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Sentís I, Melero JL, Cebria-Xart A, Grzelak M, Soto M, Michel A, Rovira Q, Rodriguez-Hernandez CJ, Caratù G, Urpi A, Sauvage C, Mendizabal-Sasieta A, Maspero D, Lavarino CE, Pascual-Reguant A, Castañeda Heredia A, Muñoz Perez JP, Mora J, Harari A, Nieto JC, Avgustinova A, Heyn H. Spatio-temporal T cell tracking for personalized TCR-T designs in childhood cancer. Ann Oncol 2025:S0923-7534(25)00733-1. [PMID: 40403847 DOI: 10.1016/j.annonc.2025.05.530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2025] [Revised: 04/21/2025] [Accepted: 05/08/2025] [Indexed: 05/24/2025] Open
Abstract
BACKGROUND Immune checkpoint inhibition (ICI) has revolutionized oncology, offering extended survival and long-term remission in previously incurable cancers. While highly effective in tumors with high mutational burden, lowly mutated cancers, including pediatric malignancies, present low response rate and limited predictive biomarkers. PATIENTS AND METHODS We present a framework for the identification and validation of tumor-reactive T cells as a biomarker to quantify ICI efficacy and as candidates for a personalized TCR-T cell therapy. Therefore, we profiled a pediatric malignant rhabdoid tumor patient with complete remission after ICI therapy using deep single-cell T cell receptor (TCR) repertoire sequencing of the tumor microenvironment (TME) and the peripheral blood. RESULTS Tracking T cell dynamics longitudinally from the tumor to cells in circulation over a time course of 12 months revealed a systemic response and durable clonal expansion of tumor-resident and ICI-induced TCR clonotypes. We functionally validated tumor reactivity of TCRs identified from the TME and the blood by co-culturing patient-derived tumor cells with TCR-engineered autologous T cells. Here, we observed unexpectedly high frequencies of tumor-reactive TCR clonotypes in the TME and confirmed T cell dynamics in the blood post-ICI to predict tumor-reactivity. CONCLUSION These findings strongly support spatio-temporal tracking of T cell activity in response to ICI to inform therapy efficacy and to serve as a source of tumor-reactive TCRs for personalized TCR-T designs.
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Affiliation(s)
- I Sentís
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institut de Recerca Sant Joan de Déu (IRSJD), Esplugues de Llobregat, Spain
| | | | - A Cebria-Xart
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institut de Recerca Sant Joan de Déu (IRSJD), Esplugues de Llobregat, Spain
| | | | - M Soto
- Omniscope, Barcelona, Spain
| | - A Michel
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Q Rovira
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institut de Recerca Sant Joan de Déu (IRSJD), Esplugues de Llobregat, Spain
| | | | - G Caratù
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - A Urpi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institut de Recerca Sant Joan de Déu (IRSJD), Esplugues de Llobregat, Spain
| | - C Sauvage
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | | | - D Maspero
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - C E Lavarino
- Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan de Déu, Barcelona, Spain
| | | | - A Castañeda Heredia
- Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan de Déu, Barcelona, Spain
| | - J P Muñoz Perez
- Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan de Déu, Barcelona, Spain
| | - J Mora
- Institut de Recerca Sant Joan de Déu (IRSJD), Esplugues de Llobregat, Spain; Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan de Déu, Barcelona, Spain
| | - A Harari
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - J C Nieto
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - A Avgustinova
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institut de Recerca Sant Joan de Déu (IRSJD), Esplugues de Llobregat, Spain.
| | - H Heyn
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain; Omniscope, Barcelona, Spain; Universitat de Barcelona (UB), Barcelona, Spain; ICREA, Barcelona, Spain.
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2
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Jiang M, Li J, Wei J, Yang X, Wang W. Advances in neoantigen-based immunotherapy for head and neck squamous cell carcinoma: a comprehensive review. Front Oncol 2025; 15:1593048. [PMID: 40444094 PMCID: PMC12119297 DOI: 10.3389/fonc.2025.1593048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2025] [Accepted: 04/17/2025] [Indexed: 06/02/2025] Open
Abstract
Head and Neck Squamous Cell Carcinoma (HNSCC), ranking among the six most prevalent malignancies worldwide, is characterized by significant heterogeneity. Conventional monotherapeutic approaches, including surgical intervention, radiotherapy, and chemotherapy, often fail to achieve complete tumor cell elimination, consequently leading to disease recurrence and metastatic progression. In this context, personalized immunotherapeutic strategies, particularly cancer vaccines and immune checkpoint inhibitors, have emerged as promising therapeutic modalities for patients with recurrent/metastatic (R/M) HNSCC. Neoantigens, which exhibit selective expression in tumor tissues while remaining absent in normal tissues, have garnered considerable attention as novel targets for HNSCC personalized immunotherapy. However, the marked heterogeneity of HNSCC, coupled with patient-specific HLA variations, necessitates precise technical identification and evaluation of neoantigens at the individual level-a significant contemporary challenge. This comprehensive review systematically explores the landscape of neoantigen-based immunotherapy in HNSCC, including neoantigen sources, screening strategies, identification methods, and their clinical applications. Additionally, it evaluates the therapeutic potential of combining neoantigen-based approaches with other immunotherapeutic modalities, particularly immune checkpoint inhibitors, providing valuable insights for future clinical practice and research directions in HNSCC treatment.
