1
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Brouwer-Visser J, Fiaschi N, Deering RP, Cygan KJ, Scott D, Jeong S, Boucher L, Gupta NT, Gupta S, Adler C, Topp MS, Bannerji R, Duell J, Advani RH, Flink DM, Chaudhry A, Thurston G, Ambati SR, Jankovic V. Molecular assessment of intratumoral immune cell subsets and potential mechanisms of resistance to odronextamab, a CD20×CD3 bispecific antibody, in patients with relapsed/refractory B-cell non-Hodgkin lymphoma. J Immunother Cancer 2024; 12:e008338. [PMID: 38519055 PMCID: PMC10961523 DOI: 10.1136/jitc-2023-008338] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2024] [Indexed: 03/24/2024] Open
Abstract
BACKGROUND Patients with relapsed/refractory B-cell non-Hodgkin lymphoma (R/R B-NHL) have a significant need for effective treatment options. Odronextamab is an Fc-silenced, human, CD20×CD3 bispecific antibody that targets CD20-expressing cells via T-cell-mediated cytotoxicity independent of T-cell/major histocompatibility complex interaction. Phase I results in patients with R/R B-NHL demonstrated that odronextamab monotherapy could achieve deep and durable responses with a generally manageable safety profile (ELM-1; NCT02290951). As part of a biomarker analysis of the same study, we investigated potential biomarkers and mechanisms of resistance to odronextamab. METHODS Patients with R/R B-NHL enrolled in ELM-1 received one time per week doses of intravenous odronextamab for 4×21 day cycles, then doses every 2 weeks thereafter. Patient tumor biopsies were obtained at baseline, on-treatment, and at progression. Immune cell markers were analyzed by immunohistochemistry, flow cytometry, single-cell RNA sequencing, and whole genome sequencing. RESULTS Baseline tumor biopsies showed that almost all patients had high proportions of B cells that expressed the CD20 target antigen, whereas expression of other B-cell surface antigens (CD19, CD22, CD79b) was more variable. Responses to odronextamab in patients with diffuse large B-cell lymphoma were not related to the relative level of baseline CD20 expression, cell of origin, or high-risk molecular subtype. A potential link was observed between greater tumor programmed cell death-ligand 1 expression and increased likelihood of response to odronextamab. Similarly, a trend was observed between clinical response and increased levels of CD8 T cells and regulatory T cells at baseline. We also identified an on-treatment pharmacodynamic shift in intratumoral immune cell subsets. Finally, loss of CD20 expression through inactivating gene mutations was identified as a potential mechanism of resistance in patients who were treated with odronextamab until progression, as highlighted in two detailed patient cases reported here. CONCLUSIONS This biomarker analysis expands on clinical findings of odronextamab in patients with R/R B-NHL, providing verification of the suitability of CD20 as a therapeutic target, as well as evidence for potential mechanisms of action and resistance.
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Affiliation(s)
| | | | | | - Kamil J Cygan
- Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Darius Scott
- Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Se Jeong
- Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Lauren Boucher
- Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Namita T Gupta
- Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Suraj Gupta
- Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | | | - Max S Topp
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Rajat Bannerji
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Johannes Duell
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Ranjana H Advani
- Department of Medicine, Stanford University, Stanford, California, USA
| | - Dina M Flink
- Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Aafia Chaudhry
- Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Gavin Thurston
- Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
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2
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Magen A, Hamon P, Fiaschi N, Soong BY, Park MD, Mattiuz R, Humblin E, Troncoso L, D'souza D, Dawson T, Kim J, Hamel S, Buckup M, Chang C, Tabachnikova A, Schwartz H, Malissen N, Lavin Y, Soares-Schanoski A, Giotti B, Hegde S, Ioannou G, Gonzalez-Kozlova E, Hennequin C, Le Berichel J, Zhao Z, Ward SC, Fiel I, Kou B, Dobosz M, Li L, Adler C, Ni M, Wei Y, Wang W, Atwal GS, Kundu K, Cygan KJ, Tsankov AM, Rahman A, Price C, Fernandez N, He J, Gupta NT, Kim-Schulze S, Gnjatic S, Kenigsberg E, Deering RP, Schwartz M, Marron TU, Thurston G, Kamphorst AO, Merad M. Intratumoral dendritic cell-CD4 + T helper cell niches enable CD8 + T cell differentiation following PD-1 blockade in hepatocellular carcinoma. Nat Med 2023; 29:1389-1399. [PMID: 37322116 PMCID: PMC11027932 DOI: 10.1038/s41591-023-02345-0] [Citation(s) in RCA: 37] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 04/10/2023] [Indexed: 06/17/2023]
Abstract
Despite no apparent defects in T cell priming and recruitment to tumors, a large subset of T cell rich tumors fail to respond to immune checkpoint blockade (ICB). We leveraged a neoadjuvant anti-PD-1 trial in patients with hepatocellular carcinoma (HCC), as well as additional samples collected from patients treated off-label, to explore correlates of response to ICB within T cell-rich tumors. We show that ICB response correlated with the clonal expansion of intratumoral CXCL13+CH25H+IL-21+PD-1+CD4+ T helper cells ("CXCL13+ TH") and Granzyme K+ PD-1+ effector-like CD8+ T cells, whereas terminally exhausted CD39hiTOXhiPD-1hiCD8+ T cells dominated in nonresponders. CD4+ and CD8+ T cell clones that expanded post-treatment were found in pretreatment biopsies. Notably, PD-1+TCF-1+ (Progenitor-exhausted) CD8+ T cells shared clones mainly with effector-like cells in responders or terminally exhausted cells in nonresponders, suggesting that local CD8+ T cell differentiation occurs upon ICB. We found that these Progenitor CD8+ T cells interact with CXCL13+ TH within cellular triads around dendritic cells enriched in maturation and regulatory molecules, or "mregDC". These results suggest that discrete intratumoral niches that include mregDC and CXCL13+ TH control the differentiation of tumor-specific Progenitor exhasuted CD8+ T cells following ICB.
