrating lymphocytes (TILs) collected from four human melanoma with low or high HLA-class II expression and we utilized TCR reconstruction and antigen specificity screening to unambiguously discover the tumor reactivity of CD4+ TILs. By testing TCR-transduced T cells against autologous patient-derived melanoma cell lines or against autologous antigen presenting cells (APCs) loaded with tumor lysates, we assessed the capacity of CD4+ TCRs to directly or indirectly recognize tumor cells. We defined the antigen-specificity of antitumor CD4+ TCRs by assessing their reactivity towards personal neoantigens (NeoAg) or public melanoma associated antigens (MAAs). Finally, we correlated NeoAg burden and HLA-class II expression in a series of 116 melanoma specimens from 4 independent cohorts of patients.ResultsAnalysis of single-cell data showed that the cluster distribution of cells within each CD4+ TCR clonotype family was highly homogeneous and appeared to follow 3 distinct major phenotypes, corresponding to non-exhausted memory cells, exhausted cells and regulatory cells (TRegs). Strikingly, clonally expanded CD4+ TReg-TILs were highly abundant within the tumor microenvironment of HLA class IIpos melanomas. We found that TCRs from exhausted cytotoxic CD4+ T cells could be directly triggered by melanoma cells not only through recognition of HLA class II restricted antigens, but also through presentation of HLA class I restricted MAAs. TReg-TCRs could be indirectly elicited through presentation of tumor antigens via APCs. Notably, numerous tumor-reactive CD4+ TReg-TCRs were directly stimulated by HLA class IIpos melanoma and demonstrated specificity for melanoma NeoAgs. In HLA class IIpos melanomas, the clonal expansion of numerous tumor-reactive and NeoAg-specific TRegs-clones appeared to be favored by a dramatically high tumor NeoAg load. Analysis of 116 melanoma specimens confirmed the association of elevated HLA-class II expression with extremely high NeoAg burden.ConclusionsOur data elucidate the landscape of infiltrating CD4+ T cells in melanoma and point to presentation of HLA-class II restricted NeoAgs and direct engagement of immunosuppressive CD4+ TRegs as a novel mechanism of immune evasion favored in HLA class IIpos melanoma.
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Tyan K, Rahma O, Giobbie-Hurder A, Brohl A, Bedard P, Renouf D, Sharon E, Streicher H, Hathaway E, Cunningham R, Manos M, Severgnini M, Rodig S, Stephen Hodi F. 374 A phase IB trial of ziv-aflibercept plus pembrolizumab in patients with advanced solid tumors. J Immunother Cancer 2021. [DOI: 10.1136/jitc-2021-sitc2021.374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BackgroundAngiogenic factors play a role in regulating immune suppression in the tumor microenvironment and driving resistance to immune checkpoint inhibitor therapy.1 Ziv-aflibercept is a soluble decoy receptor that ”traps” endogenous vascular endothelial growth factor (VEGF) with 100-fold increased binding affinity compared to Bevacizumab.2 The combination of ziv-aflibercept with either cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) or programmed cell death protein 1 (PD-1) blockade has shown promising antitumor efficacy in mouse models.3 4 We hypothesized that a novel combination of ziv-aflibercept and anti-PD-1 would be tolerable and lead to clinical benefits in tumors that traditionally do not respond to checkpoint blockade.MethodsThis is a multicenter phase 1B dose escalation study (NCT02298959) of the combination of ziv-aflibercept (at 2–4 mg/kg) plus pembrolizumab (at 2 mg/kg) administered intravenously every 2 weeks with expansion cohorts in PD-1/PD-L1 naïve melanoma, renal cell carcinoma (RCC), microsatellite stable colorectal cancer (MSS CRC), and ovarian cancer (figure 1). The primary objective was to determine the maximum tolerated dose (MTD) and recommended dose of the combination. Secondary endpoints included overall response rate (ORR) and overall survival (OS). Exploratory objectives included correlation of clinical efficacy and immune population densities in the tissue and periphery.ResultsOverall, 33 patients were enrolled during dose escalation (n=3) and dose expansion (n=30). No dose-limiting toxicities (DLTs) were reported in the initial dose level. Ziv-aflibercept 4 mg/kg plus pembrolizumab 2 mg/kg every 2 weeks was established as the MTD. Grade ≥3 treatment-related adverse events occurred in 19/33 patients (58%), the most common being hypertension (36%) and proteinuria (18%). ORR in the dose expansion cohort was 16.7% (5/30; 95% CI, 7–32%). Complete responses occurred in melanoma (n=2), partial responses occurred in RCC (n=1), mesothelioma (n=1), and melanoma (n=1). Efficacy outcomes by tumor type are shown in table 1 and figure 2. Median OS was as follows: melanoma, not reached; RCC, 15.7 months (90% CI, 2.5–15.7); CRC, 3.3 months (90% CI, 0.6–3.4), ovarian, 12.5 months (90% CI, 3.8–13.6), other solid tumors, not reached (figure 3). Activated tumor infiltrating CD8 T cells at baseline (CD8+PD1+), high CD40L expression (figure 4), and increased memory CD8 T cells in the periphery (figure 5) correlated with clinical response to the combination therapy.Abstract 374 Figure 1Study Schema of dose escalation and dose expansion. (A) Cohort 1 included the following tumors: clear cell sarcoma, triple negative breast cancer (TNBC), and mesothelioma. (B) Other solid tumors in Cohort 2 were: epithelioid mesothelioma (2) and TNBC (1).Abstract 374 Table 1Efficacy outcomes by dose level and tumor typea. Solid tumors included clear cell sarcoma (1), breast cancer (2), mesothelioma (3).b. Both patients with CR had melanoma and were in Cohort 2 (DL2).Abstract 374 Figure 2Waterfall plot of best RECIST response. Waterfall plot of maximum change from baseline in sum of target lesions for 28 patients with tumor measurements over time. Plot is color-coded by tumor type. Triangles indicate patients who developed new lesions, yellow circles indicate the 3 patients who received DL1.Abstract 374 Figure 3Progression and overall survival by tumor type. Kaplan-Meier curves for (A) progression-free survival and (B) overall survival based on tumor type.Abstract 374 Figure 4Luminex assay analysis of clinical response. Luminex analysis of baseline biomarkers. Patients were analyzed by clinical response (complete response [CR] and partial response [PR]) and durable clinical benefit (DCB) which includes patients with CR, PR, and stable disease (SD). (A) Baseline levels of IL-6 were lower in responders vs. non-responders (median 2.605 vs. 9.847 pg/mL, p = 0.009). Baseline CD40L was increased in responders (median 2,840 vs. 2,267 pg/mL, p = 0.06). (B) Baseline levels of GroB (median 1,272 vs. 592 pg/mL, p = 0.006), CXCL5 (median 547.5 vs. 296.2 pg/mL, p = 0.02), and CD40L (median 2,807 vs. 1,595 pg/mL, p = 0.001) were higher in patients with DCB vs. no DCB. P-values for baseline comparisons were obtained through Wilcoxon rank-sum test. The solid black line indicates median. Violins show range and kernel density estimate distributions of each group. (*) p < 0.05, (**) p < 0.01.Abstract 374 Figure 5Flow cytometry analysis. Flow cytometry analysis comparing T cell populations and monocytes between patients with clinical response (CR or PR, n = 5) and non-responders (n = 18) and patients with disease control (CR, PR, or SD, n = 12) and no disease control (n = 11). (A) CD4+ populations were increased in responders vs. non-responders at all time points. (B) CD8+ populations were decreased in responders vs. non-responders at all time points. (C) Treg CD4+/CD25+/FoxP3+ was decreased at baseline in responders. (D) Treg CD4+/CD25+/FoxP3+ were decreased at baseline and 1-month in patients with disease control vs. no disease control. (E) TCM CD8+/CD45RO+/CCR7+ was increased at all time points in responders vs. non-responders. (F) TEMRA CD8+/CD45RO-/CCR7- was decreased in responders at baseline. (G) Non-classical TIE2 was increased at baseline in non-responders. (H) Classical monocytes were increased at all time points in non-responders.ConclusionsThe combination of ziv-aflibercept and pembrolizumab demonstrated an acceptable safety profile with antitumor activity in solid tumors. The combination is currently being studied in sarcoma and anti-PD-1 resistant melanoma.AcknowledgementsThis trial was supported by the National Cancer Institute (NCI) and by Merck, Sharpe, and Dohme and Sanofi via Cooperative Research and Development Agreements with the NCI. PLB was supported by NCI UM1 Grant CA186644.Trial RegistrationNCT02298959ReferencesRahma OE, Hodi FS. The intersection between tumor angiogenesis and immune suppression. Clin Cancer Res September 15 2019;25(18):5449–5457. doi:10.1158/1078-0432.CCR-18-1543Holash J, Davis S, Papadopoulos N, et al. VEGF-trap: a VEGF blocker with potent antitumor effects. Proceedings of the National Academy of Sciences 2002;99(17):11393–11398. doi:10.1073/pnas.172398299Burova E, Ioffe E, Taduriyasas C, et al. Abstract 5035: blockade of VEGF with ziv-aflibercept (VEGF Trap) enhances anti-tumor efficacy of CTLA-4 blocking antibody in an Fc dependent manner. Cancer Research 2014;74(19 Supplement):5035–5035. doi:10.1158/1538-7445.am2014-5035Di Tacchio M, Macas J, Weissenberger J, et al. Tumor vessel normalization, immunostimulatory reprogramming, and improved survival in glioblastoma with combined inhibition of PD-1, angiopoietin-2, and VEGF. Cancer Immunology Research 2019;7(12):1910–1927. doi:10.1158/2326-6066.cir-18-0865Ethics ApprovalThis trial (NCT02298959) was approved by all participating IRBs.
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Gu S, Zhang W, Wang X, Jiang P, Traugh N, Li Z, Meyer C, Stewig B, Xie Y, Bu X, Manos M, Font-Tello A, Gjini E, Lako A, Lim K, Conway J, Tewari A, Zeng Z, Sahu AD, Tokheim C, Weirather J, Fu J, Zhang Y, Kroger B, Liang JH, Cejas P, Freeman G, Rodig S, Long H, Gewurz B, Stephen Hodi F, Brown M, Shirley Liu X. 700 Increasing MHC-I expression to potentiate immune checkpoint blockade therapy. J Immunother Cancer 2021. [DOI: 10.1136/jitc-2021-sitc2021.700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BackgroundCancer immunotherapy, especially immune checkpoint blockade (ICB) therapy, is leading to a paradigm shift in cancer treatment, as a small percentage of cancer patients have obtained durable remission following ICB treatment. Successful ICB responses rely on cancer cells presenting antigens to the cell surface via the major histocompatibility complex (MHC), which activates antigen-specific T-lymphocytes to kill cancer cells. Type-I MHC (MHC-I) is wildly expressed in all cell types and mediates the interaction with cytotoxic CD8 T cells. However, over 65% of cancer patients are estimated to show defects in MHC-I-mediated antigen presentation, including downregulation of its expression that can lead to primary or acquired resistance to ICB therapy, and therapeutic strategies to effectively restore or boost MHC-I are limited.MethodsHere, we employed a CRISPR screening approach with dual-marker FACS sorting to identify factors that decouple the regulation of MHC-I and PD-L1. The experimentally validated target was used to generate a KO differential expression signature. Using this signature, we analyzed transcriptome data from drug perturbation studies to identify drugs that regulate MHC-I but not PD-L1. Finally, we validated the effect of the identified drug to enhance ICB response in a T-cell-dependent manner in vivo.ResultsCRISPR screens identified TRAF3, a suppressor of the NF-κB pathway, as a negative regulator of MHC-I but not PD-L1. The Traf3-knockout (Traf3-KO) gene expression signature is associated with better survival in ICB-naive cancer patients and better ICB response. We then screened for drugs with similar transcriptional effects as this signature and identified SMAC mimetics. We experimentally validated that the SMAC mimetic birinapant upregulates MHC-I, sensitizes cancer cells to T-cell-dependent killing, and adds to ICB efficacy. However, in cancer cells with high NF-κB activity, the effect of birinapant on MHC-I is weak, indicating context-dependent MHC-I regulation.ConclusionsIn summary, Traf3 deletion specifically upregulates MHC-I without inducing PD-L1 in response to various cytokines and sensitizes cancer cells to T-cell-driven cytotoxicity. The SMAC mimetic birinapant phenocopies Traf3-knockout and sensitizes MHC-I-low melanoma to ICB therapy. Further studies are needed to elucidate the context-dependencies of MHC-I regulation. Our findings provide preclinical rationale for treating some tumors expressing low MHC-I with SMAC mimetics to enhance sensitivity to immunotherapy. The approach used in this study can be generalized to identify other drugs that enhance immunotherapy efficacy.AcknowledgementsThis study was supported by grants from the NIH (R01CA234018 to XSL, R01AI137337 to BEG, P50CA101942-12 and P50CA206963 to GJF), Breast Cancer Research Foundation (BCRF-19-100 to XSL), Burroughs Wellcome Career Award in Medical Sciences (to BEG), and Sara Elizabeth O'Brien Trust Fellowship (to SG).We thank Drs. Kai Wucherpfennig and Deng Pan for their insightful suggestions on this study.Ethics ApprovalAll mice were housed in standard cage in Dana-Farber Cancer Institute Animal Resources Facility (ARF). All animal procedures were carried out under the ARF Institutional Animal Care and Use Committee (IACUC) protocol and were in accordance with the IACUC standards for the welfare of animals.