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Affiliation(s)
- Manzhu Jiang
- College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Jiefu Li
- Guangzhou National Laboratory, Guangzhou, China
| | - Jianhua Wei
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University, Xi’an, China
| | - Xuerong Yang
- College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Weiqi Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University, Xi’an, China
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3
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Shorer O, Pinhasi A, Yizhak K. Single-cell meta-analysis of T cells reveals clonal dynamics of response to checkpoint immunotherapy. CELL GENOMICS 2025; 5:100842. [PMID: 40187353 DOI: 10.1016/j.xgen.2025.100842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Revised: 02/03/2025] [Accepted: 03/11/2025] [Indexed: 04/07/2025]
Abstract
Despite the crucial role of T cell clones in anti-tumor activity, their characterization and association with clinical outcomes following immune checkpoint inhibitors are lacking. Here, we analyzed paired single-cell RNA sequencing/T cell receptor sequencing of 767,606 T cells across 460 samples spanning 6 cancer types. We found a robust signature of response based on expanded CD8+ clones that differentiates responders from non-responders. Analysis of persistent clones showed transcriptional changes that are differentially induced by therapy in the different response groups, suggesting an improved reinvigoration capacity in responding patients. Moreover, a gene trajectory analysis revealed changes in the pseudo-temporal state of de novo clones that are associated with clinical outcomes. Lastly, we found that clones shared between tumor and blood are more abundant in non-responders and execute distinct transcriptional programs. Overall, our results highlight differences in clonal transcriptional states that are linked to patient response, offering valuable insights into the mechanisms driving effective anti-tumor immunity.
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Affiliation(s)
- Ofir Shorer
- Department of Cell Biology and Cancer Science, The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 3525422, Israel
| | - Asaf Pinhasi
- Department of Cell Biology and Cancer Science, The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 3525422, Israel
| | - Keren Yizhak
- Department of Cell Biology and Cancer Science, The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 3525422, Israel; The Taub Faculty of Computer Science, Technion - Israel Institute of Technology, Haifa 3200003, Israel.
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4
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Wiertsema P, Tan YH, Haanen JBAG, Seijkens TTP, Jedema I. Advances in TIL therapy: Expanding the horizons beyond melanoma. MED 2025:100702. [PMID: 40381620 DOI: 10.1016/j.medj.2025.100702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2025] [Revised: 04/08/2025] [Accepted: 04/22/2025] [Indexed: 05/20/2025]
Abstract
Tumor-infiltrating lymphocyte (TIL) therapy represents a breakthrough in solid tumor treatment, addressing unmet needs for patients with limited options. While its efficacy is established in advanced melanoma, TIL therapy shows early promise in non-small cell lung cancer, breast cancer, gynecological cancers, and head and neck cancers. However, challenges such as reduced T cell infiltration, lower tumor mutational burden (TMB), immunosuppressive tumor microenvironments (TME), and toxicity associated with the TIL therapy regimen hinder its broader application in these patient groups, compared with melanoma. To address these challenges, new approaches focus on the selection of tumor-reactive TIL, optimization of TIL expansion, combination of immune checkpoint inhibitors with TIL therapy to counteract immunosuppressive microenvironments, and genetic modification of TIL to enhance persistence and functionality. Larger clinical trials are essential to validate these innovations and standardize protocols. With continued advancements, TIL therapy has the potential to redefine the treatment landscape for advanced solid cancers.
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Affiliation(s)
- Pauline Wiertsema
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ya Hwee Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore; Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - John B A G Haanen
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands; Melanoma Clinic, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Tom T P Seijkens
- Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Inge Jedema
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
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5
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Trehan R, Huang P, Zhu XB, Wang X, Soliman M, Strepay D, Nur A, Kedei N, Arhin M, Ghabra S, Rodríguez-Matos F, Benmebarek MR, Ma C, Korangy F, Greten TF. SPP1 + macrophages cause exhaustion of tumor-specific T cells in liver metastases. Nat Commun 2025; 16:4242. [PMID: 40335453 PMCID: PMC12059142 DOI: 10.1038/s41467-025-59529-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Accepted: 04/25/2025] [Indexed: 05/09/2025] Open
Abstract
Functional tumor-specific CD8+ T cells are essential for effective anti-tumor immune response and immune checkpoint inhibitor therapy. Here we show that, compared to other organ sites, primary, metastatic liver tumors in murine models contain a higher number of tumor-specific CD8+ T cells which are also dysfunctional. High-dimensional, multi-omic analysis of patient samples reveals a higher frequency of exhausted tumor-reactive CD8+ T cells and enriched interactions between these cells and SPP1+ macrophages in profibrotic, alpha-SMA rich regions specifically in the liver. Differential pseudotime trajectory inference analysis reveals that extrahepatic signaling promotes an intermediate cell (IC) population in the liver, characterized by co-expression of VISG4, CSF1R, CD163, TGF-βR, IL-6R, and SPP1. Analysis of premetastatic adenocarcinoma patient samples reveals enrichment of this population may predict liver metastasis. These findings suggest a mechanism by which extrahepatic tumors drive liver metastasis by promoting an IC population that inhibits tumor-reactive CD8+ T cell function.
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Affiliation(s)
- Rajiv Trehan
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Patrick Huang
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xiao Bin Zhu
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xin Wang
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marlaine Soliman
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dillon Strepay
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Amran Nur
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Noemi Kedei
- Collaborative Protein Technology Resource, OSTR, Office of the Director, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Martin Arhin
- Neurosurgery Unit for Pituitary and Inheritable Diseases, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Shadin Ghabra
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Francisco Rodríguez-Matos
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mohamed-Reda Benmebarek
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chi Ma
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Firouzeh Korangy
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tim F Greten
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
- NCI CCR Liver Cancer Program, National Institutes of Health, Bethesda, MD, USA.