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Affiliation(s)
- Assaf Magen
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pauline Hamon
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nathalie Fiaschi
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Brian Y Soong
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew D Park
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raphaël Mattiuz
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Etienne Humblin
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Leanna Troncoso
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Darwin D'souza
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Travis Dawson
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joel Kim
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven Hamel
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mark Buckup
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christie Chang
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandra Tabachnikova
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hara Schwartz
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nausicaa Malissen
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yonit Lavin
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alessandra Soares-Schanoski
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruno Giotti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samarth Hegde
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Giorgio Ioannou
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edgar Gonzalez-Kozlova
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Clotilde Hennequin
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica Le Berichel
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhen Zhao
- The Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephen C Ward
- The Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Isabel Fiel
- The Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Baijun Kou
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Michael Dobosz
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Lianjie Li
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Christina Adler
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Min Ni
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Yi Wei
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Wei Wang
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Gurinder S Atwal
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Kunal Kundu
- VI NEXT, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Kamil J Cygan
- VI NEXT, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adeeb Rahman
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | | | - Namita T Gupta
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Seunghee Kim-Schulze
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ephraim Kenigsberg
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raquel P Deering
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Myron Schwartz
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Thomas U Marron
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Gavin Thurston
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA.
| | - Alice O Kamphorst
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Miriam Merad
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Institute for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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3
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Deering RP, Blumenberg L, Li L, Dhanik A, Jeong S, Pourpe S, Song H, Boucher L, Ragunathan S, Li Y, Zhong M, Kuhnert J, Adler C, Hawkins P, Gupta NT, Moore M, Ni M, Hansen J, Wei Y, Thurston G. Rapid TCR:Epitope Ranker (RAPTER): a primary human T cell reactivity screening assay pairing epitope and TCR at single cell resolution. Sci Rep 2023; 13:8452. [PMID: 37231180 DOI: 10.1038/s41598-023-35710-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 05/22/2023] [Indexed: 05/27/2023] Open
Abstract
Identifying epitopes that T cells respond to is critical for understanding T cell-mediated immunity. Traditional multimer and other single cell assays often require large blood volumes and/or expensive HLA-specific reagents and provide limited phenotypic and functional information. Here, we present the Rapid TCR:Epitope Ranker (RAPTER) assay, a single cell RNA sequencing (scRNA-SEQ) method that uses primary human T cells and antigen presenting cells (APCs) to assess functional T cell reactivity. Using hash-tag oligonucleotide (HTO) coding and T cell activation-induced markers (AIM), RAPTER defines paired epitope specificity and TCR sequence and can include RNA- and protein-level T cell phenotype information. We demonstrate that RAPTER identified specific reactivities to viral and tumor antigens at sensitivities as low as 0.15% of total CD8+ T cells, and deconvoluted low-frequency circulating HPV16-specific T cell clones from a cervical cancer patient. The specificities of TCRs identified by RAPTER for MART1, EBV, and influenza epitopes were functionally confirmed in vitro. In summary, RAPTER identifies low-frequency T cell reactivities using primary cells from low blood volumes, and the resulting paired TCR:ligand information can directly enable immunogenic antigen selection from limited patient samples for vaccine epitope inclusion, antigen-specific TCR tracking, and TCR cloning for further therapeutic development.
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Affiliation(s)
- Raquel P Deering
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA.