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Alessi JV, Ricciuti B, Lin-Liu Y, Gupta H, Wang X, Lamberti G, Recondo G, Vaz V, Barrichello A, Nishino M, Cherniack A, Lindsay J, Sharma B, Pfaff K, Felt K, Rodig S, Awad M. 67 Cancer aneuploidy is associated with a distinct tumor immune microenvironment and impacts outcomes to immune checkpoint inhibition in nonsquamous non-small cell lung cancer. J Immunother Cancer 2021. [DOI: 10.1136/jitc-2021-sitc2021.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BackgroundCancer aneuploidy, an unbalanced number of chromosomes, is associated with somatic mutation rate, expression of proliferative genes, and altered immune signaling. Whether aneuploidy correlates with a distinct tumor immunophenotype or impacts clinical outcomes to immune checkpoint inhibitors (ICIs) in NSCLC is unclear.MethodsAmong nonsquamous NSCLCs which underwent targeted next-generation sequencing, we retrospectively quantified aneuploidy using the fraction of chromosomal arm alterations (FAA), defined as the number of aneuploid chromosome arms divided by the number of chromosome arms assessed. An unbiased recursive partitioning algorithm was used to investigate an FAA level which best discriminated responders from non-responders to ICIs. Multiplexed immunofluorescence to quantify CD8, FOXP3, and PD-1-positive cell counts, as well as PD-L1 expression was performed on a separate cohort of nonsquamous NSCLCs to determine differences in tumor immune cells subsets according to FAA levels.ResultsAmong 1426 nonsquamous NSCLCs identified, FAA increased along with the increase of pathologic stage, and was highest among tumors harboring EGFR mutations and RET fusions, and lowest among those with KRAS, BRAF, and MET mutations. FAA inversely correlated with PD-L1 expression levels, and positively correlated with tumor mutational burden (TMB) (figure 1A-D). Among 281 NSCLCs treated with ICIs, the median FAA was significantly lower among patients with a partial response to ICI compared to those with stable or progressive disease (0.11 vs 0.21, P=0.006). A fractional aneuploidy level of 0.06 (representing the lowest quartile of FAA) was identified as an optimal cutpoint to discriminate responders from non-responders to ICI. Compared to pts with an FAA >0.06 (N=212), pts with FAA ≤0.06 (N=69) had a significantly higher ORR (42.0% vs 19.3%, P<0.001), longer median progression-free survival (mPFS 6.8 vs 3.2 months, HR: 0.64, P=0.004), and longer median overall survival (mOS 24.8 vs 13.8 months, HR: 0.65, P=0.012) with ICIs (figure 2). After adjusting for performance status, PD-L1 expression, TMB, and line of treatment, FAA retained a significant association with improved PFS (HR: 0.66, P=0.018) and OS (HR: 0.66, P=0.041) to immunotherapy. FAA had no impact on clinical outcomes among pts who received first-line platinum doublet chemotherapy without ICI (figure 3). Among 239 nonsquamous NSCLCs profiled by multiplex immunofluorescence, cancers with a low FAA (≤25th percentile) were significantly enriched in CD8+ T cells and had a higher CD8+ to FOXP3+ ratio compared to those with high FAA (>25th percentile) (figure 4).Abstract 67 Figure 1(A) Median fraction of chromosomal alterations (FAA) are shown for stages I, II, III, and IV NSCLCs. (B) Tumors with negative (<1%), low (1–49%), and high PD-L1 tumor proportion score (TPS) (≥50%) expression. (C) Pearson’s correlation coefficient between FAA and tumor mutational burden (TMB). (D) Median FAA distribution across a set of 8 targetable driver mutations (ALK, BRAF, EGFR, HER2, KRAS, MET, RET and ROS1) and none identified alteration.Abstract 67 Figure 2(A) Objective response rate, (B) progression-free survival, and (C) overall survival, in patients with a fraction of chromosomal arm alterations (FAA) ≤0.06 versus >0.06 in the immunotherapy-cohort.Abstract 67 Figure 3(A) Objective response rate and (B) progression-free survival (PFS) in patients with a fraction of chromosomal arm alterations (FAA) ≤0.06 versus >0.06 in the chemotherapy-cohort.Abstract 67 Figure 4(A) CD8+, (B) PD-1+, (C) PD-1+ CD8+ (D), FOXP3+ cells/mm2, and (E) PD-L1 distribution in nonsquamous NSCLCs with an fraction of arm-level altered (FAA) low (≤25th percentile) versus high (>25th percentile). (F) CD8+ to FOXP3+ ratio in tumors with FAA low versus FAA high.ConclusionsNonsquamous NSCLCs with low aneuploidy have a distinct immune microenvironment and more favorable outcomes to ICIs.
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Barone F, Lawler S, Aguilar L, Dwyer J, Guzik B, Soloman I, Nakashima H, Triggs D, Zhang AT, Zeng Y, Woods J, Grant J, Reardon D, Wen P, Lee EQ, Ligon K, Pisano W, Rodig S, Suva M, Wucherpfennig K, Marx S, Gritsch S, Mathewson N, Severgnini M, Giobbie-Hurder A, Krisky D, Aguilar-Cordova E, Tak P, Antonio Chiocca E. 395 Detection of viral antigen and immune activation after intra-tumor injection of CAN-3110 (ICP-34.5 expressing HSV-1 oncolytic virus) in patients with recurrent high-grade glioma. J Immunother Cancer 2021. [DOI: 10.1136/jitc-2021-sitc2021.395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BackgroundRecurrent high-grade glioma (HGG) represents a significant clinical unmet need with expected survival between 6 to 9 months. Oncolytic viruses are a new therapeutic approach for solid tumors that deploy oncolytic activity combined with local and systemic immune activation. CAN-3110 (rQNestin34.5v2) is an oncolytic herpes simplex virus (HSV), modified to encode the HSV1 ICP34.5 protein under control of the nestin promoter. Selective expression of nestin in brain tumors confers tumor-restricted replication of CAN-3110. We conducted an open-label dose-escalation phase 1 clinical trial in patients with recurrent HGG to evaluate safety, tolerability, and immunological changes after CAN-3110 treatment.MethodsThirty patients with biopsy-confirmed recurrent HGG were enrolled from September 2017 to February 2020. CAN-3110 was injected intratumorally starting at 1x106 plaque forming units (pfu) and dose-escalated by half log to 1x1010 pfu. Patients also received standard of care. Peripheral blood mononuclear cells (PBMCs), plasma and tumor samples were collected for analysis at different time-points post treatment. We evaluated HSV antigen expression in tumor tissue. RNA sequencing and T cell receptor (TCR) rearrangement analysis was performed in matched tissue and PBMCs. Cytokine profiling was completed in 29 patients at baseline, day 2, and day 28 post treatment.ResultsEighteen patients were recruited at their first recurrence and 12 at the second recurrence. Three patients presented with multifocal disease. Tumor volume ranged from 357.4 to and 54,036.1mm3 (median 7,733.9mm3, SDV 15,610.2). CAN-3110 was well-tolerated with no dose-limiting toxicity. Median overall survival was 11.7 months. We demonstrated persistence of HSV antigen and CD8+ T cell infiltrates at the site of injected tumor. Preliminary analysis revealed expansion of shared TCR clonotypes and upregulation of pro-inflammatory genes in post-treatment tumors and peripheral blood samples. Longitudinal modeling of cytokine profiling demonstrated increased levels of IL-6, VEGF alpha, CCL2 and IL1-RA and a decrease in GCP-2 levels at day 2 post-treatment (p <0.05). Significant correlations were observed between CXCL2 and CXCL6 (r=0.89 and r=0.95, respectively, at day 2 and day 28 post treatment; p<0.05), CCL2 and CXCL6 (r=0.73 and r=0.61 at days 2 and 28 post treatment; p<0.05) and between CCL2 and CXCL2 (r=0.68, p<0.05 at day 2 post treatment) in patients surviving more than 12 months.ConclusionsIntratumoral administration of CAN-3110 appears well-tolerated in recurrent HGG. Histologic, molecular, and cytokine analyses demonstrate persistence of viral antigen as well as local and systemic immune activation after treatment.Ethics ApprovalThe study was approved by the Office for Human Research Studies at Dana-Farber Cancer Institute, Protocol Number 16–557.
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Akturk G, Parra ER, Gjini E, Lako A, Lee JJ, Neuberg D, Zhang J, Yao S, Laface I, Rogic A, Chen PH, Sanchez-Espiridion B, Valle DMD, Moravec R, Kinders R, Hudgens C, Wu C, Wistuba II, Thurin M, Hewitt SM, Rodig S, Gnjatic S, Tetzlaff MT. Multiplex Tissue Imaging Harmonization: A Multicenter Experience from CIMAC-CIDC Immuno-Oncology Biomarkers Network. Clin Cancer Res 2021; 27:5072-5083. [PMID: 34253580 PMCID: PMC9777693 DOI: 10.1158/1078-0432.ccr-21-2051] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE The Cancer Immune Monitoring and Analysis Centers - Cancer Immunologic Data Commons (CIMAC-CIDC) network supported by the NCI Cancer Moonshot initiative was established to provide correlative analyses for clinical trials in cancer immunotherapy, using state-of-the-art technology. Fundamental to this initiative is implementation of multiplex IHC assays to define the composition and distribution of immune infiltrates within tumors in the context of their potential role as biomarkers. A critical unanswered question involves the relative fidelity of such assays to reliably quantify tumor-associated immune cells across different platforms. EXPERIMENTAL DESIGN Three CIMAC sites compared across their laboratories: (i) image analysis algorithms, (ii) image acquisition platforms, (iii) multiplex staining protocols. Two distinct high-dimensional approaches were employed: multiplexed IHC consecutive staining on single slide (MICSSS) and multiplexed immunofluorescence (mIF). To eliminate variables potentially impacting assay performance, we completed a multistep harmonization process, first comparing assay performance using independent protocols followed by the integration of laboratory-specific protocols and finally, validating this harmonized approach in an independent set of tissues. RESULTS Data generated at the final validation step showed an intersite Spearman correlation coefficient (r) of ≥0.85 for each marker within and across tissue types, with an overall low average coefficient of variation ≤0.1. CONCLUSIONS Our results support interchangeability of protocols and platforms to deliver robust, and comparable data using similar tissue specimens and confirm that CIMAC-CIDC analyses may therefore be used with confidence for statistical associations with clinical outcomes largely independent of site, antibody selection, protocol, and platform across different sites.
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Affiliation(s)
- Guray Akturk
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Edwin R Parra
- Translational Molecular Pathology-Dermatopathology Laboratory, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Evisa Gjini
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ana Lako
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - J Jack Lee
- Translational Molecular Pathology-Dermatopathology Laboratory, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Jiexin Zhang
- Translational Molecular Pathology-Dermatopathology Laboratory, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shen Yao
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Ilaria Laface
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Anita Rogic
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, New York
| | | | - Beatriz Sanchez-Espiridion
- Translational Molecular Pathology-Dermatopathology Laboratory, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Diane M Del Valle
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Radim Moravec
- Kelly Services; Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, Maryland
| | - Robert Kinders
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Courtney Hudgens
- Translational Molecular Pathology-Dermatopathology Laboratory, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Catherine Wu
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ignacio I Wistuba
- Translational Molecular Pathology-Dermatopathology Laboratory, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Magdalena Thurin
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, Maryland
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Scott Rodig
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sacha Gnjatic
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Michael T Tetzlaff
- Translational Molecular Pathology-Dermatopathology Laboratory, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Mahadevan NR, Knelson EH, Wolff JO, Vajdi A, Saigí M, Campisi M, Hong D, Thai TC, Piel B, Han S, Reinhold BB, Duke-Cohan JS, Poitras MJ, Taus LJ, Lizotte PH, Portell A, Quadros V, Santucci AD, Murayama T, Cañadas I, Kitajima S, Akitsu A, Fridrikh M, Watanabe H, Reardon B, Gokhale PC, Paweletz CP, Awad MM, Van Allen EM, Lako A, Wang XT, Chen B, Hong F, Sholl LM, Tolstorukov MY, Pfaff K, Jänne PA, Gjini E, Edwards R, Rodig S, Reinherz EL, Oser MG, Barbie DA. Intrinsic Immunogenicity of Small Cell Lung Carcinoma Revealed by Its Cellular Plasticity. Cancer Discov 2021; 11:1952-1969. [PMID: 33707236 PMCID: PMC8338750 DOI: 10.1158/2159-8290.cd-20-0913] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 01/06/2021] [Accepted: 03/05/2021] [Indexed: 12/26/2022]
Abstract
Small cell lung carcinoma (SCLC) is highly mutated, yet durable response to immune checkpoint blockade (ICB) is rare. SCLC also exhibits cellular plasticity, which could influence its immunobiology. Here we discover that a distinct subset of SCLC uniquely upregulates MHC I, enriching for durable ICB benefit. In vitro modeling confirms epigenetic recovery of MHC I in SCLC following loss of neuroendocrine differentiation, which tracks with derepression of STING. Transient EZH2 inhibition expands these nonneuroendocrine cells, which display intrinsic innate immune signaling and basally restored antigen presentation. Consistent with these findings, murine nonneuroendocrine SCLC tumors are rejected in a syngeneic model, with clonal expansion of immunodominant effector CD8 T cells. Therapeutically, EZH2 inhibition followed by STING agonism enhances T-cell recognition and rejection of SCLC in mice. Together, these data identify MHC I as a novel biomarker of SCLC immune responsiveness and suggest novel immunotherapeutic approaches to co-opt SCLC's intrinsic immunogenicity. SIGNIFICANCE: SCLC is poorly immunogenic, displaying modest ICB responsiveness with rare durable activity. In profiling its plasticity, we uncover intrinsically immunogenic MHC Ihi subpopulations of nonneuroendocrine SCLC associated with durable ICB benefit. We also find that combined EZH2 inhibition and STING agonism uncovers this cell state, priming cells for immune rejection.This article is highlighted in the In This Issue feature, p. 1861.