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6
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Hugaboom MB, Wirth LV, Street K, Ruthen N, Jegede OA, Schindler NR, Shah V, Zaemes JP, Ahmar NE, Matar S, Savla V, Choueiri TK, Denize T, West DJ, McDermott DF, Plimack ER, Sosman JA, Haas NB, Stein MN, Alter R, Bilen MA, Hurwitz ME, Hammers H, Signoretti S, Atkins MB, Wu CJ, Braun DA. Presence of Tertiary Lymphoid Structures and Exhausted Tissue-Resident T Cells Determines Clinical Response to PD-1 Blockade in Renal Cell Carcinoma. Cancer Discov 2025; 15:948-968. [PMID: 39992403 PMCID: PMC12048281 DOI: 10.1158/2159-8290.cd-24-0991] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 01/08/2025] [Accepted: 02/21/2025] [Indexed: 02/25/2025]
Abstract
SIGNIFICANCE We describe a paradigm wherein combined high TLS and low tissue-resident exhausted CD8+ T cells are required for optimal response to PD-1 blockade in RCC. This analysis identifies key determinants of response to PD-1 blockade in advanced RCC and suggests avenues for future immune modulation through rational combination therapy strategies.
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Affiliation(s)
- Miya B. Hugaboom
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Lena V. Wirth
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Kelly Street
- Division of Biostatistics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Neil Ruthen
- Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Opeyemi A. Jegede
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Valisha Shah
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacob P. Zaemes
- Georgetown Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | - Nourhan El Ahmar
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Sayed Matar
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Varunika Savla
- 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
| | - Thomas Denize
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Destiny J. West
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - David F. McDermott
- Division of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | - Jeffrey A. Sosman
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | - Naomi B. Haas
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Mark N. Stein
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Robert Alter
- Hackensack University Medical Center, Hackensack, NJ, USA
| | - Mehmet A. Bilen
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Michael E. Hurwitz
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Hans Hammers
- Department of Internal Medicine, Division of Hematology and Oncology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Michael B. Atkins
- Georgetown Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David A. Braun
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
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Boxer E, Feigin N, Tschernichovsky R, Darnell NG, Greenwald AR, Hoefflin R, Kovarsky D, Simkin D, Turgeman S, Zhang L, Tirosh I. Emerging clinical applications of single-cell RNA sequencing in oncology. Nat Rev Clin Oncol 2025; 22:315-326. [PMID: 40021788 DOI: 10.1038/s41571-025-01003-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2025] [Indexed: 03/03/2025]
Abstract
Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of complex tissues both in health and in disease. Over the past decade, scRNA-seq has been applied to tumour samples obtained from patients with cancer in hundreds of studies, thereby advancing the view that each tumour is a complex ecosystem and uncovering the diverse states of both cancer cells and the tumour microenvironment. Such studies have primarily investigated and provided insights into the basic biology of cancer, although considerable research interest exists in leveraging these findings towards clinical applications. In this Review, we summarize the available data from scRNA-seq studies investigating samples from patients with cancer with a particular focus on findings that are of potential clinical relevance. We highlight four main research objectives of scRNA-seq studies and describe some of the most relevant findings towards such goals. We also describe the limitations of scRNA-seq, as well as future approaches in this field that are anticipated to further advance clinical applicability.
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Affiliation(s)
- Emily Boxer
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nisan Feigin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Roi Tschernichovsky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Davidoff Cancer Center, Rabin Medical Center, Petah Tikva, Israel
| | - Noam Galili Darnell
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alissa R Greenwald
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rouven Hoefflin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Daniel Kovarsky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Dor Simkin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shira Turgeman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Lingling Zhang
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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8
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Hitscherich K, Noussome D, Dinerman A, Dulemba V, Lowery F, Nilubol N. A Pan-Cancer Comparative Analysis of The Cancer Genome Atlas Transcriptomic TIL-Immune Signatures. RESEARCH SQUARE 2025:rs.3.rs-6441170. [PMID: 40313762 PMCID: PMC12045360 DOI: 10.21203/rs.3.rs-6441170/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2025]
Abstract
Efforts to understand the tumor microenvironment (TME) through basic science research and The Cancer Genome Atlas (TCGA) data analysis have led to the creation of unique immune transcriptomic signatures from tumor-infiltrating lymphocytes (TIL). However, no pan-cancer analysis has been conducted to compare the prognostic performance of these signatures using overall survival (OS) or progression-free interval (PFI) as endpoints. We compiled a library of 146 TIL-immune signatures and evaluated gene signature score correlation with OS and PFI for 9,961 available TCGA samples across 33 cancer types. Zhang CD8 TCS demonstrated higher accuracy in prognosticating both OS and PFI across the pan-cancer landscape, however, variability was seen across cancer types and germ cell origin. Cluster analysis compiled a group of six signatures (Oh.Cd8.MAIT, Grog.8KLRB1, Oh.TIL_CD4.GZMK, Grog.CD4.TCF7, Oh.CD8.RPL, Grog.CD4.RPL32) whose association with OS and PFI could potentially be conserved across multiple cancer types.