| | - Lili Blumenberg
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Lianjie Li
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Ankur Dhanik
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Se Jeong
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Stephane Pourpe
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Hang Song
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Lauren Boucher
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Shoba Ragunathan
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Yanxia Li
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Maggie Zhong
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Jessica Kuhnert
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Christina Adler
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Peter Hawkins
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Namita T Gupta
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Michael Moore
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Min Ni
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Johanna Hansen
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Yi Wei
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Gavin Thurston
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
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4
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Kwart D, He J, Srivatsan S, Lett C, Golubov J, Oswald EM, Poon P, Ye X, Waite J, Zaretsky AG, Haxhinasto S, Au-Yeung E, Gupta NT, Chiu J, Adler C, Cherravuru S, Malahias E, Negron N, Lanza K, Coppola A, Ni M, Song H, Wei Y, Atwal GS, Macdonald L, Oristian NS, Poueymirou W, Jankovic V, Fury M, Lowy I, Murphy AJ, Sleeman MA, Wang B, Skokos D. Cancer cell-derived type I interferons instruct tumor monocyte polarization. Cell Rep 2022; 41:111769. [PMID: 36476866 DOI: 10.1016/j.celrep.2022.111769] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 06/29/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Monocytes are highly plastic immune cells that modulate antitumor immunity. Therefore, identifying factors that regulate tumor monocyte functions is critical for developing effective immunotherapies. Here, we determine that endogenous cancer cell-derived type I interferons (IFNs) control monocyte functional polarization. Guided by single-cell transcriptomic profiling of human and mouse tumors, we devise a strategy to distinguish and separate immunostimulatory from immunosuppressive tumor monocytes by surface CD88 and Sca-1 expression. Leveraging this approach, we show that cGAS-STING-regulated cancer cell-derived IFNs polarize immunostimulatory monocytes associated with anti-PD-1 immunotherapy response in mice. We also demonstrate that immunosuppressive monocytes convert into immunostimulatory monocytes upon cancer cell-intrinsic cGAS-STING activation. Consistently, we find that human cancer cells can produce type I IFNs that polarize monocytes, and our immunostimulatory monocyte gene signature is enriched in patient tumors that respond to anti-PD-1 immunotherapy. Our work exposes a role for cancer cell-derived IFNs in licensing monocyte functions that influence immunotherapy outcomes.
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Affiliation(s)
- Dylan Kwart
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Jing He
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | | | | | - Patrick Poon
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Xuan Ye
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | | | | | | | - Joyce Chiu
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | | | | | | | | | - Min Ni
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Hang Song
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Yi Wei
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | | | | | | | - Matthew Fury
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Israel Lowy
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | - Bei Wang
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA.
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5
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Marron TU, Fiel MI, Hamon P, Fiaschi N, Kim E, Ward SC, Zhao Z, Kim J, Kennedy P, Gunasekaran G, Tabrizian P, Doroshow D, Legg M, Hammad A, Magen A, Kamphorst AO, Shareef M, Gupta NT, Deering R, Wang W, Wang F, Thanigaimani P, Mani J, Troncoso L, Tabachnikova A, Chang C, Akturk G, Buckup M, Hamel S, Ioannou G, Hennequin C, Jamal H, Brown H, Bonaccorso A, Labow D, Sarpel U, Rosenbloom T, Sung MW, Kou B, Li S, Jankovic V, James N, Hamon SC, Cheung HK, Sims JS, Miller E, Bhardwaj N, Thurston G, Lowy I, Gnjatic S, Taouli B, Schwartz ME, Merad M. Neoadjuvant cemiplimab for resectable hepatocellular carcinoma: a single-arm, open-label, phase 2 trial. Lancet Gastroenterol Hepatol 2022; 7:219-229. [PMID: 35065058 PMCID: PMC9901534 DOI: 10.1016/s2468-1253(21)00385-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 01/05/2023]
Abstract
BACKGROUND Surgical resection of early stage hepatocellular carcinoma is standard clinical practice; however, most tumours recur despite surgery, and no perioperative intervention has shown a survival benefit. Neoadjuvant immunotherapy has induced pathological responses in multiple tumour types and might decrease the risk of postoperative recurrence in hepatocellular carcinoma. We aimed to evaluate the clinical activity of neoadjuvant cemiplimab (an anti-PD-1) in patients with resectable hepatocellular carcinoma. METHODS For this single-arm, open-label, phase 2 trial, patients with resectable hepatocellular carcinoma (stage Ib, II, and IIIb) were enrolled and received two cycles of neoadjuvant cemiplimab 350 mg intravenously every 3 weeks followed by surgical resection. Eligible patients were aged 18 years or older, had confirmed resectable hepatocellular carcinoma, an Eastern Cooperative Oncology Group performance status of 0 or 1, and adequate liver function. Patients were excluded if they had metastatic disease, if the surgery was not expected to be curative, if they had a known additional malignancy requiring active treatment, or if they required systemic steroid treatment or any other immunosuppressive therapy. After resection, patients received an additional eight cycles of cemiplimab 350 mg intravenously every 3 weeks in the adjuvant setting. The primary endpoint was significant tumour necrosis on pathological examination (defined as >70% necrosis of the resected tumour). Secondary endpoints included delay of surgery, the proportion of patients with an overall response, change in CD8+ T-cell density, and adverse events. Tumour necrosis and response were analysed in all patients who received at least one dose of cemiplimab and completed surgical resection; safety and other endpoints were analysed in the intention-to-treat population. Patients underwent pre-treatment biopsies and blood collection throughout treatment. This trial is registered with ClinicalTrials.gov (NCT03916627, Cohort B) and is ongoing. FINDINGS Between Aug 5, 2019, and Nov 25, 2020, 21 patients were enrolled. All patients received neoadjuvant cemiplimab, and 20 patients underwent successful resection. Of the 20 patients with resected tumours, four (20%) had significant tumour necrosis. Three (15%) of 20 patients had a partial response, and all other patients maintained stable disease. 20 (95%) patients had a treatment-emergent adverse event of any grade during the neoadjuvant treatment period. The most common adverse events of any grade were increased aspartate aminotransferase (in four patients), increased blood creatine phosphokinase (in three), constipation (in three), and fatigue (in three). Seven patients had grade 3 adverse events, including increased blood creatine phosphokinase (in two patients) and hypoalbuminaemia (in one). No grade 4 or 5 events were observed. One patient developed pneumonitis, which led to a delay in surgery by 2 weeks. INTERPRETATION This report is, to our knowledge, the largest clinical trial of a neoadjuvant anti-PD-1 monotherapy reported to date in hepatocellular carcinoma. The observed pathological responses to cemiplimab in this cohort support the design of larger trials to identify the optimal treatment duration and definitively establish the clinical benefit of preoperative PD-1 blockade in patients with hepatocellular carcinoma. FUNDING Regeneron Pharmaceuticals.