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Affiliation(s)
- Navin R Mahadevan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Erik H Knelson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jacquelyn O Wolff
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Amir Vajdi
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Maria Saigí
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Marco Campisi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Deli Hong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Tran C Thai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Brandon Piel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Saemi Han
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Bruce B Reinhold
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jonathan S Duke-Cohan
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Michael J Poitras
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Experimental Therapeutics Core, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Luke J Taus
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Patrick H Lizotte
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Andrew Portell
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Victor Quadros
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alison D Santucci
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Takahiko Murayama
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Israel Cañadas
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Shunsuke Kitajima
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Aoi Akitsu
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Maya Fridrikh
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Hideo Watanabe
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Brendan Reardon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Prafulla C Gokhale
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Experimental Therapeutics Core, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Cloud P Paweletz
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mark M Awad
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ana Lako
- Translational Pathology, Bristol Myers Squibb, Trenton, New Jersey
| | - Xi-Tao Wang
- Translational Pathology, Bristol Myers Squibb, Trenton, New Jersey
| | - Benjamin Chen
- Translational Pathology, Bristol Myers Squibb, Trenton, New Jersey
| | - Fangxin Hong
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Michael Y Tolstorukov
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kathleen Pfaff
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Evisa Gjini
- Translational Pathology, Bristol Myers Squibb, Trenton, New Jersey
| | - Robin Edwards
- Translational Pathology, Bristol Myers Squibb, Trenton, New Jersey
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ellis L Reinherz
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - David A Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
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26
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Alessi JV, Ricciuti B, Li YY, Gupta H, Lamberti G, Recondo G, Nishino M, Sholl LM, Cherniak AD, Lindsay J, Sharma B, Pfaff K, Felt K, Rodig S, Awad MM. Abstract 26: Association of aneuploidy score with clinical outcomes to immunotherapy in NSCLC. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Cancer aneuploidy, an unbalanced number of chromosomes, is associated with somatic mutation rate, expression of proliferative genes, and altered immune signaling. Whether aneuploidy impacts clinical outcomes to immune checkpoint inhibitors (ICIs) in NSCLC is unknown.
Methods: In NSCLCs which underwent targeted next-generation sequencing (NGS), we retrospectively analyzed the aneuploidy score (AS), defined as the sum of the number of altered chromosome arms, among patients treated with immune checkpoint inhibitors. An unbiased recursive partitioning (URP) algorithm was used to investigate an optimal AS cut-off with respect to objective response rate (ORR). Multiplexed immunofluorescence (mIF) to quantify CD8+, FOXP3+, PD-1+ immune cells, and PD-L1 was performed to determine differences in tumor immune cells subsets according to AS cut-off.
Results: Among 279 patients with NSCLC treated with ICIs, the median AS was 6 (range 0 to 23). The AS was significantly lower among patients with a partial response to ICI compared to those with stable or progressive disease (4 vs 7, P=0.004). An unbiased recursive partitioning analysis identified an AS of 2 as the strongest discriminator of objective response to ICI. Compared to patients with an AS >2 (N= 207, 74.2%), patients with AS ≤2 (N=72, 25.8%) had a significantly higher overall response rate (ORR 43.0% vs 19.8%, P<0.001), a significantly longer median progression free survival (mPFS 6.2 months vs 2.9 months, HR: 0.70 [95% CI: 0.52-0.94], P=0.02), and a significantly longer median overall survival (mOS 19.8 months versus 13.8 months, HR: 0.66 [95% CI: 0.47-0.94], P=0.02) to treatment with ICIs. After adjusting for other variables such as performance status, presence of oncogenic driver mutation, PD-L1 expression, tumor mutational burden, and line of treatment, AS was significantly associated with improved mPFS (HR: 0.72 [95% CI: 0.52-0.99], P=0.04) and mOS (HR: 0.64 [95% CI: 0.44-0.94], P=0.02). Among 179 NSCLCs profiled by multiplex immunofluorescence, compared to cancers with an AS >2, those with low aneuploidy (AS ≤2) had significantly higher numbers of CD8+, FOXP3+, PD-1+ immune cells, and PD-1+ CD8+ T cells, both intratumorally and when looking at the total numbers of cells within the tumor and the tumor-stroma interface. There was no significant difference in PD-L1 expression levels or tumor mutational burden on tumor cells or on immune cells according to aneuploidy score.
Conclusion: NSCLCs with low aneuploidy have a distinct immune microenvironment and more favorable outcomes to ICIs.
Citation Format: João Victor Alessi, Biagio Ricciuti, Yvonne Y. Li, Hersh Gupta, Giuseppe Lamberti, Gonzalo Recondo, Mizuki Nishino, Lynette M. Sholl, Andrew D. Cherniak, James Lindsay, Bijaya Sharma, Kathleen Pfaff, Kristen Felt, Scott Rodig, Mark M. Awad. Association of aneuploidy score with clinical outcomes to immunotherapy in NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 26.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Bijaya Sharma
- 3Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, MA
| | - Kathleen Pfaff
- 3Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, MA
| | - Kristen Felt
- 3Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, MA
| | - Scott Rodig
- 4Brigham and Women's Hospital and Dana-Farber Cancer Institute, Boston, MA
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27
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Gu SS, Zhang W, Wang X, Jiang P, Traugh N, Li Z, Meyer C, Stewig B, Xie Y, Bu X, Manos MP, Font-Tello A, Gjini E, Lako A, Lim K, Conway J, Tewari AK, Zeng Z, Sahu AD, Tokheim C, Weirather JL, Fu J, Zhang Y, Kroger B, Liang JH, Cejas P, Freeman GJ, Rodig S, Long HW, Gewurz BE, Hodi FS, Brown M, Liu XS. Therapeutically Increasing MHC-I Expression Potentiates Immune Checkpoint Blockade. Cancer Discov 2021; 11:1524-1541. [PMID: 33589424 DOI: 10.1158/2159-8290.cd-20-0812] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 11/13/2020] [Accepted: 01/13/2021] [Indexed: 11/16/2022]
Abstract
Immune checkpoint blockade (ICB) therapy revolutionized cancer treatment, but many patients with impaired MHC-I expression remain refractory. Here, we combined FACS-based genome-wide CRISPR screens with a data-mining approach to identify drugs that can upregulate MHC-I without inducing PD-L1. CRISPR screening identified TRAF3, a suppressor of the NFκB pathway, as a negative regulator of MHC-I but not PD-L1. The Traf3-knockout gene expression signature is associated with better survival in ICB-naïve patients with cancer and better ICB response. We then screened for drugs with similar transcriptional effects as this signature and identified Second Mitochondria-derived Activator of Caspase (SMAC) mimetics. We experimentally validated that the SMAC mimetic birinapant upregulates MHC-I, sensitizes cancer cells to T cell-dependent killing, and adds to ICB efficacy. Our findings provide preclinical rationale for treating tumors expressing low MHC-I expression with SMAC mimetics to enhance sensitivity to immunotherapy. The approach used in this study can be generalized to identify other drugs that enhance immunotherapy efficacy. SIGNIFICANCE: MHC-I loss or downregulation in cancer cells is a major mechanism of resistance to T cell-based immunotherapies. Our study reveals that birinapant may be used for patients with low baseline MHC-I to enhance ICB response. This represents promising immunotherapy opportunities given the biosafety profile of birinapant from multiple clinical trials.This article is highlighted in the In This Issue feature, p. 1307.
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Affiliation(s)
- Shengqing Stan Gu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Wubing Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,School of Life Science and Technology, Tongji University, Shanghai, China
| | - Xiaoqing Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Peng Jiang
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Nicole Traugh
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ziyi Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,School of Life Science and Technology, Tongji University, Shanghai, China
| | - Clifford Meyer
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Blair Stewig
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Yingtian Xie
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Xia Bu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Michael P Manos
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alba Font-Tello
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Evisa Gjini
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ana Lako
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Klothilda Lim
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jake Conway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alok K Tewari
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Zexian Zeng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Avinash Das Sahu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Collin Tokheim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Jason L Weirather
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jingxin Fu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,School of Life Science and Technology, Tongji University, Shanghai, China
| | - Yi Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Benjamin Kroger
- The University of Texas Southwestern Medical School, Dallas, Texas
| | - Jin Hua Liang
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Scott Rodig
- Department of Pathologic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Benjamin E Gewurz
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
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28
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Barroso-Sousa R, Forman J, Weber ZT, Collier K, Kao KZ, Richardson ET, Keenan T, Cohen O, Manos MP, Brennick RC, Ott P, Hodi FS, Dillon DA, Lin NU, Van Allen EE, Rodig S, Winer EP, Mittendorf EA, Wu CJ, Stover D, Wagle N, Shukla S, Tolaney S. Abstract PS4-25: Comprehensive genomic analysis reveals molecular correlates of response to immune checkpoint inhibitors (ICI) in metastatic triple-negative breast cancer (mTNBC). Cancer Res 2021. [DOI: 10.1158/1538-7445.sabcs20-ps4-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Genomic mechanisms associated with response to ICI in mTNBC are largely unknown. The aim of this work is to assess the genomic and immune profiles of mTNBC samples collected from patients (pts) treated with ICI. Methods: We identified 31 women with mTNBC treated with ICI (pembrolizumab, n=6, NCT02447003; atezolizumab, n=4, NCT01375842; nivolumab + cabozantinib, n = 6, NCT03316586; pembrolizumab + eribulin, n=8, NCT02513472; atezolizumab + nab-paclitaxel, n=7, NCT01633970) who had tumor tissue or blood available for sequencing obtained before and after ICI. Clinical benefit (CB), here defined as any objective response or stable disease (SD) for > 24 weeks, was observed in 20 pts (65%). An extraordinary responder was defined as having CB ≥ 2 yrs; 5 pts were considered extraordinary responders (range 26-60months). Whole exome sequencing (WES) was done on each tumor and on germline DNA from blood (23 pts had successful WES performed on samples collected before ICI; 5 of these had WES on samples taken after disease progression). RNA sequencing (RNAseq) was successfully performed in 18 of the tumors with WES performed on samples before ICI; and 3 of these had RNAseq on samples taken after disease progression. 18 pts had tumors assessed by multiplex immunofluorescence (mIF) panels encompassing CD4, CD8, PD-1, PD-L1, and cytokeratin on samples collected before ICI. WES, deep targeted panel and low coverage whole genome sequencing were performed on serially collected plasma samples from 22 pts to evaluate tumor fraction and specific mutations. The association between biomarkers and clinical benefit to ICI was assessed. Results: 21 of 31 pts (67%) had received ≥1 prior lines of systemic therapy in the metastatic setting before starting ICI. Among the most frequently mutated genes at baseline are: TP53 (57%); PIK3CA (18%); DNAH5, MYH8 (both 13%); KMT2C, AKT1, LAMA2 (all 9%). Pts with CB had a higher tumor mutational burden (TMB) than pts with no CB (p=0.018). Differential expression analysis of RNAseq data revealed an upregulation of several immune-related genes in pts with CB, indicating increased immune infiltration in that group. Gene set enrichment analysis of this expression data using hallmark and canonical pathway gene sets from MSigDB (nominal p-val < 0.05) showed that, compared to samples from pts without CB, extraordinary responders had elevated transcriptional signatures of several cancer-related pathways associated with cell survival, proliferation and metabolism, as well as genes associated with increased immune infiltration and upregulation of inflammatory response programs. The mIF showed that the tumor microenvironment (TME) of pts with CB were enriched in Cytokeratin-negative/PD-L1-positive cells compared to those without CB (p=0.014). Expression of CD4, CD8 and PD-1 was not significantly different between pts with and without CB. Genomic analysis of circulating tumor DNA, and tumor evolutionary analysis for pts with both pre- and post-ICI samples (acquired resistance) will be presented. Conclusions: Clinical benefit to ICI in mTNBC was associated with upregulation of immune-related pathways, enrichment of non-tumoral PD-L1-positive cells in TME, and high TMB.
Citation Format: Romualdo Barroso-Sousa, Juliet Forman, Zachary T. Weber, Katherine Collier, Katrina Z. Kao, Edward T. Richardson, III, Tanya Keenan, Ofir Cohen, Michael P. Manos, Ryan C. Brennick, Patrick Ott, F. Steve Hodi, Deborah A. Dillon, Nancy U. Lin, Eliezer E. Van Allen, Scott Rodig, Eric P. Winer, Elizabeth A. Mittendorf, Catherine J. Wu, Daniel Stover, Nikhil Wagle, Sachet Shukla, Sara Tolaney. Comprehensive genomic analysis reveals molecular correlates of response to immune checkpoint inhibitors (ICI) in metastatic triple-negative breast cancer (mTNBC) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS4-25.