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Lim SH, An M, Lee H, Heo YJ, Min BH, Mehta A, Wright S, Kim KM, Kim ST, Klempner SJ, Lee J. Determinants of Response to Sequential Pembrolizumab with Trastuzumab plus Platinum/5-FU in HER2-Positive Gastric Cancer: A Phase II Chemoimmunotherapy Trial. Clin Cancer Res 2025; 31:1476-1490. [PMID: 40100100 PMCID: PMC11995005 DOI: 10.1158/1078-0432.ccr-24-3528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Revised: 12/16/2024] [Accepted: 02/10/2025] [Indexed: 03/20/2025]
Abstract
PURPOSE Adding pembrolizumab to first-line fluoropyrimidine (5-FU)/platinum chemotherapy plus trastuzumab improves outcomes in advanced HER2+ gastroesophageal adenocarcinomas, but the benefit is largely confined to dual HER2+ and PD-L1+ patients. To assess the contributions of components, we conducted a phase II trial evaluating 5-FU/platinum/trastuzumab and added pembrolizumab in cycle 2 in patients with metastatic HER2+ disease. PATIENTS AND METHODS Treatment-naïve patients with advanced HER2+ gastroesophageal cancer underwent a baseline biopsy and received a single dose of 5-FU/platinum with trastuzumab followed by repeat biopsy. Pembrolizumab was added, and a third biopsy was performed after six cycles. The primary endpoint was the objective response rate. Secondary endpoints included progression-free and overall survival. Exploratory biomarker analysis and dynamic changes in HER2 and PD-L1 were prespecified. RESULTS Sixteen patients were enrolled. The objective response rate was 69%, and the median progression-free survival was 11.9 months. Serial whole-exome, single-cell RNA, T-cell receptor sequencing, and spatial transcriptomics from pretreatment and on-treatment samples revealed early trastuzumab-induced NK cell infiltration in HER2+ tumor beds and an increase in Fc receptor gamma III expression in macrophages, suggesting that trastuzumab directs Fc receptor-mediated antibody-dependent cytotoxicity. This favorable remodeling was enhanced by the addition of pembrolizumab, primarily in PD-L1+ samples. We observed TGF-β signaling in HER2-negative tumor regions, which was associated with nonresponder status. CONCLUSIONS These data highlight the biology of intratumoral heterogeneity and the impact of tumor and immune cell features on clinical outcomes and may partly explain the lesser magnitude of pembrolizumab benefit in HER2+ and PD-L1-negative subgroups.
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Affiliation(s)
- Sung Hee Lim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Minae An
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyuk Lee
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | | | - Byung-Hoon Min
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Arnav Mehta
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Samuel Wright
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Kyoung-Mee Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seung Tae Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Samuel J. Klempner
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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10
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Li H, Zandberg DP, Kulkarni A, Chiosea SI, Santos PM, Isett BR, Joy M, Sica GL, Contrera KJ, Tatsuoka CM, Brand M, Duvvuri U, Kim S, Kubik M, Sridharan S, Tu F, Chen J, Bruno TC, Vignali DAA, Cillo AR, Bao R, Wang JH, Vujanovic L, Ferris RL. Distinct CD8 + T cell dynamics associate with response to neoadjuvant cancer immunotherapies. Cancer Cell 2025; 43:757-775.e8. [PMID: 40086437 DOI: 10.1016/j.ccell.2025.02.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 07/30/2024] [Accepted: 02/24/2025] [Indexed: 03/16/2025]
Abstract
We leverage a clinical trial (NCT04080804) that compared neoadjuvant anti-PD-1, anti-PD-1+CTLA-4, and anti-PD-1+LAG-3 therapies in head and neck squamous cell carcinoma patients. Combination therapies promote higher pathologic response rates versus monotherapy, and major pathologic response is associated with better survival. To address whether successful immune checkpoint inhibitor (ICI) regimens act through similar or distinct pathways, we robustly and longitudinally characterize transcriptional and proteomic dynamics of CD8+ tumor-infiltrating lymphocytes (TILs) in a clonal manner. Anti-PD-1+LAG-3 reprograms CD8+ TIL with type-I interferon response and exhaustion gene programs into effector memory and resident memory (TEM/TRM). In contrast, anti-PD-1+CTLA-4 activates and expands pre-existing TEM/TRM CD8+ TIL, but does not rejuvenate exhausted phenotypes into T effector cells. Anti-PD-1+LAG-3, but not anti-PD-1+CTLA-4, induces widespread TCR sharing among the different transcriptional states, as well as increased TCR diversity in responding patients. Our data suggest doublet regimen-specific transcriptional and clonal dynamics of tumor-reactive CD8+ T cells.
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Affiliation(s)
- Housaiyin Li
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Molecular Genetics and Development Biology Graduate Program, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dan P Zandberg
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Aditi Kulkarni
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Simion I Chiosea
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Patricia M Santos
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Brian R Isett
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Marion Joy
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Gabriel L Sica
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kevin J Contrera
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Curtis M Tatsuoka
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Biostatistics Facility, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Matthias Brand
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Umamaheswar Duvvuri
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Otolaryngology, NYU Grossman School of Medicine, New York, NY, USA
| | - Seungwon Kim
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mark Kubik
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shaum Sridharan
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Fei Tu
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jie Chen
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Molecular Genetics and Development Biology Graduate Program, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tullia C Bruno
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA; Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Dario A A Vignali
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA; Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Anthony R Cillo
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA; Center for Systems Immunology, University of Pittsburgh, Pittsburgh, PA, USA; Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Riyue Bao
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jing Hong Wang
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA; Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Lazar Vujanovic
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Robert L Ferris
- UNC Lineberger Comprehensive Cancer Center, UNC Health Care System, Chapel Hill, NC, USA.