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MESH Headings
- Aged
- Aged, 80 and over
- Antibodies, Monoclonal, Humanized/administration & dosage
- Antibodies, Monoclonal, Humanized/adverse effects
- Antineoplastic Agents, Immunological/administration & dosage
- Antineoplastic Agents, Immunological/adverse effects
- Aspartate Aminotransferases/blood
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/pathology
- Carcinoma, Hepatocellular/surgery
- Creatine Kinase/blood
- Female
- Humans
- Liver Neoplasms/drug therapy
- Liver Neoplasms/pathology
- Liver Neoplasms/surgery
- Male
- Middle Aged
- Neoadjuvant Therapy
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Affiliation(s)
- Thomas U Marron
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Early Phase Trials Unit, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center of Excellence for Liver and Bile Duct Cancer, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases and RM Transplant Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Maria Isabel Fiel
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center of Excellence for Liver and Bile Duct Cancer, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases and RM Transplant Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pauline Hamon
- The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Edward Kim
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center of Excellence for Liver and Bile Duct Cancer, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases and RM Transplant Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephen C Ward
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center of Excellence for Liver and Bile Duct Cancer, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases and RM Transplant Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhen Zhao
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joel Kim
- The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paul Kennedy
- Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; BioMedical Engineering and Imaging Institute (BMEII), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ganesh Gunasekaran
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center of Excellence for Liver and Bile Duct Cancer, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases and RM Transplant Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Surgical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Parissa Tabrizian
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center of Excellence for Liver and Bile Duct Cancer, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases and RM Transplant Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Surgical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Deborah Doroshow
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Early Phase Trials Unit, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Meredith Legg
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Early Phase Trials Unit, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ashley Hammad
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Early Phase Trials Unit, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Assaf Magen
- The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alice O Kamphorst
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center of Excellence for Liver and Bile Duct Cancer, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases and RM Transplant Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Muhammed Shareef
- Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Wei Wang
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Fang Wang
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | | | | | - Leanna Troncoso
- The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandra Tabachnikova
- The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christie Chang
- The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Guray Akturk
- The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Human Immune Monitoring Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mark Buckup
- The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven Hamel
- The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Human Immune Monitoring Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Giorgio Ioannou
- The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Human Immune Monitoring Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Clotilde Hennequin
- The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hajra Jamal
- The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Haley Brown
- The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Antoinette Bonaccorso
- The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center of Excellence for Liver and Bile Duct Cancer, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases and RM Transplant Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Surgical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Labow
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center of Excellence for Liver and Bile Duct Cancer, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases and RM Transplant Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Surgical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Umut Sarpel
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center of Excellence for Liver and Bile Duct Cancer, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases and RM Transplant Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Surgical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Talia Rosenbloom
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Early Phase Trials Unit, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Max W Sung
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center of Excellence for Liver and Bile Duct Cancer, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases and RM Transplant Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Baijun Kou
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Siyu Li
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | | | | | | | | | | | | | - Nina Bhardwaj
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center of Excellence for Liver and Bile Duct Cancer, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases and RM Transplant Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Israel Lowy
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Sacha Gnjatic
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Human Immune Monitoring Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bachir Taouli
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center of Excellence for Liver and Bile Duct Cancer, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases and RM Transplant Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; BioMedical Engineering and Imaging Institute (BMEII), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Myron E Schwartz
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center of Excellence for Liver and Bile Duct Cancer, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases and RM Transplant Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Surgical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The neoAdjuvant Research Group to Evaluate Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center of Excellence for Liver and Bile Duct Cancer, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases and RM Transplant Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Human Immune Monitoring Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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6
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Zhang W, Hawkins PG, He J, Gupta NT, Liu J, Choonoo G, Jeong SW, Chen CR, Dhanik A, Dillon M, Deering R, Macdonald LE, Thurston G, Atwal GS. A framework for highly multiplexed dextramer mapping and prediction of T cell receptor sequences to antigen specificity. Sci Adv 2021; 7:7/20/eabf5835. [PMID: 33990328 PMCID: PMC8121425 DOI: 10.1126/sciadv.abf5835] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/25/2021] [Indexed: 05/04/2023]
Abstract
T cell receptor (TCR) antigen-specific recognition is essential for the adaptive immune system. However, building a TCR-antigen interaction map has been challenging due to the staggering diversity of TCRs and antigens. Accordingly, highly multiplexed dextramer-TCR binding assays have been recently developed, but the utility of the ensuing large datasets is limited by the lack of robust computational methods for normalization and interpretation. Here, we present a computational framework comprising a novel method, ICON (Integrative COntext-specific Normalization), for identifying reliable TCR-pMHC (peptide-major histocompatibility complex) interactions and a neural network-based classifier TCRAI that outperforms other state-of-the-art methods for TCR-antigen specificity prediction. We further demonstrated that by combining ICON and TCRAI, we are able to discover novel subgroups of TCRs that bind to a given pMHC via different mechanisms. Our framework facilitates the identification and understanding of TCR-antigen-specific interactions for basic immunological research and clinical immune monitoring.