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Affiliation(s)
| | | | | | | | | | | | | | - Ofir Cohen
- 2Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | | | | | - Scott Rodig
- 4Dana-Farber Cancer Institute/Brigham Women's Hospital, Boston, MA
| | | | | | | | - Daniel Stover
- 3Ohio State University College of Medicine, Columbus, OH
| | | | - Sachet Shukla
- 4Dana-Farber Cancer Institute/Brigham Women's Hospital, Boston, MA
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29
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Alon S, Goodwin DR, Sinha A, Wassie AT, Chen F, Daugharthy ER, Bando Y, Kajita A, Xue AG, Marrett K, Prior R, Cui Y, Payne AC, Yao CC, Suk HJ, Wang R, Yu CCJ, Tillberg P, Reginato P, Pak N, Liu S, Punthambaker S, Iyer EPR, Kohman RE, Miller JA, Lein ES, Lako A, Cullen N, Rodig S, Helvie K, Abravanel DL, Wagle N, Johnson BE, Klughammer J, Slyper M, Waldman J, Jané-Valbuena J, Rozenblatt-Rosen O, Regev A, Church GM, Marblestone AH, Boyden ES. Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems. Science 2021; 371:eaax2656. [PMID: 33509999 PMCID: PMC7900882 DOI: 10.1126/science.aax2656] [Citation(s) in RCA: 157] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/13/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022]
Abstract
Methods for highly multiplexed RNA imaging are limited in spatial resolution and thus in their ability to localize transcripts to nanoscale and subcellular compartments. We adapt expansion microscopy, which physically expands biological specimens, for long-read untargeted and targeted in situ RNA sequencing. We applied untargeted expansion sequencing (ExSeq) to the mouse brain, which yielded the readout of thousands of genes, including splice variants. Targeted ExSeq yielded nanoscale-resolution maps of RNAs throughout dendrites and spines in the neurons of the mouse hippocampus, revealing patterns across multiple cell types, layer-specific cell types across the mouse visual cortex, and the organization and position-dependent states of tumor and immune cells in a human metastatic breast cancer biopsy. Thus, ExSeq enables highly multiplexed mapping of RNAs from nanoscale to system scale.
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Affiliation(s)
- Shahar Alon
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
- Faculty of Engineering, Gonda Brain Research Center and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Daniel R Goodwin
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
| | - Anubhav Sinha
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Asmamaw T Wassie
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Fei Chen
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Evan R Daugharthy
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Yosuke Bando
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- Kioxia Corporation, Minato-ku, Tokyo, Japan
| | | | - Andrew G Xue
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
| | | | | | - Yi Cui
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
| | - Andrew C Payne
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chun-Chen Yao
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ho-Jun Suk
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Ru Wang
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
| | - Chih-Chieh Jay Yu
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Paul Tillberg
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
| | - Paul Reginato
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Nikita Pak
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
- Department of Mechanical Engineering, MIT, Cambridge, MA, USA
| | - Songlei Liu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Sukanya Punthambaker
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Eswar P R Iyer
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Richie E Kohman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | | | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Ana Lako
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicole Cullen
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott Rodig
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Karla Helvie
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Daniel L Abravanel
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Nikhil Wagle
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bruce E Johnson
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Michal Slyper
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Waldman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Department of Biology, MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | | | - Edward S Boyden
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA.
- McGovern Institute, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Department of Biology, MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
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30
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Mehta AK, Cheney EM, Hartl CA, Pantelidou C, Oliwa M, Castrillon JA, Lin JR, Hurst KE, de Oliveira Taveira M, Johnson NT, Oldham WM, Kalocsay M, Berberich MJ, Boswell SA, Kothari A, Johnson S, Dillon DA, Lipschitz M, Rodig S, Santagata S, Garber JE, Tung N, Yélamos J, Thaxton JE, Mittendorf EA, Sorger PK, Shapiro GI, Guerriero JL. Targeting immunosuppressive macrophages overcomes PARP inhibitor resistance in BRCA1-associated triple-negative breast cancer. Nat Cancer 2021; 2:66-82. [PMID: 33738458 PMCID: PMC7963404 DOI: 10.1038/s43018-020-00148-7] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 10/27/2020] [Indexed: 12/26/2022]
Abstract
Despite objective responses to PARP inhibition and improvements in progression-free survival compared to standard chemotherapy in patients with BRCA-associated triple-negative breast cancer (TNBC), benefits are transitory. Using high dimensional single-cell profiling of human TNBC, here we demonstrate that macrophages are the predominant infiltrating immune cell type in BRCA-associated TNBC. Through multi-omics profiling we show that PARP inhibitors enhance both anti- and pro-tumor features of macrophages through glucose and lipid metabolic reprogramming driven by the sterol regulatory element-binding protein 1 (SREBP-1) pathway. Combined PARP inhibitor therapy with CSF-1R blocking antibodies significantly enhanced innate and adaptive anti-tumor immunity and extends survival in BRCA-deficient tumors in vivo and is mediated by CD8+ T-cells. Collectively, our results uncover macrophage-mediated immune suppression as a liability of PARP inhibitor treatment and demonstrate combined PARP inhibition and macrophage targeting therapy induces a durable reprogramming of the tumor microenvironment, thus constituting a promising therapeutic strategy for TNBC.
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Affiliation(s)
- Anita K Mehta
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Emily M Cheney
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christina A Hartl
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Constantia Pantelidou
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Madisson Oliwa
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jessica A Castrillon
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jia-Ren Lin
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Katie E Hurst
- Department of Orthopedics and Physical Medicine, Medical University of South Carolina, Charleston, SC, USA
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, SC, USA
| | - Mateus de Oliveira Taveira
- Division of Hematology/Oncology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
- Department of Imaging, AC Camargo Cancer Center, São Paulo, Brazil
| | - Nathan T Johnson
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - William M Oldham
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Marian Kalocsay
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Matthew J Berberich
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sarah A Boswell
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Aditi Kothari
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Shawn Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Deborah A Dillon
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mikel Lipschitz
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sandro Santagata
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | - Judy E Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nadine Tung
- Division of Hematology/Oncology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - José Yélamos
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Jessica E Thaxton
- Department of Orthopedics and Physical Medicine, Medical University of South Carolina, Charleston, SC, USA
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, SC, USA
- Hollings Cancer Center, Charleston, SC, USA
| | - Elizabeth A Mittendorf
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA, USA
- Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | - Geoffrey I Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, USA
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jennifer L Guerriero
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA.
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA.
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA, USA.
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Gstalder C, Liu D, Miao D, Lutterbach B, DeVine AL, Lin C, Shettigar M, Pancholi P, Buchbinder EI, Carter SL, Manos MP, Rojas-Rudilla V, Brennick R, Gjini E, Chen PH, Lako A, Rodig S, Yoon CH, Freeman GJ, Barbie DA, Hodi FS, Miles W, Van Allen EM, Haq R. Inactivation of Fbxw7 Impairs dsRNA Sensing and Confers Resistance to PD-1 Blockade. Cancer Discov 2020; 10:1296-1311. [PMID: 32371478 PMCID: PMC8802534 DOI: 10.1158/2159-8290.cd-19-1416] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 04/04/2020] [Accepted: 04/30/2020] [Indexed: 11/16/2022]
Abstract
The molecular mechanisms leading to resistance to PD-1 blockade are largely unknown. Here, we characterize tumor biopsies from a patient with melanoma who displayed heterogeneous responses to anti-PD-1 therapy. We observe that a resistant tumor exhibited a loss-of-function mutation in the tumor suppressor gene FBXW7, whereas a sensitive tumor from the same patient did not. Consistent with a functional role in immunotherapy response, inactivation of Fbxw7 in murine tumor cell lines caused resistance to anti-PD-1 in immunocompetent animals. Loss of Fbxw7 was associated with altered immune microenvironment, decreased tumor-intrinsic expression of the double-stranded RNA (dsRNA) sensors MDA5 and RIG1, and diminished induction of type I IFN and MHC-I expression. In contrast, restoration of dsRNA sensing in Fbxw7-deficient cells was sufficient to sensitize them to anti-PD-1. Our results thus establish a new role for the commonly inactivated tumor suppressor FBXW7 in viral sensing and sensitivity to immunotherapy. SIGNIFICANCE: Our findings establish a role of the commonly inactivated tumor suppressor FBXW7 as a genomic driver of response to anti-PD-1 therapy. Fbxw7 loss promotes resistance to anti-PD-1 through the downregulation of viral sensing pathways, suggesting that therapeutic reactivation of these pathways could improve clinical responses to checkpoint inhibitors in genomically defined cancer patient populations.This article is highlighted in the In This Issue feature, p. 1241.
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MESH Headings
- Aged
- Animals
- Antibodies, Monoclonal, Humanized/pharmacology
- Antibodies, Monoclonal, Humanized/therapeutic use
- Cell Line, Tumor/transplantation
- DEAD Box Protein 58/genetics
- DEAD Box Protein 58/metabolism
- Disease Models, Animal
- Drug Resistance, Neoplasm/genetics
- F-Box-WD Repeat-Containing Protein 7/genetics
- F-Box-WD Repeat-Containing Protein 7/metabolism
- Gene Expression Regulation, Neoplastic/immunology
- HeLa Cells
- Humans
- Immune Checkpoint Inhibitors/pharmacology
- Immune Checkpoint Inhibitors/therapeutic use
- Interferon-Induced Helicase, IFIH1/genetics
- Interferon-Induced Helicase, IFIH1/metabolism
- Loss of Function Mutation
- Male
- Mice
- Mutagenesis, Site-Directed
- Programmed Cell Death 1 Receptor/antagonists & inhibitors
- RNA, Double-Stranded/immunology
- RNA, Double-Stranded/metabolism
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Skin Neoplasms/drug therapy
- Skin Neoplasms/genetics
- Skin Neoplasms/immunology
- Skin Neoplasms/pathology
- Tumor Microenvironment/genetics
- Tumor Microenvironment/immunology
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Affiliation(s)
- Cécile Gstalder
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Division of Population Sciences, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Diana Miao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Bart Lutterbach
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alexander L DeVine
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Chenyu Lin
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio
| | - Megha Shettigar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Priya Pancholi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Elizabeth I Buchbinder
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Scott L Carter
- Department of Data Sciences, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Division of Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Michael P Manos
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Vanesa Rojas-Rudilla
- Department of CAMD Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ryan Brennick
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Evisa Gjini
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Pei-Hsuan Chen
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Ana Lako
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Scott Rodig
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Charles H Yoon
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - David A Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Wayne Miles
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Rizwan Haq
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
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Giavina-Bianchi M, Giavina-Bianchi P, Sotto MN, Rodig S, Mihm M, Festa Neto C, Duncan LM, Kalil J. Nodular primary cutaneous melanoma is associated with PD-L1 expression. Eur J Dermatol 2020; 30:352-357. [PMID: 32969795 DOI: 10.1684/ejd.2020.3846] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND In previous studies, patients with Stage III melanomas expressing PD-L1 in more than 5% of their neoplastic cells had improved recurrence-free survival with anti-PD1 adjuvant therapy. OBJECTIVES We examined PD-L1 expression as a possible biomarker of primary cutaneous melanomas in the vertical growth phase. MATERIALS AND METHODS This was a retrospective study including 66 patients with invasive primary cutaneous melanomas. We assessed patient clinical and histopathological data and performed immunohistochemical assays with melanoma specimens from the patients to evaluate PD-L1, PD-1, CD3, CD8 and FoxP3 expression. RESULTS We observed PD-L1 expression in 21% (14/66) of our samples, and this expression correlated with increased melanoma thickness (p = 0.002) and nodular-type melanoma (p = 0.001). After adjusting for tumor thickness using a logistic regression test, the association of PD-L1 with nodular-type melanoma persisted. Nodular-type melanoma was 6.48 times more likely to be positive for PD-L1 than other histological types (p = 0.014; 95% CI: 1.46-28.82). As expected, PD-L1 expression correlated with the number of PD-1-expressing cells in the tumor-infiltrating lymphocyte population (p = 0.04). No correlation with PD-L1 was observed for age, sex, tumor site, skin phototype, ulceration status, sentinel lymph node status, metastasis development or survival. Regarding the immune profile of the tumor-infiltrating lymphocytes of PD-L1-positive and -negative groups, no significant differences were observed in the numbers of CD3 + , CD8 + FoxP3-, CD8-FoxP3+ and CD8 + FoxP3+ cells by immunohistochemistry. CONCLUSION Nodular-type melanoma is associated with PD-L1 expression and may be a suitable candidate for adjuvant therapy of primary melanomas treated with immunotherapy.
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Affiliation(s)
- Mara Giavina-Bianchi
- Department of Dermatology, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 255, 3 andar, 05403-900, São Paulo SP, Brazil, Division of Clinical Immunology and Allergy, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 255, 8 andar, 05403-900, São Paulo SP, Brazil
| | - Pedro Giavina-Bianchi
- Division of Clinical Immunology and Allergy, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 255, 8 andar, 05403-900, São Paulo SP, Brazil
| | - Mirian Nacagamo Sotto
- Department of Dermatology, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 255, 3 andar, 05403-900, São Paulo SP, Brazil
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 15 Shattuck Street, Boston MA, 02115, USA
| | - Martin Mihm
- Mihm Cutaneous Pathology Consultative Service, Emmanuel College, 41 Louis Pasteur Street, Room 360, Boston MA, 02115, USA
| | - Cyro Festa Neto
- Department of Dermatology, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 255, 3 andar, 05403-900, São Paulo SP, Brazil
| | - Lyn M Duncan
- Dermatopathology Unit, Pathology Service, Massachusetts General Hospital, Harvard Medical School, Warren Building 825, 55 Fruit Street, Boston MA 02114, USA
| | - Jorge Kalil
- Division of Clinical Immunology and Allergy, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 255, 8 andar, 05403-900, São Paulo SP, Brazil
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Jain N, Hartert K, Tadros S, Fiskus W, Havranek O, Ma MCJ, Bouska A, Heavican T, Kumar D, Deng Q, Moore D, Pak C, Liu CL, Gentles AJ, Hartmann E, Kridel R, Smedby KE, Juliusson G, Rosenquist R, Gascoyne RD, Rosenwald A, Giancotti F, Neelapu SS, Westin J, Vose JM, Lunning MA, Greiner T, Rodig S, Iqbal J, Alizadeh AA, Davis RE, Bhalla K, Green MR. Targetable genetic alterations of TCF4 ( E2-2) drive immunoglobulin expression in diffuse large B cell lymphoma. Sci Transl Med 2020; 11:11/497/eaav5599. [PMID: 31217338 DOI: 10.1126/scitranslmed.aav5599] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/31/2019] [Accepted: 05/15/2019] [Indexed: 12/12/2022]
Abstract
The activated B cell (ABC-like) subtype of diffuse large B cell lymphoma (DLBCL) is characterized by chronic activation of signaling initiated by immunoglobulin μ (IgM). By analyzing the DNA copy number profiles of 1000 DLBCL tumors, we identified gains of 18q21.2 as the most frequent genetic alteration in ABC-like DLBCL. Using integrative analysis of matched gene expression profiling data, we found that the TCF4 (E2-2) transcription factor gene was the target of these alterations. Overexpression of TCF4 in ABC-like DLBCL cell lines led to its occupancy on immunoglobulin (IGHM) and MYC gene enhancers and increased expression of these genes at the transcript and protein levels. Inhibition of TCF4 activity with dominant-negative constructs was synthetically lethal to ABC-like DLBCL cell lines harboring TCF4 DNA copy gains, highlighting these gains as an attractive potential therapeutic target. Furthermore, the TCF4 gene was one of the top BRD4-regulated genes in DLBCL cell lines. BET proteolysis-targeting chimera (PROTAC) ARV771 extinguished TCF4, MYC, and IgM expression and killed ABC-like DLBCL cells in vitro. In DLBCL xenograft models, ARV771 treatment reduced tumor growth and prolonged survival. This work highlights a genetic mechanism for promoting immunoglobulin signaling in ABC-like DLBCL and provides a functional rationale for the use of BET inhibitors in this disease.