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11
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Moravec Ž, Haanen JBAG, Schumacher TN, Scheper W. Learning the language of T cell receptors through large-scale screening. Cancer Cell 2025:S1535-6108(25)00133-3. [PMID: 40250445 DOI: 10.1016/j.ccell.2025.03.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2025] [Revised: 03/24/2025] [Accepted: 03/28/2025] [Indexed: 04/20/2025]
Abstract
T cells perform critical roles in orchestrating immunity in health and disease. However, decoding what individual T cells recognize has long been challenging due to the immense diversity of both T cell receptors (TCRs) and potential antigens. Recent advances in high-throughput TCR screening approaches now provide an opportunity to map the antigen specificity landscape of T cells with unprecedented depth. Here, we outline these recent developments in screening methodologies and discuss how these can help advance our fundamental understanding of T cell-based immunity.
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Affiliation(s)
- Živa Moravec
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - John B A G Haanen
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ton N Schumacher
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands; Oncode Institute, Utrecht, the Netherlands.
| | - Wouter Scheper
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands.
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12
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Goff SL, Rosenberg SA. Tumor-infiltrating lymphocyte immunotherapy comes of age: a journey of development in the Surgery Branch, NCI. J Immunother Cancer 2025; 13:e011734. [PMID: 40210239 PMCID: PMC11987153 DOI: 10.1136/jitc-2025-011734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2025] [Accepted: 04/01/2025] [Indexed: 04/12/2025] Open
Abstract
The early development of tumor-infiltrating lymphocytes into an effective clinical strategy was fundamentally the work of hundreds of scientists and clinicians within the Surgery Branch of the National Cancer Institute under the leadership of Steven Rosenberg. That journey brought new insights into the tumor-immune cell interface and ultimately helped create a new first-in-class therapeutic for patients with metastatic cancer.
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Affiliation(s)
- Stephanie L Goff
- Surgery Branch, National Cancer Institute Center for Cancer Research, Bethesda, Maryland, USA
| | - Steven A Rosenberg
- Surgery Branch, National Cancer Institute Center for Cancer Research, Bethesda, Maryland, USA
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13
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Li X, Nguyen J, Korkut A. Recurrent Composite Markers of Cell Types and States. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2023.07.17.549344. [PMID: 37503180 PMCID: PMC10370072 DOI: 10.1101/2023.07.17.549344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Biological function is mediated by the hierarchical organization of cell types and states within tissue ecosystems. Identifying interpretable composite marker sets that both define and distinguish hierarchical cell identities is essential for decoding biological complexity, yet remains a major challenge. Here, we present RECOMBINE, an algorithm that identifies recurrent composite marker sets to define hierarchical cell identities. Validation using both simulated and biological datasets demonstrates that RECOMBINE achieves higher accuracy in identifying discriminative markers compared to existing approaches, including differential gene expression analysis. When applied to single-cell data and validated with spatial transcriptomics data from the mouse visual cortex, RECOMBINE identified key cell type markers and generated a robust gene panel for targeted spatial profiling. It also uncovered markers of CD8+; T cell states, including GZMK+;HAVCR2-; effector memory cells associated with anti-PD-1 therapy response, and revealed a rare intestinal subpopulation with composite markers in mice. Finally, using data from the Tabula Sapiens project, RECOMBINE identified composite marker sets across a broad range of human tissues. Together, these results highlight RECOMBINE as a robust, data-driven framework for optimized marker selection, enabling the discovery and validation of hierarchical cell identities across diverse tissue contexts.
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14
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Lowery FJ, Goff SL, Gasmi B, Parkhurst MR, Ratnam NM, Halas HK, Shelton TE, Langhan MM, Bhasin A, Dinerman AJ, Dulemba V, Goldlust IS, Gustafson AM, Hakim AA, Hitscherich KJ, Kenney LM, Levy L, Rault-Wang JG, Bera A, Ray S, Seavey CD, Hoang CD, Hernandez JM, Gartner JJ, Sindiri S, Prickett TD, McIntyre LS, Krishna S, Robbins PF, Klemen ND, Kwong MLM, Yang JC, Rosenberg SA. Neoantigen-specific tumor-infiltrating lymphocytes in gastrointestinal cancers: a phase 2 trial. Nat Med 2025:10.1038/s41591-025-03627-5. [PMID: 40169866 DOI: 10.1038/s41591-025-03627-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Accepted: 03/03/2025] [Indexed: 04/03/2025]
Abstract
Adoptive transfer of unselected autologous tumor-infiltrating lymphocytes (TILs) has mediated meaningful clinical responses in patients with metastatic melanoma but not in cancers of gastrointestinal epithelial origin. In an evolving single-arm phase 2 trial design, TILs were derived from and administered to 91 patients with treatment-refractory mismatch repair proficient metastatic gastrointestinal cancers in a schema with lymphodepleting chemotherapy and high-dose interleukin-2 (three cohorts of an ongoing trial). The primary endpoint of this study was the objective response rate as measured using Response Evaluation Criteria in Solid Tumors 1.0; safety was a descriptive secondary endpoint. In the pilot phase, no clinical responses were observed in 18 patients to bulk, unselected TILs; however, when TILs were screened and selected for neoantigen recognition (SEL-TIL), three responses were seen in 39 patients (7.7% (95% confidence interval (CI): 2.7-20.3)). Based on the high levels of programmed cell death protein 1 in the infused TILs, pembrolizumab was added to the regimen (SEL-TIL + P), and eight objective responses were seen in 34 patients (23.5% (95% CI: 12.4-40.0)). All patients experienced transient severe hematologic toxicities from chemotherapy. Seven (10%) patients required critical care support. Exploratory analyses for laboratory and clinical correlates of response were performed for the SEL-TIL and SEL-TIL + P treatment arms. Response was associated with recognition of an increased number of targeted neoantigens and an increased number of administered CD4+ neoantigen-reactive TILs. The current strategy (SEL-TIL + P) exceeded the parameters of the trial design for patients with colorectal cancer, and an expansion phase is accruing. These results could potentially provide a cell-based treatment in a population not traditionally expected to respond to immunotherapy. ClinicalTrials.gov identifier: NCT01174121 .