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Affiliation(s)
- Wen Zhang
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA.
| | - Peter G Hawkins
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Jing He
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Namita T Gupta
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Jinrui Liu
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Gabrielle Choonoo
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Se W Jeong
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Calvin R Chen
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Ankur Dhanik
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Myles Dillon
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Raquel Deering
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Lynn E Macdonald
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Gavin Thurston
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Gurinder S Atwal
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA.
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7
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Benitez AA, Khalil-Agüero S, Nandakumar A, Gupta NT, Zhang W, Atwal GS, Murphy AJ, Sleeman MA, Haxhinasto S. Absence of central tolerance in Aire-deficient mice synergizes with immune-checkpoint inhibition to enhance antitumor responses. Commun Biol 2020; 3:355. [PMID: 32641748 PMCID: PMC7343867 DOI: 10.1038/s42003-020-1083-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 06/19/2020] [Indexed: 02/06/2023] Open
Abstract
The endogenous anti-tumor responses are limited in part by the absence of tumor-reactive T cells, an inevitable consequence of thymic central tolerance mechanisms ensuring prevention of autoimmunity. Here we show that tumor rejection induced by immune checkpoint blockade is significantly enhanced in Aire-deficient mice, the epitome of central tolerance breakdown. The observed synergy in tumor rejection extended to different tumor models, was accompanied by increased numbers of activated T cells expressing high levels of Gzma, Gzmb, Perforin, Cxcr3, and increased intratumoural levels of Cxcl9 and Cxcl10 compared to wild-type mice. Consistent with Aire's central role in T cell repertoire selection, single cell TCR sequencing unveiled expansion of several clones with high tumor reactivity. The data suggest that breakdown in central tolerance synergizes with immune checkpoint blockade in enhancing anti-tumor immunity and may serve as a model to unmask novel anti-tumor therapies including anti-tumor TCRs, normally purged during central tolerance.
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Affiliation(s)
- Asiel A Benitez
- Regeneron Pharmaceuticals, Inc. 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Sara Khalil-Agüero
- Regeneron Pharmaceuticals, Inc. 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Anjali Nandakumar
- Regeneron Pharmaceuticals, Inc. 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Namita T Gupta
- Regeneron Pharmaceuticals, Inc. 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Wen Zhang
- Regeneron Pharmaceuticals, Inc. 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Gurinder S Atwal
- Regeneron Pharmaceuticals, Inc. 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Andrew J Murphy
- Regeneron Pharmaceuticals, Inc. 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Matthew A Sleeman
- Regeneron Pharmaceuticals, Inc. 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Sokol Haxhinasto
- Regeneron Pharmaceuticals, Inc. 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA.
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8
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Laidlaw BJ, Lu Y, Amezquita RA, Weinstein JS, Vander Heiden JA, Gupta NT, Kleinstein SH, Kaech SM, Craft J. Interleukin-10 from CD4 + follicular regulatory T cells promotes the germinal center response. Sci Immunol 2018; 2:2/16/eaan4767. [PMID: 29054998 DOI: 10.1126/sciimmunol.aan4767] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 09/13/2017] [Indexed: 02/06/2023]
Abstract
CD4+ follicular regulatory T (Tfr) cells suppress B cell responses through modulation of follicular helper T (Tfh) cells and germinal center (GC) development. We found that Tfr cells can also promote the GC response through provision of interleukin-10 (IL-10) after acute infection with lymphocytic choriomeningitis virus (LCMV). Sensing of IL-10 by B cells was necessary for optimal development of the GC response. GC B cells formed in the absence of Treg cell-derived IL-10 displayed an altered dark zone state and decreased expression of the transcription factor Forkhead box protein 1 (FOXO1). IL-10 promoted nuclear translocation of FOXO1 in activated B cells. These data indicate that Tfr cells play a multifaceted role in the fine-tuning of the GC response and identify IL-10 as an important mediator by which Tfr cells support the GC reaction.