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Affiliation(s)
- Neeraj Jain
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Keenan Hartert
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Saber Tadros
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Warren Fiskus
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ondrej Havranek
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Man Chun John Ma
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alyssa Bouska
- Department of Pathology and Immunology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Tayla Heavican
- Department of Pathology and Immunology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Dhiraj Kumar
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Qing Deng
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dalia Moore
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Christine Pak
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chih Long Liu
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Andrew J Gentles
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - Elena Hartmann
- Institute of Pathology, University of Würzburg, Würzburg 97080, Germany.,Comprehensive Cancer Center Mainfranken, Wurzburg 97080, Germany
| | - Robert Kridel
- Princess Margaret Cancer Center, University of Toronto, Toronto, ON M5G 2C4, Canada
| | - Karin Ekstrom Smedby
- Department of Medicine, Solna, Clinical Epidemiology Unit, Karolinska Institutet, and Hematology Center, Karolinska University Hospital, Stockholm SE-171 76, Sweden
| | - Gunnar Juliusson
- Department of Laboratory Medicine, Stem Cell Center, Lund University, Lund SE-221 00, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Universitetssjukhuset, Stockholm SE-171 76, Sweden
| | - Randy D Gascoyne
- Center for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada
| | - Andreas Rosenwald
- Institute of Pathology, University of Würzburg, Würzburg 97080, Germany.,Comprehensive Cancer Center Mainfranken, Wurzburg 97080, Germany
| | - Filippo Giancotti
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sattva S Neelapu
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jason Westin
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Julie M Vose
- Division of Hematology and Oncology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Matthew A Lunning
- Division of Hematology and Oncology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Timothy Greiner
- Department of Pathology and Immunology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Javeed Iqbal
- Department of Pathology and Immunology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ash A Alizadeh
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - R Eric Davis
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kapil Bhalla
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael R Green
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. .,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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34
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Akturk G, Parra Cuentas ER, Lako A, Gjini E, Espiridion BS, Wistuba II, Thurin M, Hewitt SM, Rodig S, Zhang J, Neuberg DS, Lee JJ, Gnjatic S, Tetzlaff MT. CIMAC-CIDC tissue imaging harmonization. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.3125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3125 Background: The Cancer Immune Monitoring and Analysis Centers Cancer Immunology Data Commons (CIMAC-CIDC) network is a NCI Cancer Moonshots initiative to provide state-of-the-art technology and expertise for immunotherapy clinical trials. Multiplex tissue immunostaining is an integral assay provided that examines density and spatial distribution of immune cells and markers in tissues, for their prognostic or predictive value. Two approaches were evaluated for sensitivity, specificity, and reproducibility and subsequently harmonized: chromogenic-based Multiplex Immunohistochemical Consecutive Staining on Single Slide (MICSSS) and Multiplex Immunofluorescence (mIF) based tyramide signal amplification system. Methods: Harmonization was performed across CIMACs (Mount Sinai, Dana Farber Cancer Institute, MD Anderson Cancer Center) in multiple steps to prove that comparable data can be generated independent of site and platform. Goals: 1) harmonize image analysis platforms alone using tissues pre-stained with single chromogenic IHC for CD3 (membrane), Ki67 (nuclear), and CD68 (cytoplasmic), 2) compare image acquisition platforms, 3) streamline Antibody (Ab) clones and assess PD-L1 detection in relation to CLIA- assays, 4) harmonize staining protocols, image acquisition, and analysis platforms on 2 test head and neck tumor samples using MICSSS and mIF, 5) validate harmonization results with a tissue microarray on 27 tissues representing multiple tumors. For last steps, each CIMAC used their platforms for PD-L1, PD-1, CD3, CD8, and pan-cytokeratin (PanCK) staining on one of three consecutive slides from serial sections and compared densities of each marker. Results: Variables as PD-1 Ab clone, positive control reference tissues, sigma value for nuclear segmentation, and use of machine-learning based cell classifier were found to be key to produce accurate, reliable, comparable data. After visual quality control assessment and comparisons of each Region Of Interest (ROI), an overall inter-site Spearman correlation coefficient of ≥0.85 was achieved per marker within each tissue and across tissue types (expect pan-Cytokeratin, ≥0.7), with average coefficient of variation ≤0.1. Conclusions: These results show for the first time that two platforms can deliver harmonized data, despite differences in protocols, platforms, reagents, and analysis tools. Data resulting from retrospective and prospective CIMAC-CIDC analyses may be used with confidence for statistical associations with clinical parameters and outcome.
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Affiliation(s)
- Guray Akturk
- Icahn School of Medicine at Mount Sinai, New York City, NY
| | | | - Ana Lako
- Dana-Farber Cancer Center, Boston, MA
| | | | | | | | | | | | - Scott Rodig
- Department of Pathology and Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Jiexin Zhang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Donna S. Neuberg
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - J. Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
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35
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Färkkilä A, Gulhan DC, Casado J, Jacobson CA, Nguyen H, Kochupurakkal B, Maliga Z, Yapp C, Chen YA, Schapiro D, Zhou Y, Graham JR, Dezube BJ, Munster P, Santagata S, Garcia E, Rodig S, Lako A, Chowdhury D, Shapiro GI, Matulonis UA, Park PJ, Hautaniemi S, Sorger PK, Swisher EM, D'Andrea AD, Konstantinopoulos PA. Author Correction: Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer. Nat Commun 2020; 11:2543. [PMID: 32424117 PMCID: PMC7235235 DOI: 10.1038/s41467-020-16344-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Anniina Färkkilä
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.,Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA.,Research Program in Systems Oncology, University of Helsinki, Haartmaninkatu 8, 00014, Helsinki, Finland.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Doga C Gulhan
- Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
| | - Julia Casado
- Research Program in Systems Oncology, University of Helsinki, Haartmaninkatu 8, 00014, Helsinki, Finland
| | - Connor A Jacobson
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Huy Nguyen
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Bose Kochupurakkal
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Zoltan Maliga
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Clarence Yapp
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Yu-An Chen
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Denis Schapiro
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Yinghui Zhou
- TESARO: A GSK company, 1000 Winter Street, Waltham, MA, 02451, USA
| | - Julie R Graham
- TESARO: A GSK company, 1000 Winter Street, Waltham, MA, 02451, USA
| | - Bruce J Dezube
- TESARO: A GSK company, 1000 Winter Street, Waltham, MA, 02451, USA
| | - Pamela Munster
- Helen Diller Family Comprehensive Cancer Center, 1450 3rd Street, San Francisco, CA, 94158, USA
| | - Sandro Santagata
- Brigham and Women's Hospital, Laboratory for Systems Pharmacology, 75 Francis Street, Boston, MA, 02115, USA
| | - Elizabeth Garcia
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Ana Lako
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Dipanjan Chowdhury
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Geoffrey I Shapiro
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Ursula A Matulonis
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, University of Helsinki, Haartmaninkatu 8, 00014, Helsinki, Finland
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | | | - Alan D D'Andrea
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.
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Färkkilä A, Gulhan DC, Casado J, Jacobson CA, Nguyen H, Kochupurakkal B, Maliga Z, Yapp C, Chen YA, Schapiro D, Zhou Y, Graham JR, Dezube BJ, Munster P, Santagata S, Garcia E, Rodig S, Lako A, Chowdhury D, Shapiro GI, Matulonis UA, Park PJ, Hautaniemi S, Sorger PK, Swisher EM, D'Andrea AD, Konstantinopoulos PA. Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer. Nat Commun 2020; 11:1459. [PMID: 32193378 PMCID: PMC7081234 DOI: 10.1038/s41467-020-15315-8] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/26/2020] [Indexed: 11/09/2022] Open
Abstract
Combined PARP and immune checkpoint inhibition has yielded encouraging results in ovarian cancer, but predictive biomarkers are lacking. We performed immunogenomic profiling and highly multiplexed single-cell imaging on tumor samples from patients enrolled in a Phase I/II trial of niraparib and pembrolizumab in ovarian cancer (NCT02657889). We identify two determinants of response; mutational signature 3 reflecting defective homologous recombination DNA repair, and positive immune score as a surrogate of interferon-primed exhausted CD8 + T-cells in the tumor microenvironment. Presence of one or both features associates with an improved outcome while concurrent absence yields no responses. Single-cell spatial analysis reveals prominent interactions of exhausted CD8 + T-cells and PD-L1 + macrophages and PD-L1 + tumor cells as mechanistic determinants of response. Furthermore, spatial analysis of two extreme responders shows differential clustering of exhausted CD8 + T-cells with PD-L1 + macrophages in the first, and exhausted CD8 + T-cells with cancer cells harboring genomic PD-L1 and PD-L2 amplification in the second.
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Affiliation(s)
- Anniina Färkkilä
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.,Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA.,Research Program in Systems Oncology, University of Helsinki, Haartmaninkatu 8, 00014, Helsinki, Finland.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Doga C Gulhan
- Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
| | - Julia Casado
- Research Program in Systems Oncology, University of Helsinki, Haartmaninkatu 8, 00014, Helsinki, Finland
| | - Connor A Jacobson
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Huy Nguyen
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Bose Kochupurakkal
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Zoltan Maliga
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Clarence Yapp
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Yu-An Chen
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Denis Schapiro
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Yinghui Zhou
- TESARO: A GSK company, 1000 Winter Street, Waltham, MA, 02451, USA
| | - Julie R Graham
- TESARO: A GSK company, 1000 Winter Street, Waltham, MA, 02451, USA
| | - Bruce J Dezube
- TESARO: A GSK company, 1000 Winter Street, Waltham, MA, 02451, USA
| | - Pamela Munster
- Helen Diller Family Comprehensive Cancer Center, 1450 3rd Street, San Francisco, CA, 94158, USA
| | - Sandro Santagata
- Brigham and Women's Hospital, Laboratory for Systems Pharmacology, 75 Francis Street, Boston, MA, 02115, USA
| | - Elizabeth Garcia
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Ana Lako
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Dipanjan Chowdhury
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Geoffrey I Shapiro
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Ursula A Matulonis
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, University of Helsinki, Haartmaninkatu 8, 00014, Helsinki, Finland
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | | | - Alan D D'Andrea
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.
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Gstalder C, Liu D, Miao D, Devine A, Lutterbach B, Pancholi P, Shettigar M, Buchbinder E, Carter S, Manos M, Rojas-Rudilla V, Brennick R, Gjini E, Lako A, Rodig S, Yoon C, Freeman G, Hodi FS, Van Allen EM, Haq R. Abstract A48: Inactivation of Fbxw7 impairs dsRNA sensing and confers resistance to PD-1 blockade. Cancer Immunol Res 2020. [DOI: 10.1158/2326-6074.tumimm19-a48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Immunotherapies such as anti-PD-1 antibodies can induce durable responses in a subset of cancer patients, but intrinsic or acquired resistance occurs in most cases. Understanding the molecular mechanisms that drive resistance and response to immunotherapies could therefore lead to alternative treatment strategies exhibiting greater efficacy and precision. To identify new tumor cell-intrinsic mechanisms of resistance to PD-1 blockade, we evaluated metastatic melanoma patients who exhibited complete regression of all but one metastatic site following anti-PD-1 therapy. In one patient, we observed a loss-of-function mutation in the tumor suppressor gene F-Box and WD repeat domain containing 7 (FBXW7)—specifically in the resistant tumor. Using an immunocompetent, anti-PD-1 sensitive melanoma mouse model, we demonstrated that Fbxw7 loss of function in tumor cells causes resistance to PD-1 blockade. We showed that the genetic deletion of Fbxw7 in tumor cells alters the tumor immune microenvironment—including decreased effector cells and increased suppressive cells—in addition to diminished responses to viral sensing and interferon signaling pathways in vivo. Mechanistically, we found that Fbxw7 is necessary for the expression of the dsRNA sensors Mda5 and Rig-I. As a consequence, Fbxw7 is required for dsRNA-induced type I interferon production and interferon signaling in tumor cells. Conversely, restoration of the dsRNA signaling pathway in Fbxw7-deficient cells is sufficient to increase MHC-I expression and to suppress growth of Fbxw7-deficient tumors, thereby promoting antitumor immunity. Our findings establish a hitherto unrecognized role of the tumor suppressor gene FBXW7 in tumor immunity and sensitivity to immunotherapy. Collectively, these findings establish a novel tumor-intrinsic pathway of resistance and suggest that therapeutic reactivation of viral sensing pathways could improve clinical responses to checkpoint inhibitors in genomically defined populations.