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Affiliation(s)
- Frank J Lowery
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Stephanie L Goff
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA.
| | - Billel Gasmi
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Maria R Parkhurst
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Nivedita M Ratnam
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Hyunmi K Halas
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Thomas E Shelton
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Michelle M Langhan
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Aarushi Bhasin
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Aaron J Dinerman
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Victoria Dulemba
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Ian S Goldlust
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Alexandra M Gustafson
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Abraham A Hakim
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Kyle J Hitscherich
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Lisa M Kenney
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Lior Levy
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Juliette G Rault-Wang
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Alakesh Bera
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Satyajit Ray
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Courtney D Seavey
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Chuong D Hoang
- National Cancer Institute, Center for Cancer Research, Thoracic Surgery Branch, Bethesda, MD, USA
| | - Jonathan M Hernandez
- National Cancer Institute, Center for Cancer Research, Surgical Oncology Program, Bethesda, MD, USA
| | - Jared J Gartner
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Sivasish Sindiri
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Todd D Prickett
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Lori S McIntyre
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Sri Krishna
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Paul F Robbins
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Nicholas D Klemen
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Mei Li M Kwong
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - James C Yang
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA
| | - Steven A Rosenberg
- National Cancer Institute, Center for Cancer Research, Surgery Branch, Bethesda, MD, USA.
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15
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Martínez-Jiménez F, Chowell D. Genetic immune escape in cancer: timing and implications for treatment. Trends Cancer 2025; 11:286-294. [PMID: 39632211 PMCID: PMC11981860 DOI: 10.1016/j.trecan.2024.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2024] [Revised: 11/04/2024] [Accepted: 11/04/2024] [Indexed: 12/07/2024]
Abstract
Genetic immune escape (GIE) alterations pose a significant challenge in cancer by enabling tumors to evade immune detection. These alterations, which can vary significantly across cancer types, may often arise early in clonal evolution and contribute to malignant transformation. As tumors evolve, GIE alterations are positively selected, allowing immune-resistant clones to proliferate. In addition to genetic changes, the tumor microenvironment (TME) and non-genetic factors such as inflammation, smoking, and environmental exposures play crucial roles in promoting immune evasion. Understanding the timing and mechanisms of GIE, alongside microenvironmental influences, is crucial for improving early detection and developing more effective therapeutic interventions. This review highlights the implications of GIE in cancer development and immunotherapy resistance, and emphasizes the need for integrative approaches.
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Affiliation(s)
- Francisco Martínez-Jiménez
- Systems Oncology Program, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; Hartwig Medical Foundation, Amsterdam, The Netherlands.
| | - Diego Chowell
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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16
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Qin R, Zhang Y, Shi J, Wu P, An C, Li Z, Liu N, Wan Z, Hua T, Li X, Lou J, Yin W, Chen W. TCR catch bonds nonlinearly control CD8 cooperation to shape T cell specificity. Cell Res 2025; 35:265-283. [PMID: 40011760 PMCID: PMC11958657 DOI: 10.1038/s41422-025-01077-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 01/14/2025] [Indexed: 02/28/2025] Open
Abstract
Naturally evolved T-cell receptors (TCRs) exhibit remarkably high specificity in discriminating non-self antigens from self-antigens under dynamic biomechanical modulation. In contrast, engineered high-affinity TCRs often lose this specificity, leading to cross-reactivity with self-antigens and off-target toxicity. The underlying mechanism for this difference remains unclear. Our study reveals that natural TCRs exploit mechanical force to form optimal catch bonds with their cognate antigens. This process relies on a mechanically flexible TCR-pMHC binding interface, which enables force-enhanced CD8 coreceptor binding to MHC-α1α2 domains through sequential conformational changes induced by force in both the MHC and CD8. Conversely, engineered high-affinity TCRs create rigid, tightly bound interfaces with cognate pMHCs of their parental TCRs. This rigidity prevents the force-induced conformational changes necessary for optimal catch-bond formation. Paradoxically, these high-affinity TCRs can form moderate catch bonds with non-stimulatory pMHCs of their parental TCRs, leading to off-target cross-reactivity and reduced specificity. We have also developed comprehensive force-dependent TCR-pMHC kinetics-function maps capable of distinguishing functional and non-functional TCR-pMHC pairs and identifying toxic, cross-reactive TCRs. These findings elucidate the mechano-chemical basis of the specificity of natural TCRs and highlight the critical role of CD8 in targeting cognate antigens. This work provides valuable insights for engineering TCRs with enhanced specificity and potency against non-self antigens, particularly for applications in cancer immunotherapy and infectious disease treatment, while minimizing the risk of self-antigen cross-reactivity.