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Affiliation(s)
- Brian J Laidlaw
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yisi Lu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Robert A Amezquita
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jason S Weinstein
- Department of Internal Medicine (Rheumatology), Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jason A Vander Heiden
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Namita T Gupta
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Steven H Kleinstein
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA.,Interdepartmental Program in Computational Biology and Bioinformatics, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Susan M Kaech
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Joe Craft
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA. .,Department of Internal Medicine (Rheumatology), Yale University School of Medicine, New Haven, CT 06520, USA
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9
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Gupta NT, Adams KD, Briggs AW, Timberlake SC, Vigneault F, Kleinstein SH. Hierarchical Clustering Can Identify B Cell Clones with High Confidence in Ig Repertoire Sequencing Data. J Immunol 2017; 198:2489-2499. [PMID: 28179494 DOI: 10.4049/jimmunol.1601850] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/04/2017] [Indexed: 12/18/2022]
Abstract
Adaptive immunity is driven by the expansion, somatic hypermutation, and selection of B cell clones. Each clone is the progeny of a single B cell responding to Ag, with diversified Ig receptors. These receptors can now be profiled on a large scale by next-generation sequencing. Such data provide a window into the microevolutionary dynamics that drive successful immune responses and the dysregulation that occurs with aging or disease. Clonal relationships are not directly measured, but they must be computationally inferred from these sequencing data. Although several hierarchical clustering-based methods have been proposed, they vary in distance and linkage methods and have not yet been rigorously compared. In this study, we use a combination of human experimental and simulated data to characterize the performance of hierarchical clustering-based methods for partitioning sequences into clones. We find that single linkage clustering has high performance, with specificity, sensitivity, and positive predictive value all >99%, whereas other linkages result in a significant loss of sensitivity. Surprisingly, distance metrics that incorporate the biases of somatic hypermutation do not outperform simple Hamming distance. Although errors were more likely in sequences with short junctions, using the entire dataset to choose a single distance threshold for clustering is near optimal. Our results suggest that hierarchical clustering using single linkage with Hamming distance identifies clones with high confidence and provides a fully automated method for clonal grouping. The performance estimates we develop provide important context to interpret clonal analysis of repertoire sequencing data and allow for rigorous testing of other clonal grouping algorithms.
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Affiliation(s)
- Namita T Gupta
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520
| | | | | | | | | | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520; .,Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520; and.,Department of Pathology, Yale School of Medicine, New Haven, CT 06520
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10
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Toby IT, Levin MK, Salinas EA, Christley S, Bhattacharya S, Breden F, Buntzman A, Corrie B, Fonner J, Gupta NT, Hershberg U, Marthandan N, Rosenfeld A, Rounds W, Rubelt F, Scarborough W, Scott JK, Uduman M, Vander Heiden JA, Scheuermann RH, Monson N, Kleinstein SH, Cowell LG. VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. BMC Bioinformatics 2016; 17:333. [PMID: 27766961 PMCID: PMC5073965 DOI: 10.1186/s12859-016-1214-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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] [Indexed: 12/31/2022] Open
Abstract
Background The genes that produce antibodies and the immune receptors expressed on lymphocytes are not germline encoded; rather, they are somatically generated in each developing lymphocyte by a process called V(D)J recombination, which assembles specific, independent gene segments into mature composite genes. The full set of composite genes in an individual at a single point in time is referred to as the immune repertoire. V(D)J recombination is the distinguishing feature of adaptive immunity and enables effective immune responses against an essentially infinite array of antigens. Characterization of immune repertoires is critical in both basic research and clinical contexts. Recent technological advances in repertoire profiling via high-throughput sequencing have resulted in an explosion of research activity in the field. This has been accompanied by a proliferation of software tools for analysis of repertoire sequencing data. Despite the widespread use of immune repertoire profiling and analysis software, there is currently no standardized format for output files from V(D)J analysis. Researchers utilize software such as IgBLAST and IMGT/High V-QUEST to perform V(D)J analysis and infer the structure of germline rearrangements. However, each of these software tools produces results in a different file format, and can annotate the same result using different labels. These differences make it challenging for users to perform additional downstream analyses. Results To help address this problem, we propose a standardized file format for representing V(D)J analysis results. The proposed format, VDJML, provides a common standardized format for different V(D)J analysis applications to facilitate downstream processing of the results in an application-agnostic manner. The VDJML file format specification is accompanied by a support library, written in C++ and Python, for reading and writing the VDJML file format. Conclusions The VDJML suite will allow users to streamline their V(D)J analysis and facilitate the sharing of scientific knowledge within the community. The VDJML suite and documentation are available from https://vdjserver.org/vdjml/. We welcome participation from the community in developing the file format standard, as well as code contributions.