Citation Format: Cécile Gstalder, David Liu, Diana Miao, Alexander Devine, Bart Lutterbach, Priya Pancholi, Megha Shettigar, Elizabeth Buchbinder, Scott Carter, Michael Manos, Vanesa Rojas-Rudilla, Ryan Brennick, Evisa Gjini, Ana Lako, Scott Rodig, Charles Yoon, Gordon Freeman, F. Stephen Hodi, Eliezer M. Van Allen, Rizwan Haq. Inactivation of Fbxw7 impairs dsRNA sensing and confers resistance to PD-1 blockade [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr A48.
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Affiliation(s)
| | - David Liu
- 1Dana-Farber Cancer Institute, Boston, MA,
| | - Diana Miao
- 1Dana-Farber Cancer Institute, Boston, MA,
| | | | | | | | | | | | | | | | | | | | | | - Ana Lako
- 2Brigham and Women’s Hospital, Boston, MA
| | | | | | | | | | | | - Rizwan Haq
- 1Dana-Farber Cancer Institute, Boston, MA,
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Guerriero JL, Mehta AK, Cheney EM, Castrillon JA, Lin JR, Taveira MDO, Sonzogni O, Pantelidou C, Hartl CA, Oldham WM, Johnson NT, Boswell SA, Kalocsay M, Berberich MJ, Mei S, Wang D, Johnson S, Gross B, Dillon DA, Lipschitz M, Gjini E, Rodig S, Santagata S, Garber JE, Tung N, Sorger P, Shapiro GI, Wulf GM, Mittendorf EA. Abstract P5-04-01: PARP inhibition modulates the infiltration, phenotype and function of tumor-associated macrophages (TAMs) in BRCA-associated breast cancer and can be augmented by harnessing the anti-tumor potential of TAMs. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p5-04-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Patients with BRCA-associated triple negative breast cancer (TNBC) have few effective treatment options. PARP inhibitors are promising, and we recently showed they induce an influx of white blood cells, including CD8+ T-cells and macrophages into the tumor. The influx of CD8+ cells, mediated by activation of the STING pathway in tumor cells, contributes substantially to efficacy of PARP inhibition in mice. Strikingly, in these studies, the greatest infiltration of immune cells into the tumor was macrophages. Given objective responses to PARP inhibition have been observed in clinical trials but the benefits are transitory, we hypothesized that this was presumably due to a suppressive tumor microenvironment, driven by tumor macrophages. To better understand the molecular basis of resistance to PARP inhibitors, we used high dimensional single-cell immune profiling on human TNBC. We observed a ≥10-fold increase in TAMs in BRCA-associated TNBC compared to BRCA-wildtype TNBC. Using a pre-clinical model of BRCA1-deficient triple-negative breast cancer, we found that PARP inhibitors not only further increased TAM abundance but also induced functional and phenotypic changes associated with STING pathway activation, antigen presentation, and chemokine and cytokine signaling. PARP inhibitors increased the frequency of TAMs expressing co-stimulatory molecules CD80 and CD86 as well as the activation and maturation marker CD40, which are indicative of an anti-tumor phenotype. We also identified a novel negative feedback mechanism which limits the functionality of the anti-tumor TAMs, and is consistent with induction of an immune suppressive macrophage population. Utilizing transcriptomic, proteomic and metabolic profiling of ex vivo cultured human myeloid cells, we identified multiple biological processes associate with PARP inhibition, showing that these drugs directly affect macrophage states and phenotypes. Remarkably, in the pre-clinical BRCA1-deficient TNBC model, the novel combination of PARP inhibition with macrophage modulation significantly extended remissions obtained with PARP inhibitor therapy only, and this advantage persisted when treatment was discontinued, suggestive of a durable reprogramming of the tumor microenvironment. Moreover, CD8+ cells were required for the extension of PARP inhibitor-induced remissions, suggesting that targeting macrophages lifted the constraints imposed by pro-tumor macrophages on CD8+ T cell-mediated tumor cell killing. We identify mechanisms related to macrophage and T-cell activation that increase PFS and provide evidence that TAMs may serve as targets for new therapeutic interventions designed to overcome PARP inhibitor resistance in BRCA-associated TNBC.
Citation Format: Jennifer L Guerriero, Anita K Mehta, Emily M Cheney, Jessica A. Castrillon, Jia-Ren Lin, Mateus de Oliveira Taveira, Olmo Sonzogni, Constantia Pantelidou, Christina A Hartl, William M Oldham, Nathan T Johnson, Sarah A Boswell, Marian Kalocsay, Matthew J Berberich, Sholin Mei, Dan Wang, Shawn Johnson, Brett Gross, Deborah A Dillon, Mikel Lipschitz, Evisa Gjini, Scott Rodig, Sandro Santagata, Judy E Garber, Nadine Tung, Peter Sorger, Geoffrey I Shapiro, Gerburg M Wulf, Elizabeth A Mittendorf. PARP inhibition modulates the infiltration, phenotype and function of tumor-associated macrophages (TAMs) in BRCA-associated breast cancer and can be augmented by harnessing the anti-tumor potential of TAMs [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-04-01.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Dan Wang
- 3Beth Israel Deaconess Medical Center, Boston, MA
| | | | | | | | | | | | | | | | | | - Nadine Tung
- 3Beth Israel Deaconess Medical Center, Boston, MA
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Armand P, Rodig S, Melnichenko V, Thieblemont C, Bouabdallah K, Tumyan G, Özcan M, Portino S, Fogliatto L, Caballero MD, Walewski J, Gulbas Z, Ribrag V, Christian B, Perini GF, Salles G, Svoboda J, Zain J, Patel S, Chen PH, Ligon AH, Ouyang J, Neuberg D, Redd R, Chatterjee A, Balakumaran A, Orlowski R, Shipp M, Zinzani PL. Pembrolizumab in Relapsed or Refractory Primary Mediastinal Large B-Cell Lymphoma. J Clin Oncol 2019; 37:3291-3299. [PMID: 31609651 PMCID: PMC6881098 DOI: 10.1200/jco.19.01389] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
PURPOSE Patients with relapsed or refractory primary mediastinal large B-cell lymphoma (rrPMBCL) have a poor prognosis, and their treatment represents an urgent and unmet need. Because PMBCL is associated with genetic aberrations at 9p24 and overexpression of programmed cell death-1 (PD-1) ligands (PD-L1), it is hypothesized to be susceptible to PD-1 blockade. METHODS In the phase IB KEYNOTE-013 (ClinicalTrials.gov identifier: NCT01953692) and phase II KEYNOTE-170 (ClinicalTrials.gov identifier: NCT02576990) studies, adults with rrPMBCL received pembrolizumab for up to 2 years or until disease progression or unacceptable toxicity. The primary end points were safety and objective response rate in KEYNOTE-013 and objective response rate in KEYNOTE-170. Secondary end points included duration of response, progression-free survival, overall survival, and safety. Exploratory end points included association between biomarkers and pembrolizumab activity. RESULTS The objective response rate was 48% (7 complete responses; 33%) among 21 patients in KEYNOTE-013 and 45% (7 complete responses; 13%) among 53 patients in KEYNOTE-170. After a median follow-up time of 29.1 months in KEYNOTE-013 and 12.5 months in KEYNOTE-170, the median duration of response was not reached in either study. No patient with complete response experienced progression, including 2 patients with complete response for at least 1 year off therapy. Treatment-related adverse events occurred in 24% of patients in KEYNOTE-013 and 23% of patients in KEYNOTE-170. There were no treatment-related deaths. Among 42 evaluable patients, the magnitude of the 9p24 gene abnormality was associated with PD-L1 expression, which was itself significantly associated with progression-free survival. CONCLUSION Pembrolizumab is associated with high response rate, durable activity, and a manageable safety profile in patients with rrPMBCL.
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Affiliation(s)
| | | | | | | | | | - Gayane Tumyan
- N.N. Blokhin Russian Cancer Research Center, Moscow, Russia
| | - Muhit Özcan
- Ankara University Medical School, Ankara, Turkey
| | | | | | | | - Jan Walewski
- Maria Sklodowska-Curie Institute Oncology Center, Warszawa, Poland
| | | | | | - Beth Christian
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Pier Luigi Zinzani
- Institute of Hematology, Seràgnoli University of Bologna, Bologna, Italy
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Gurjao C, Liu D, Hofree M, AlDubayan SH, Wakiro I, Su MJ, Felt K, Gjini E, Brais LK, Rotem A, Rosenthal MH, Rozenblatt-Rosen O, Rodig S, Ng K, Van Allen EM, Corsello SM, Ogino S, Regev A, Nowak JA, Giannakis M. Intrinsic Resistance to Immune Checkpoint Blockade in a Mismatch Repair-Deficient Colorectal Cancer. Cancer Immunol Res 2019; 7:1230-1236. [PMID: 31217164 PMCID: PMC6679789 DOI: 10.1158/2326-6066.cir-18-0683] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/13/2019] [Accepted: 06/12/2019] [Indexed: 12/12/2022]
Abstract
Immunotherapy with checkpoint inhibitors, such as the programmed death-1 (PD-1) antibodies pembrolizumab and nivolumab, are effective in a variety of tumors, yet not all patients respond. Tumor microsatellite instability-high (MSI-H) has emerged as a biomarker of response to checkpoint blockade, leading to the tissue agnostic approval of pembrolizumab in MSI-H cancers. Here we describe a patient with MSI-H colorectal cancer that was treated with this immune checkpoint inhibitor and exhibited progression of disease. We examined this intrinsic resistance through genomic, transcriptional, and pathologic characterization of the patient's tumor and the associated immune microenvironment. The tumor had typical MSI-H molecular features, including a high neoantigen load. We also identified biallelic loss of the gene for β2-microglobulin (B2M), whose product is critical for antigen presentation. Immune infiltration deconvolution analysis of bulk transcriptome data from this anti-PD-1-resistant tumor and hundreds of other colorectal cancer specimens revealed a high natural killer cell and M2 macrophage infiltration in the patient's cancer. This was confirmed by single-cell transcriptome analysis and multiplex immunofluorescence. Our study provides insight into resistance in MSI-H tumors and suggests immunotherapeutic strategies in additional genomic contexts of colorectal cancer.
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Affiliation(s)
- Carino Gurjao
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Matan Hofree
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Saud H AlDubayan
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Isaac Wakiro
- The Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mei-Ju Su
- Biotherapeutic and Medicinal Sciences, Biogen, Cambridge, Massachusetts
| | - Kristen Felt
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Evisa Gjini
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lauren K Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Asaf Rotem
- The Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Michael H Rosenthal
- Department of Radiology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | | | - Scott Rodig
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- The Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Steven M Corsello
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Shuji Ogino
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Jonathan A Nowak
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts.
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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Waks AG, Stover DG, Guerriero JL, Dillon D, Barry WT, Gjini E, Hartl C, Lo W, Savoie J, Brock J, Wesolowski R, Li Z, Damicis A, Philips AV, Wu Y, Yang F, Sullivan A, Danaher P, Brauer HA, Osmani W, Lipschitz M, Hoadley KA, Goldberg M, Perou CM, Rodig S, Winer EP, Krop IE, Mittendorf EA, Tolaney SM. The Immune Microenvironment in Hormone Receptor-Positive Breast Cancer Before and After Preoperative Chemotherapy. Clin Cancer Res 2019; 25:4644-4655. [PMID: 31061067 DOI: 10.1158/1078-0432.ccr-19-0173] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/05/2019] [Accepted: 05/01/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Hormone receptor-positive/HER2-negative (HR+/HER2-) breast cancer is associated with low levels of stromal tumor-infiltrating lymphocytes (sTIL) and PD-L1, and demonstrates poor responses to checkpoint inhibitor therapy. Evaluating the effect of standard chemotherapy on the immune microenvironment may suggest new opportunities for immunotherapy-based approaches to treating HR+/HER2- breast tumors. EXPERIMENTAL DESIGN HR+/HER2- breast tumors were analyzed before and after neoadjuvant chemotherapy. sTIL were assessed histologically; CD8+ cells, CD68+ cells, and PD-L1 staining were assessed immunohistochemically; whole transcriptome sequencing and panel RNA expression analysis (NanoString) were performed. RESULTS Ninety-six patients were analyzed from two cohorts (n = 55, Dana-Farber cohort; n = 41, MD Anderson cohort). sTIL, CD8, and PD-L1 on tumor cells were higher in tumors with basal PAM50 intrinsic subtype. Higher levels of tissue-based lymphocyte (sTIL, CD8, PD-L1) and macrophage (CD68) markers, as well as gene expression markers of lymphocyte or macrophage phenotypes (NanoString or CIBERSORT), correlated with favorable response to neoadjuvant chemotherapy, but not with improved distant metastasis-free survival in these cohorts or a large gene expression dataset (N = 302). In paired pre-/postchemotherapy samples, sTIL and CD8+ cells were significantly decreased after treatment, whereas expression analyses (NanoString) demonstrated significant increase of multiple myeloid signatures. Single gene expression implicated increased expression of immunosuppressive (M2-like) macrophage-specific genes after chemotherapy. CONCLUSIONS The immune microenvironment of HR+/HER2- tumors differs according to tumor biology. This cohort of paired pre-/postchemotherapy samples suggests a critical role for immunosuppressive macrophage expansion in residual disease. The role of macrophages in chemoresistance should be explored, and further evaluation of macrophage-targeting therapy is warranted.