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Affiliation(s)
- Rui Qin
- Department of Cardiology of the Second Affiliated Hospital and Department of Cell Biology, Zhejiang University School of Medicine, Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yong Zhang
- State Key Laboratory of Epigenetic Regulation and Intervention, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiawei Shi
- Key Laboratory for Biomedical Engineering of the Ministry of Education, and Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, and College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Peng Wu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Chenyi An
- School of Biology and Engineering, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zhenhai Li
- Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Institute of Applied Mathematics and Mechanics, School of Mechanics and Engineering Science, Shanghai University, Shanghai, China
| | - Nuo Liu
- Department of Hematology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- National Key Laboratory of Immune Response and Immunotherapy & MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Ziyan Wan
- Department of Hematology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- National Key Laboratory of Immune Response and Immunotherapy & MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Ting Hua
- Department of Hematology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- National Key Laboratory of Immune Response and Immunotherapy & MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Xiaolong Li
- Department of Hematology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- National Key Laboratory of Immune Response and Immunotherapy & MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Jizhong Lou
- State Key Laboratory of Epigenetic Regulation and Intervention, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Weiwei Yin
- Key Laboratory for Biomedical Engineering of the Ministry of Education, and Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, and College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Wei Chen
- Department of Cardiology of the Second Affiliated Hospital and Department of Cell Biology, Zhejiang University School of Medicine, Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China.
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou, Zhejiang, China.
- MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University, Hangzhou, Zhejiang, China.
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17
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Rausch L, Kallies A. Molecular Mechanisms Governing CD8 T Cell Differentiation and Checkpoint Inhibitor Response in Cancer. Annu Rev Immunol 2025; 43:515-543. [PMID: 40279308 DOI: 10.1146/annurev-immunol-082223-044122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2025]
Abstract
CD8 T cells play a critical role in antitumor immunity. However, over time, they often become dysfunctional or exhausted and ultimately fail to control tumor growth. To effectively harness CD8 T cells for cancer immunotherapy, a detailed understanding of the mechanisms that govern their differentiation and function is crucial. This review summarizes our current knowledge of the molecular pathways that regulate CD8 T cell heterogeneity and function in chronic infection and cancer and outlines how T cells respond to therapeutic checkpoint blockade. We explore how T cell-intrinsic and -extrinsic factors influence CD8 T cell differentiation, fate choices, and functional states and ultimately dictate their response to therapy. Identifying cells that orchestrate long-term antitumor immunity and understanding the mechanisms that govern their development and persistence are critical steps toward improving cancer immunotherapy.
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Affiliation(s)
- Lisa Rausch
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia;
| | - Axel Kallies
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia;
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18
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Oh MS, Abascal J, Rennels AK, Salehi-Rad R, Dubinett SM, Liu B. Tumor Heterogeneity and the Immune Response in Non-Small Cell Lung Cancer: Emerging Insights and Implications for Immunotherapy. Cancers (Basel) 2025; 17:1027. [PMID: 40149360 PMCID: PMC11941341 DOI: 10.3390/cancers17061027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2024] [Revised: 03/13/2025] [Accepted: 03/15/2025] [Indexed: 03/29/2025] Open
Abstract
Resistance to immune checkpoint inhibitors (ICIs) represents a major challenge for the effective treatment of non-small cell lung cancer (NSCLC). Tumor heterogeneity has been identified as an important mechanism of treatment resistance in cancer and has been increasingly implicated in ICI resistance. The diversity and clonality of tumor neoantigens, which represent the target epitopes for tumor-specific immune cells, have been shown to impact the efficacy of immunotherapy. Advances in genomic techniques have further enhanced our understanding of clonal landscapes within NSCLC and their evolution in response to therapy. In this review, we examine the role of tumor heterogeneity during immune surveillance in NSCLC and highlight its spatial and temporal evolution as revealed by modern technologies. We explore additional sources of heterogeneity, including epigenetic and metabolic factors, that have come under greater scrutiny as potential mediators of the immune response. We finally discuss the implications of tumor heterogeneity on the efficacy of ICIs and highlight potential strategies for overcoming therapeutic resistance.
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Affiliation(s)
- Michael S. Oh
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (M.S.O.); (J.A.); (A.K.R.); (R.S.-R.); (S.M.D.)
| | - Jensen Abascal
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (M.S.O.); (J.A.); (A.K.R.); (R.S.-R.); (S.M.D.)
| | - Austin K. Rennels
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (M.S.O.); (J.A.); (A.K.R.); (R.S.-R.); (S.M.D.)
| | - Ramin Salehi-Rad
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (M.S.O.); (J.A.); (A.K.R.); (R.S.-R.); (S.M.D.)
- Department of Medicine, VA Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA
| | - Steven M. Dubinett
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (M.S.O.); (J.A.); (A.K.R.); (R.S.-R.); (S.M.D.)
- Department of Medicine, VA Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA
| | - Bin Liu
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (M.S.O.); (J.A.); (A.K.R.); (R.S.-R.); (S.M.D.)