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Affiliation(s)
- Inimary T Toby
- Department of Clinical Sciences, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9066, USA
| | - Mikhail K Levin
- Bank of America Corporate Center, 100 North Tryon Street, Charlotte, NC, 28202, USA
| | | | - Scott Christley
- Department of Clinical Sciences, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9066, USA
| | - Sanchita Bhattacharya
- Institute for Computational Health Sciences, University of California San Francisco, Mission Hall, 550 16th Street, 4th Floor, Box 0110, San Francisco, CA, 94158, USA
| | - Felix Breden
- Department of Biological Sciences and The IRMACS Centre, Simon Fraser University, 8888 University Drive, Burnaby, V5A 1S6, British Columbia, Canada
| | - Adam Buntzman
- Department of Immunobiology, University of Arizona School of Medicine, 1656 E. Mabel Street, P.O. Box 245221, Tucson, AZ, 85724-5221, USA
| | - Brian Corrie
- New Zealand eScience Infrastructure, University of Auckland, Level 10, 49 Symonds Street, Auckland, New Zealand
| | - John Fonner
- Texas Advanced Computing Center, Research Office Complex 1.101, J.J. Pickle Research Campus, Building 196, 10100 Burnet Road (R8700), Austin, TX, 78758-4497, USA
| | - Namita T Gupta
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 505, New Haven, CT, 06511, USA
| | - Uri Hershberg
- School of Biomedical Engineering, Science and Health Systems and Department of Microbiology and Immunology, College of Medicine, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104, USA
| | - Nishanth Marthandan
- The IRMACS Centre (ASB 10905), Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Aaron Rosenfeld
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104, USA
| | - William Rounds
- Department of Neurology and Neurotherapeutics, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9036, USA
| | - Florian Rubelt
- Stanford University School of Medicine, 279 Campus Drive, Stanford, CA, 94305-5101, USA
| | - Walter Scarborough
- Texas Advanced Computing Center, Research Office Complex 1.101, J.J. Pickle Research Campus, Building 196, 10100 Burnet Road (R8700), Austin, TX, 78758-4497, USA
| | - Jamie K Scott
- Department of Molecular Biology and Biochemistry and Faculty of Health Sciences, Simon Fraser University, Blusson Hall, Room 11300, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Mohamed Uduman
- Department of Pathology, Yale School of Medicine, 300 George Street, Suite 505, New Haven, CT, 06511, USA
| | - Jason A Vander Heiden
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 505, New Haven, CT, 06511, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA.,Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.,Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Nancy Monson
- Department of Neurology and Neurotherapeutics, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9036, USA
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 505, New Haven, CT, 06511, USA.,Department of Pathology, Yale School of Medicine, 300 George Street, Suite 505, New Haven, CT, 06511, USA.,Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Lindsay G Cowell
- Department of Clinical Sciences, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9066, USA.
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11
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Di Niro R, Snir O, Kaukinen K, Yaari G, Lundin KEA, Gupta NT, Kleinstein SH, Cols M, Cerutti A, Mäki M, Shlomchik MJ, Sollid LM. Responsive population dynamics and wide seeding into the duodenal lamina propria of transglutaminase-2-specific plasma cells in celiac disease. Mucosal Immunol 2016; 9:254-64. [PMID: 26153762 PMCID: PMC4703456 DOI: 10.1038/mi.2015.57] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [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: 10/16/2014] [Accepted: 05/12/2015] [Indexed: 02/04/2023]
Abstract
A hallmark of celiac disease is autoantibodies to transglutaminase 2 (TG2). By visualizing TG2-specific antibodies by antigen staining of affected gut tissue, we identified TG2-specific plasma cells in the lamina propria as well as antibodies in the subepithelial layer, inside the epithelium, and at the brush border. The frequency of TG2-specific plasma cells were found not to correlate with serum antibody titers, suggesting that antibody production at other sites may contribute to serum antibody levels. Upon commencement of a gluten-free diet, the frequency of TG2-specific plasma cells in the lesion dropped dramatically within 6 months, yet some cells remained. The frequency of TG2-specific plasma cells in the celiac lesion is thus dynamically regulated in response to gluten exposure. Laser microdissection of plasma cell patches, followed by antibody gene sequencing, demonstrated that clonal cells were seeded in distinct areas of the mucosa. This was confirmed by immunoglobulin heavy chain repertoire analysis of plasma cells isolated from individual biopsies of two untreated patients, both for TG2-specific and non-TG2-specific cells. Our results shed new light on the processes underlying the B-cell response in celiac disease, and the approach of staining for antigen-specific antibodies should be applicable to other antibody-mediated diseases.
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Affiliation(s)
- R Di Niro
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,
| | - O Snir
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - K Kaukinen
- Departments of Internal Medicine and Gastroenterology, Tampere University Hospital and School of Medicine, University of Tampere, Tampere, Finland
| | - G Yaari
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - K E A Lundin
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway,Centre for Immune Regulation and Department of Gastroenterology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - N T Gupta
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
| | - S H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA,Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - M Cols
- Immunology Institute, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - A Cerutti
- Immunology Institute, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - M Mäki
- Tampere Centre for Child Health Research, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - M J Shlomchik
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - L M Sollid
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
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12
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Tsioris K, Gupta NT, Ogunniyi AO, Zimnisky RM, Qian F, Yao Y, Wang X, Stern JNH, Chari R, Briggs AW, Clouser CR, Vigneault F, Church GM, Garcia MN, Murray KO, Montgomery RR, Kleinstein SH, Love JC. Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing. Integr Biol (Camb) 2015; 7:1587-97. [PMID: 26481611 PMCID: PMC4754972 DOI: 10.1039/c5ib00169b] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [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] [Indexed: 12/29/2022]
Abstract
West Nile virus (WNV) infection is an emerging mosquito-borne disease that can lead to severe neurological illness and currently has no available treatment or vaccine. Using microengraving, an integrated single-cell analysis method, we analyzed a cohort of subjects infected with WNV - recently infected and post-convalescent subjects - and efficiently identified four novel WNV neutralizing antibodies. We also assessed the humoral response to WNV on a single-cell and repertoire level by integrating next generation sequencing (NGS) into our analysis. The results from single-cell analysis indicate persistence of WNV-specific memory B cells and antibody-secreting cells in post-convalescent subjects. These cells exhibited class-switched antibody isotypes. Furthermore, the results suggest that the antibody response itself does not predict the clinical severity of the disease (asymptomatic or symptomatic). Using the nucleotide coding sequences for WNV-specific antibodies derived from single cells, we revealed the ontogeny of expanded WNV-specific clones in the repertoires of recently infected subjects through NGS and bioinformatic analysis. This analysis also indicated that the humoral response to WNV did not depend on an anamnestic response, due to an unlikely previous exposure to the virus. The innovative and integrative approach presented here to analyze the evolution of neutralizing antibodies from natural infection on a single-cell and repertoire level can also be applied to vaccine studies, and could potentially aid the development of therapeutic antibodies and our basic understanding of other infectious diseases.