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Affiliation(s)
- Adrienne G Waks
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Daniel G Stover
- Division of Medical Oncology, Ohio State University College of Medicine, Columbus, Ohio
| | - Jennifer L Guerriero
- Breast Tumor Immunology Laboratory, Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Deborah Dillon
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - William T Barry
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Evisa Gjini
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Christina Hartl
- Breast Tumor Immunology Laboratory, Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Wesley Lo
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jennifer Savoie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jane Brock
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Robert Wesolowski
- Division of Medical Oncology, Ohio State University College of Medicine, Columbus, Ohio
| | - Zaibo Li
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio
| | - Adrienne Damicis
- Department of Biostatistics, Ohio State University College of Public Health, Columbus, Ohio
| | - Anne V Philips
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yun Wu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Fei Yang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | | | - Wafa Osmani
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mikel Lipschitz
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Katherine A Hoadley
- University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Michael Goldberg
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Charles M Perou
- University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Eric P Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ian E Krop
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Elizabeth A Mittendorf
- Breast Tumor Immunology Laboratory, Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Boston, Massachusetts
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - Sara M Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
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42
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Monjazeb A, Giobbie-Hurder A, Lako A, Tesfaye AA, Stroiney A, Gentzler RD, Jabbour S, Alese OB, Rahma OE, Cleary JM, Sharon E, Raben D, Mamon HJ, Streicher H, Chen HX, Ahmed M, Gjini E, Rodig S, Hodi FS, Schoenfeld JD. Analysis of colorectal cancer patients treated on ETCTN 10021: A multicenter randomized trial of combined PD-L1 and CTLA-4 inhibition with targeted low-dose or hypofractionated radiation. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.8_suppl.49] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
49 Background: Pre-clinical and clinical evidence support immune effects of targeted radiation (RT) resulting in synergy with immune checkpoint therapy. However, prospective data are lacking in regards to safety, efficacy and immunologic impacts of different doses of RT given in conjunction with PD-L1 and CTLA-4 blockade. Methods: ETCTN 10021 is a multicenter randomized phase 2 study evaluating repeated low-dose fractionated RT (LDFRT) or hypofractionated RT (HFRT) in combination with PD-L1 and CTLA-4 inhibition in metastatic microsatellite-stable colorectal cancer (CRC) refractory to first-line chemotherapy, or non-small cell lung cancer progressive on prior PD-1 inhibition. The primary endpoint is objective response excluding irradiated lesions. Pre- and on-treatment biopsies were analyzed using multiplex immunofluorescence (IF) evaluating multiple immune markers. We report the prespecified analysis of the CRC cohort. Results: Twenty CRC patients were randomized, 19 of whom were treated with immunotherapy and RT, and 18 of whom were evaluable for response. Median lines of prior therapy were 4 (range 1-7). There were 16 patients with toxicity potentially related to treatment (84%), and 8 patients with possibly associated grade 3-5 toxicity (42%). Best response was stable disease in one patient with an abscopal out-of-field response who developed new lesions after HFRT and 4 cycles with decreasing overall disease burden. Correlative IF performed on 5 sample pairs revealed that HFRT, but not LDFRT, increased infiltration of CD8+, and CD8+/PD1+/Ki67+ T-cells in the RT field. Conclusions: We demonstrate the feasibility of a multicenter randomized study adding different RT regimens to PD-L1/CTLA-4 blockade. Toxicity was, in general, consistent with PD-L1/CTLA-4 inhibition with no significant RT-related toxicities noted. Although the best response of stable disease doesn’t support the use of PD-L1/CTLA-4 inhibition with HFRT or LDFRT in this population using these RT regimens and schedule, integrated biomarkers provide support that HFRT impacts the local immune microenvironment. Clinical trial information: NCT02888743.
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Affiliation(s)
| | | | - Ana Lako
- Dana-Farber Cancer Center, Boston, MA
| | | | | | | | - Salma Jabbour
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ
| | | | | | | | | | - David Raben
- Department of Radiation Oncology, Aurora, CO
| | | | - Howard Streicher
- Division of Cancer Treatment and Diagnosis, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD
| | | | | | | | - Scott Rodig
- Department of Pathology and Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
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43
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Reardon D, Keskin D, Tirosh I, Anandappa A, Mathewson N, Sun J, Shukla S, Gjini E, Li S, Giobbie-Hurder A, McCluskey C, Chiocca EA, Neuberg D, Wucherpfennig K, Suva M, Fritsch E, Rodig S, Ligon K, Wen P, Livak K, Regev A, Hacohen N, Wu C, Ott P. ATIM-32. PERSONALIZED NEOANTIGEN-TARGETING VACCINE GENERATES ROBUST SYSTEMIC AND INTRATUMORAL T CELL RESPONSES IN GLIOBLASTOMA (GBM) PATIENTS. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy148.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | - Itay Tirosh
- Weizmann Institute of Science, Rehovot, Tel Aviv, Israel
| | | | | | - Jing Sun
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Evisa Gjini
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shuqiang Li
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - E Antonio Chiocca
- Department of Neurosurgery, Brigham and Womens Hospital, Boston, MA, USA
| | | | | | - Mario Suva
- Massachusetts General Hospital, Boston, MA, USA
| | | | - Scott Rodig
- Brigham and Women’s Hospital, Boston, MA, USA
| | - Keith Ligon
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Patrick Wen
- Center For Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Nir Hacohen
- Massachusetts General Hospital, Boston, MA, USA
| | | | - Patrick Ott
- Dana-Farber Cancer Institute, Boston, MA, USA
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44
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Cañadas I, Thummalapalli R, Kim JW, Kitajima S, Jenkins RW, Christensen CL, Campisi M, Kuang Y, Zhang Y, Gjini E, Zhang G, Tian T, Sen DR, Miao D, Imamura Y, Thai T, Piel B, Terai H, Aref AR, Hagan T, Koyama S, Watanabe M, Baba H, Adeni AE, Lydon CA, Tamayo P, Wei Z, Herlyn M, Barbie TU, Uppaluri R, Sholl LM, Sicinska E, Sands J, Rodig S, Wong KK, Paweletz CP, Watanabe H, Barbie DA. Tumor innate immunity primed by specific interferon-stimulated endogenous retroviruses. Nat Med 2018; 24:1143-1150. [PMID: 30038220 PMCID: PMC6082722 DOI: 10.1038/s41591-018-0116-5] [Citation(s) in RCA: 179] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 06/04/2018] [Indexed: 12/17/2022]
Abstract
Mesenchymal tumor subpopulations secrete pro-tumorigenic cytokines and promote treatment resistance1–4. This phenomenon has been implicated in chemorefractory small cell lung cancer (SCLC) and resistance to targeted therapies5–8, but remains incompletely defined. Here we identify a subclass of endogenous retroviruses (ERVs) that engages innate immune signaling in these cells. Stimulated 3 Prime Antisense Retroviral Coding Sequences (SPARCS) are oriented inversely in 3′UTRs of specific genes enriched for regulation by STAT1 and EZH2. De-repression of these loci results in dsRNA generation following IFNγ exposure due to bi-directional transcription from the STAT1-activated gene promoter and the 5′ LTR of the antisense ERV. Engagement of MAVS and STING activates downstream TBK1, IRF3, and STAT1 signaling, sustaining a positive feedback loop. SPARCS induction in human tumors is tightly associated with MHC class 1 expression, mesenchymal markers, and downregulation of chromatin modifying enzymes, including EZH2. Analysis of cell lines with high inducible SPARCS expression reveals strong association with an AXL/MET positive mesenchymal cell state. While SPARCS high tumors are immune infiltrated, they also exhibit multiple features of an immune suppressed microenviroment. Together, these data unveil a subclass of ERVs whose de-repression triggers pathologic innate immune signaling in cancer, with important implications for cancer immunotherapy.
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Affiliation(s)
- Israel Cañadas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rohit Thummalapalli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jong Wook Kim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Shunsuke Kitajima
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Russell William Jenkins
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Division of Medical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | | | - Marco Campisi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yanan Kuang
- Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yanxi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Evisa Gjini
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Gao Zhang
- Melanoma Research Center and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Tian Tian
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA
| | - Debattama Rai Sen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Diana Miao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yu Imamura
- Gastroenterological Surgery, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Tran Thai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brandon Piel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hideki Terai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amir Reza Aref
- Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Timothy Hagan
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shohei Koyama
- Department of Respiratory Medicine, Allergy and Rheumatic Diseases, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Masayuki Watanabe
- Gastroenterological Surgery, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Anika Elise Adeni
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Pablo Tamayo
- Moores Cancer Center and School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA
| | - Meenhard Herlyn
- Melanoma Research Center and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Thanh Uyen Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Ravindra Uppaluri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Ewa Sicinska
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacob Sands
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Kwok Kin Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Cloud Peter Paweletz
- Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hideo Watanabe
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David Allen Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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45
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Reardon DA, Neuberg DS, Keskin DB, Tirosh I, Anandappa A, Mathewson ND, Sun J, Shukla SA, Gjini E, Li S, Giobbie-Hurder A, Wucherpfennig K, Suva M, Fritsch E, Rodig S, Ligon KL, Livak KJ, Hacohen N, Wu CJ, Ott PA. Effect of dexamethasone in glioblastoma (GBM) patients on systemic and intratumoral T-cell responses induced by personalized neoantigen-targeting vaccine. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- David A. Reardon
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | | | | | | | | | | | - Jing Sun
- Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | - Mario Suva
- Massachusetts General Hospital, Boston, MA
| | | | - Scott Rodig
- Department of Pathology and Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Keith L. Ligon
- Dana-Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA
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46
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Waks AG, Tolaney SM, Schnitt SJ, Dillon D, Gjini E, Abdelrahman S, Marino-Enriquez A, Helvie K, Marini L, Cohen O, Kim D, Wander SA, Stover DG, Rodig S, Krop IE, Winer EP, Lin NU, Wagle N. The tumor-immune microenvironment (TME) in HR+/HER2- metastatic breast cancer (mBC): Relationship to non-metastatic (met) tumors and prior treatment (tx) received. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.1054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ofir Cohen
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Dewey Kim
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | - Scott Rodig
- Department of Pathology and Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
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47
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Wu X, Giobbie-Hurder A, Connolly EM, Li J, Liao X, Severgnini M, Zhou J, Rodig S, Hodi FS. Anti-CTLA-4 based therapy elicits humoral immunity to galectin-3 in patients with metastatic melanoma. Oncoimmunology 2018; 7:e1440930. [PMID: 29900046 PMCID: PMC5993498 DOI: 10.1080/2162402x.2018.1440930] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/08/2018] [Accepted: 02/10/2018] [Indexed: 01/13/2023] Open
Abstract
The combination of CTLA-4 blockade ipilimumab (Ipi) with VEGF-A blocking antibody bevacizumab (Bev) has demonstrated favorable clinical outcomes in patients with advanced melanoma. Galectin-3 (Gal-3) plays a prominent role in tumor growth, metastasis, angiogenesis, and immune evasion. Here we report that Ipi plus Bev (Ipi-Bev) therapy increased Gal-3 antibody titers by 50% or more in approximately one third of treated patients. Antibody responses to Gal-3 were associated with higher complete and partial responses and better overall survival. Ipi alone also elicited antibody responses to Gal-3 at a frequency comparable to the Ipi-Bev combination. However, an association of elicited antibody responses to Gal-3 with clinical outcomes was not observed in Ipi alone treated patients. In contrast to being neutralized in Ipi-Bev treated patients, circulating VEGF-A increased by 100% or more in a subset of patients after Ipi treatment, with most having progressive disease. Among the Ipi treated patients with therapy-induced Gal-3 antibody increases, circulating VEGF-A was increased in 3 of 6 nonresponders but in none of 4 responders as a result of treatment. Gal-3 antibody responses occurred significantly less frequently (3.2%) in a cohort of patients receiving PD-1 blockade where high pre-treatment serum Gal-3 was associated with reduced OS and response rates. Our findings suggest that anti-CTLA-4 elicited humoral immune responses to Gal-3 in melanoma patients which may contribute to the antitumor effect in the presence of an anti-VEGF-A combination. Furthermore, pre-treatment circulating Gal-3 may potentially have prognostic and predictive value for immune checkpoint therapy.