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Affiliation(s)
- Konstantinos Tsioris
- Department of Chemical Engineering, Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Bldg. 76-253, Cambridge, MA 02139, USA.
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13
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Di Niro R, Lee SJ, Vander Heiden JA, Elsner RA, Trivedi N, Bannock JM, Gupta NT, Kleinstein SH, Vigneault F, Gilbert TJ, Meffre E, McSorley SJ, Shlomchik MJ. Salmonella Infection Drives Promiscuous B Cell Activation Followed by Extrafollicular Affinity Maturation. Immunity 2015; 43:120-31. [PMID: 26187411 DOI: 10.1016/j.immuni.2015.06.013] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 03/25/2015] [Accepted: 06/16/2015] [Indexed: 12/25/2022]
Abstract
The B cell response to Salmonella typhimurium (STm) occurs massively at extrafollicular sites, without notable germinal centers (GCs). Little is known in terms of its specificity. To expand the knowledge of antigen targets, we screened plasmablast (PB)-derived monoclonal antibodies (mAbs) for Salmonella specificity, using ELISA, flow cytometry, and antigen microarray. Only a small fraction (0.5%-2%) of the response appeared to be Salmonella-specific. Yet, infection of mice with limited B cell receptor (BCR) repertoires impaired the response, suggesting that BCR specificity was important. We showed, using laser microdissection, that somatic hypermutation (SHM) occurred efficiently at extrafollicular sites leading to affinity maturation that in turn led to detectable STm Ag-binding. These results suggest a revised vision of how clonal selection and affinity maturation operate in response to Salmonella. Clonal selection initially is promiscuous, activating cells with virtually undetectable affinity, yet SHM and selection occur during the extrafollicular response yielding higher affinity, detectable antibodies.
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Affiliation(s)
- Roberto Di Niro
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Laboratory Medicine and Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Seung-Joo Lee
- Center for Comparative Medicine, University of California, Davis, CA 95616, USA
| | - Jason A Vander Heiden
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Rebecca A Elsner
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Nikita Trivedi
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jason M Bannock
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Namita T Gupta
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | | | | | - Eric Meffre
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Stephen J McSorley
- Center for Comparative Medicine, University of California, Davis, CA 95616, USA
| | - Mark J Shlomchik
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Laboratory Medicine and Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA.
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14
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Gupta NT, Vander Heiden JA, Uduman M, Gadala-Maria D, Yaari G, Kleinstein SH. Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. Bioinformatics 2015; 31:3356-8. [PMID: 26069265 DOI: 10.1093/bioinformatics/btv359] [Citation(s) in RCA: 464] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 06/05/2015] [Indexed: 12/11/2022] Open
Abstract
UNLABELLED Advances in high-throughput sequencing technologies now allow for large-scale characterization of B cell immunoglobulin (Ig) repertoires. The high germline and somatic diversity of the Ig repertoire presents challenges for biologically meaningful analysis, which requires specialized computational methods. We have developed a suite of utilities, Change-O, which provides tools for advanced analyses of large-scale Ig repertoire sequencing data. Change-O includes tools for determining the complete set of Ig variable region gene segment alleles carried by an individual (including novel alleles), partitioning of Ig sequences into clonal populations, creating lineage trees, inferring somatic hypermutation targeting models, measuring repertoire diversity, quantifying selection pressure, and calculating sequence chemical properties. All Change-O tools utilize a common data format, which enables the seamless integration of multiple analyses into a single workflow. AVAILABILITY AND IMPLEMENTATION Change-O is freely available for non-commercial use and may be downloaded from http://clip.med.yale.edu/changeo. CONTACT steven.kleinstein@yale.edu.
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Affiliation(s)
- Namita T Gupta
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Jason A Vander Heiden
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Mohamed Uduman
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06511, USA and
| | - Daniel Gadala-Maria
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Gur Yaari
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, Department of Pathology, Yale University School of Medicine, New Haven, CT 06511, USA and
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