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Affiliation(s)
- Xinqi Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | - Anita Giobbie-Hurder
- Center for Immuno-oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA.,Department of Biostatistics & Computational Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Erin M Connolly
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | - Jingjing Li
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | - Xiaoyun Liao
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | - Mariano Severgnini
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA.,Center for Immuno-oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | - Jun Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | - Scott Rodig
- Department of Pathology Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston, MA
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA.,Melanoma Disease Center, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA.,Center for Immuno-oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
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48
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Ricklefs FL, Alayo Q, Krenzlin H, Mahmoud AB, Speranza MC, Nakashima H, Hayes JL, Lee K, Balaj L, Passaro C, Rooj AK, Krasemann S, Carter BS, Chen CC, Steed T, Treiber J, Rodig S, Yang K, Nakano I, Lee H, Weissleder R, Breakefield XO, Godlewski J, Westphal M, Lamszus K, Freeman GJ, Bronisz A, Lawler SE, Chiocca EA. Immune evasion mediated by PD-L1 on glioblastoma-derived extracellular vesicles. Sci Adv 2018; 4:eaar2766. [PMID: 29532035 PMCID: PMC5842038 DOI: 10.1126/sciadv.aar2766] [Citation(s) in RCA: 368] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Binding of programmed death ligand-1 (PD-L1) to programmed cell death protein-1 (PD1) leads to cancer immune evasion via inhibition of T cell function. One of the defining characteristics of glioblastoma, a universally fatal brain cancer, is its profound local and systemic immunosuppression. Glioblastoma has also been shown to generate extracellular vesicles (EVs), which may play an important role in tumor progression. We thus hypothesized that glioblastoma EVs may be important mediators of immunosuppression and that PD-L1 could play a role. We show that glioblastoma EVs block T cell activation and proliferation in response to T cell receptor stimulation. PD-L1 was expressed on the surface of some, but not of all, glioblastoma-derived EVs, with the potential to directly bind to PD1. An anti-PD1 receptor blocking antibody significantly reversed the EV-mediated blockade of T cell activation but only when PD-L1 was present on EVs. When glioblastoma PD-L1 was up-regulated by IFN-γ, EVs also showed some PD-L1-dependent inhibition of T cell activation. PD-L1 expression correlated with the mesenchymal transcriptome profile and was anatomically localized in the perinecrotic and pseudopalisading niche of human glioblastoma specimens. PD-L1 DNA was present in circulating EVs from glioblastoma patients where it correlated with tumor volumes of up to 60 cm3. These results suggest that PD-L1 on EVs may be another mechanism for glioblastoma to suppress antitumor immunity and support the potential of EVs as biomarkers in tumor patients.
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Affiliation(s)
- Franz L. Ricklefs
- Harvey Cushing Neuro-Oncology Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Quazim Alayo
- Harvey Cushing Neuro-Oncology Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Harald Krenzlin
- Harvey Cushing Neuro-Oncology Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ahmad B. Mahmoud
- Harvey Cushing Neuro-Oncology Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- College of Applied Medical Sciences, Taibah University, Madinah Munawwarah, Saudi Arabia
| | - Maria C. Speranza
- Harvey Cushing Neuro-Oncology Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Hiroshi Nakashima
- Harvey Cushing Neuro-Oncology Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Josie L. Hayes
- School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kyungheon Lee
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Carmela Passaro
- Harvey Cushing Neuro-Oncology Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Arun K. Rooj
- Harvey Cushing Neuro-Oncology Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Susanne Krasemann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bob S. Carter
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Clark C. Chen
- Department of Neurosurgery, University of California, San Diego, La Jolla, CA 92121, USA
| | - Tyler Steed
- Department of Neurosurgery, University of California, San Diego, La Jolla, CA 92121, USA
| | - Jeffrey Treiber
- Department of Neurosurgery, University of California, San Diego, La Jolla, CA 92121, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Katherine Yang
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ichiro Nakano
- Comprehensive Cancer Center, University of Birmingham, Birmingham, AL 35294, USA
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xandra O. Breakefield
- Departments of Neurology and Radiology, Massachusetts General Hospital and Program in Neuroscience, Harvard Medical School, Boston, MA 02114, USA
| | - Jakub Godlewski
- Harvey Cushing Neuro-Oncology Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Manfred Westphal
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gordon J. Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Agnieszka Bronisz
- Harvey Cushing Neuro-Oncology Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sean E. Lawler
- Harvey Cushing Neuro-Oncology Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Corresponding author. (E.A.C.); (S.E.L.)
| | - E. Antonio Chiocca
- Harvey Cushing Neuro-Oncology Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Corresponding author. (E.A.C.); (S.E.L.)
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49
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Masugi Y, Nishihara R, Yang J, Mima K, da Silva A, Shi Y, Inamura K, Cao Y, Song M, Nowak JA, Liao X, Nosho K, Chan AT, Giannakis M, Bass AJ, Hodi FS, Freeman GJ, Rodig S, Fuchs CS, Qian ZR, Ogino S. Tumour CD274 (PD-L1) expression and T cells in colorectal cancer. Gut 2017; 66:1463-1473. [PMID: 27196573 PMCID: PMC5097696 DOI: 10.1136/gutjnl-2016-311421] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/22/2016] [Accepted: 04/03/2016] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Evidence suggests that CD274 (programmed death-ligand 1, B7-H1) immune checkpoint ligand repress antitumour immunity through its interaction with the PDCD1 (programmed cell death 1, PD-1) receptor of T lymphocytes in various tumours. We hypothesised that tumour CD274 expression levels might be inversely associated with T-cell densities in colorectal carcinoma tissue. DESIGN We evaluated tumour CD274 expression by immunohistochemistry in 823 rectal and colon cancer cases within the Nurses' Health Study and Health Professionals Follow-up Study. We conducted multivariable ordinal logistic regression analyses to examine the association of tumour CD274 expression with CD3+, CD8+, CD45RO (PTPRC)+ or FOXP3+ cell density in tumour tissue, controlling for potential confounders including tumour status of microsatellite instability (MSI), CpG island methylator phenotype, long interspersed nucleotide element-1 methylation level and KRAS, BRAF and PIK3CA mutations. RESULTS CD274 expression in tumour cells or stromal cells (including immune cells) was detected in 731 (89%) or 44 (5%) cases, respectively. Tumour CD274 expression level correlated inversely with FOXP3+ cell density in colorectal cancer tissue (outcome) (ptrend=0.0002). For a unit increase in outcome quartile categories, multivariable OR in the highest (vs lowest) CD274 expression score was 0.22 (95% CI 0.10 to 0.47). Tumour CD274 expression was inversely associated with MSI-high status (p=0.001). CD274 expression was not significantly associated with CD3+, CD8+ or CD45RO+ cell density, pathological lymphocytic reactions or patient survival prognosis. CONCLUSIONS Tumour CD274 expression is inversely associated with FOXP3+ cell density in colorectal cancer tissue, suggesting a possible influence of CD274-expressing carcinoma cells on regulatory T cells in the tumour microenvironment.
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Affiliation(s)
- Yohei Masugi
- Department of Medical Oncology, Dana-Farber Cancer Institute and
Harvard Medical School, Boston, Massachusetts, USA
| | - Reiko Nishihara
- Department of Medical Oncology, Dana-Farber Cancer Institute and
Harvard Medical School, Boston, Massachusetts, USA,Department of Nutrition, Harvard T.H. Chan School of Public Health,
Boston, Massachusetts, USA,Department of Epidemiology, Harvard T.H. Chan School of Public
Health, Boston, Massachusetts, USA,Department of Biostatistics, Harvard T.H. Chan School of Public
Health, Boston, Massachusetts, USA
| | - Juhong Yang
- Department of Medical Oncology, Dana-Farber Cancer Institute and
Harvard Medical School, Boston, Massachusetts, USA,Collaborative Innovation Center of Tianjin for Medical Epigenetics,
Key Laboratory of Hormone and Development, Metabolic Disease Hospital & Tianjin
Institute of Endocrinology, Tianjin Medical University, Tianjin, China
| | - Kosuke Mima
- Department of Medical Oncology, Dana-Farber Cancer Institute and
Harvard Medical School, Boston, Massachusetts, USA
| | - Annacarolina da Silva
- Department of Medical Oncology, Dana-Farber Cancer Institute and
Harvard Medical School, Boston, Massachusetts, USA
| | - Yan Shi
- Department of Medical Oncology, Dana-Farber Cancer Institute and
Harvard Medical School, Boston, Massachusetts, USA
| | - Kentaro Inamura
- Division of Pathology, Cancer Institute, Japanese Foundation For
Cancer Research, Tokyo, Japan
| | - Yin Cao
- Department of Nutrition, Harvard T.H. Chan School of Public Health,
Boston, Massachusetts, USA,Clinical and Translational Epidemiology Unit, Massachusetts General
Hospital and Harvard Medical School, Boston, Massachusetts, USA,Division of Gastroenterology, Massachusetts General Hospital,
Boston, Massachusetts, USA
| | - Mingyang Song
- Department of Nutrition, Harvard T.H. Chan School of Public Health,
Boston, Massachusetts, USA,Clinical and Translational Epidemiology Unit, Massachusetts General
Hospital and Harvard Medical School, Boston, Massachusetts, USA,Division of Gastroenterology, Massachusetts General Hospital,
Boston, Massachusetts, USA
| | - Jonathan A. Nowak
- Division of MPE Molecular Pathological Epidemiology, Department of
Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston,
Massachusetts, USA
| | - Xiaoyun Liao
- Department of Medical Oncology, Dana-Farber Cancer Institute and
Harvard Medical School, Boston, Massachusetts, USA,Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston,
Massachusetts, USA
| | - Katsuhiko Nosho
- Department of Gastroenterology, Rheumatology and Clinical
Immunology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Andrew T. Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General
Hospital and Harvard Medical School, Boston, Massachusetts, USA,Division of Gastroenterology, Massachusetts General Hospital,
Boston, Massachusetts, USA,Channing Division of Network Medicine, Department of Medicine,
Brigham and Women’s Hospital and Harvard Medical School, Boston,
Massachusetts, USA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute and
Harvard Medical School, Boston, Massachusetts, USA,Broad Institute of MIT and Harvard, Cambridge, Massachusetts,
USA,Department of Medicine, Brigham and Women’s Hospital and
Harvard Medical School, Boston, Massachusetts, USA
| | - Adam J. Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute and
Harvard Medical School, Boston, Massachusetts, USA,Broad Institute of MIT and Harvard, Cambridge, Massachusetts,
USA,Department of Medicine, Brigham and Women’s Hospital and
Harvard Medical School, Boston, Massachusetts, USA
| | - F. Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute and
Harvard Medical School, Boston, Massachusetts, USA,Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston,
Massachusetts, USA
| | - Gordon J. Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute and
Harvard Medical School, Boston, Massachusetts, USA,Department of Medicine, Brigham and Women’s Hospital and
Harvard Medical School, Boston, Massachusetts, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women’s Hospital and
Harvard Medical School, Boston, Massachusetts, USA
| | - Charles S. Fuchs
- Department of Medical Oncology, Dana-Farber Cancer Institute and
Harvard Medical School, Boston, Massachusetts, USA,Channing Division of Network Medicine, Department of Medicine,
Brigham and Women’s Hospital and Harvard Medical School, Boston,
Massachusetts, USA
| | - Zhi Rong Qian
- Department of Medical Oncology, Dana-Farber Cancer Institute and
Harvard Medical School, Boston, Massachusetts, USA
| | - Shuji Ogino
- Department of Medical Oncology, Dana-Farber Cancer Institute and
Harvard Medical School, Boston, Massachusetts, USA,Department of Epidemiology, Harvard T.H. Chan School of Public
Health, Boston, Massachusetts, USA,Division of MPE Molecular Pathological Epidemiology, Department of
Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston,
Massachusetts, USA
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50
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Fanale M, Engert A, Younes A, Armand P, Ansell S, Zinzani P, Timmerman J, Collins G, Ramchandren R, Cohen J, De Boer J, Kuruvilla J, Savage K, Trneny M, Rodig S, Shipp M, Kato K, Sumbul A, Farsaci B, Santoro A. NIVOLUMAB FOR RELAPSED/REFRACTORY CLASSICAL HODGKIN LYMPHOMA AFTER AUTOLOGOUS TRANSPLANT: FULL RESULTS AFTER EXTENDED FOLLOW-UP OF THE PHASE 2 CHECKMATE 205 TRIAL. Hematol Oncol 2017. [DOI: 10.1002/hon.2437_124] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- M. Fanale
- Department of Lymphoma/Myeloma; University of Texas MD Anderson Cancer Center; Houston USA
| | - A. Engert
- Department of Internal Medicine I; University Hospital of Cologne; Cologne Germany
| | - A. Younes
- Lymphoma Service; Memorial Sloan Kettering Cancer Center; New York USA
| | - P. Armand
- Medical Oncology; Dana-Farber Cancer Institute; Boston USA
| | - S. Ansell
- Division of Hematology; Mayo Clinic; Rochester USA
| | - P.L. Zinzani
- Institute of Hematology “L. e A. Seràgnoli; University of Bologna; Bologna Italy
| | - J.M. Timmerman
- Division of Hematology and Oncology; University of California, Los Angeles; Los Angeles USA
| | - G.P. Collins
- Oxford Cancer and Haematology Center; Churchill Hospital; Headington Oxford UK
| | - R. Ramchandren
- Department of Hematology/Oncology; Barbara Ann Karmanos Cancer Institute; Detroit USA
| | - J.B. Cohen
- Department of Hematology and Medical Oncology, Winship Cancer Institute; Emory University; Atlanta USA
| | - J.P. De Boer
- Department of Medical Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital; Amsterdam Netherlands
| | - J. Kuruvilla
- Department of Medical Oncology and Hematology; University of Toronto and Princess Margaret Cancer Centre; Toronto Canada
| | - K.J. Savage
- Department of Medical Oncology; British Columbia Cancer Agency; Vancouver Canada
| | - M. Trneny
- Department of Hematology; Charles University in Prague and General University Hospital in Prague; Prague Czech Republic
| | - S. Rodig
- Department of Pathology; Brigham and Women's Hospital; Boston USA
| | - M. Shipp
- Center for Hematologic Oncology; Dana-Farber Cancer Institute; Boston USA
| | - K. Kato
- Global Clinical Research; Bristol-Myers Squibb; Lawrenceville USA
| | - A. Sumbul
- Global Biostatistics; Bristol-Myers Squibb; Lawrenceville USA
| | - B. Farsaci
- Oncology Biomarkers; Bristol-Myers Squibb; Lawrenceville USA
| | - A. Santoro
- Department of Medical Oncology and Hematology, Humanitas Cancer Center; Humanitas University; Rozzano Milan Italy
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