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA
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19
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Raphael I, Xiong Z, Sneiderman CT, Raphael RA, Mash M, Schwegman L, Jackson SA, O'Brien C, Anderson KJ, Sever RE, Hendrikse LD, Vincze SR, Diaz A, Felker J, Nazarian J, Nechemia-Arbely Y, Hu B, Kammula US, Agnihotri S, Rich JN, Broniscer A, Drappatz J, Abel TJ, Uttam S, Hwang EI, Pearce TM, Taylor MD, Nisnboym M, Forsthuber TG, Pollack IF, Chikina M, Rajasundaram D, Kohanbash G. The T cell receptor landscape of childhood brain tumors. Sci Transl Med 2025; 17:eadp0675. [PMID: 40106578 DOI: 10.1126/scitranslmed.adp0675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 10/01/2024] [Accepted: 02/18/2025] [Indexed: 03/22/2025]
Abstract
The diverse T cell receptor (TCR) repertoire confers the ability to recognize an almost unlimited array of antigens. Characterization of antigen specificity of tumor-infiltrating lymphocytes (TILs) is key for understanding antitumor immunity and for guiding the development of effective immunotherapies. Here, we report a large-scale comprehensive examination of the TCR landscape of TILs across the spectrum of pediatric brain tumors, the leading cause of cancer-related mortality in children. We show that a T cell clonality index can inform patient prognosis, where more clonality is associated with more favorable outcomes. Moreover, TCR similarity groups' assessment revealed patient clusters with defined human leukocyte antigen associations. Computational analysis of these clusters identified putative tumor antigens and peptides as targets for antitumor T cell immunity, which were functionally validated by T cell stimulation assays in vitro. Together, this study presents a framework for tumor antigen prediction based on in situ and in silico TIL TCR analyses. We propose that TCR-based investigations should inform tumor classification and precision immunotherapy development.
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Affiliation(s)
- Itay Raphael
- Department of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Zujian Xiong
- Department of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Chaim T Sneiderman
- Department of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Rebecca A Raphael
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Moshe Mash
- Robotics Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Lance Schwegman
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Sydney A Jackson
- Department of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Casey O'Brien
- Division of Health Informatics, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Kevin J Anderson
- Division of Health Informatics, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - ReidAnn E Sever
- Department of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Liam D Hendrikse
- Arthur and Sonia Labatt Brain Tumor Research Centre, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Developmental & Stem Cell Biology Program, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Sarah R Vincze
- Department of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Aaron Diaz
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - James Felker
- Pediatric Neuro-Oncology Program, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Javad Nazarian
- Department of Pediatrics, University of Zurich, 8001 Zurich, Switzerland
| | - Yael Nechemia-Arbely
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Baoli Hu
- Department of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Udai S Kammula
- UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
- Division of Surgical Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Sameer Agnihotri
- Department of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Jeremy N Rich
- UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Alberto Broniscer
- Pediatric Neuro-Oncology Program, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Jan Drappatz
- Neuro-oncology Program, Division of Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Taylor J Abel
- Department of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Shikhar Uttam
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Eugene I Hwang
- Department of Pediatrics, Division of Oncology, Children's National Hospital, Washington, DC 20010, USA
| | - Thomas M Pearce
- Division of Neuropathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Michael D Taylor
- Arthur and Sonia Labatt Brain Tumor Research Centre, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Developmental & Stem Cell Biology Program, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 3K3, Canada
- Division of Neurosurgery, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Michal Nisnboym
- Department of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
- Neuro-oncology Program, Division of Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
- Department of Neurology, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
- Department of Neurosurgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Thomas G Forsthuber
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Ian F Pollack
- Department of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Maria Chikina
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Dhivyaa Rajasundaram
- Division of Health Informatics, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Gary Kohanbash
- Department of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15260, USA
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20
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Zhang Y, Yan L, Sun H, Zhang Z, Shen F, Sun L. Targeted Delivery of Personalized Cancer Vaccines Based on Antibody-Antigen Complexes. Vaccines (Basel) 2025; 13:324. [PMID: 40266219 PMCID: PMC11946472 DOI: 10.3390/vaccines13030324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2024] [Revised: 03/15/2025] [Accepted: 03/16/2025] [Indexed: 04/24/2025] Open
Abstract
BACKGROUND Personalized cancer vaccines based on tumor neoantigens show great potential in cancer immunotherapy due to their high safety and specificity. However, it is inherently difficult to realize the efficiently targeted delivery of personalized cancer vaccines to antigen-presenting cells (APCs). METHODS This study aimed to address these challenges by developing and evaluating a personalized cancer vaccine based on antibody-antigen complexes, which was designed to enhance antitumor effects by increasing the utilization of tumor neoantigens by APCs. Mice were immunized with a carrier protein, keyhole limpet hemocyanin (KLH), to induce the production of antibodies against KLH. Subsequently, mice were immunized with KLH loaded with tumor neoantigens and the immunoadjuvant CpG ODN and underwent immunological analysis to evaluate the immune and antitumor effects. RESULTS The results showed that preimmunization with KLH could promote the uptake of the personalized KLH-based tumor vaccine, which was enhanced by dendritic cells (DCs) and macrophages (Mφs), by strengthening the T-cell immune responses to tumors. CONCLUSIONS Collectively, this work provides a new idea for the targeted delivery of personalized cancer vaccines.
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Affiliation(s)
- Yaling Zhang
- School of Life Sciences, Shanghai University, Shanghai 200444, China (L.Y.)
| | - Lingling Yan
- School of Life Sciences, Shanghai University, Shanghai 200444, China (L.Y.)
| | - He Sun
- School of Life Sciences, Shanghai University, Shanghai 200444, China (L.Y.)
| | - Ziyi Zhang
- School of Life Sciences, Shanghai University, Shanghai 200444, China (L.Y.)
| | - Fengyun Shen
- Institute of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Lele Sun
- Institute of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
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21
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Lennerz V, Doppler C, Fatho M, Dröge A, Schaper S, Gennermann K, Genzel N, Plassmann S, Weismann D, Lukowski SW, Bents D, Beushausen C, Kriese K, Herbst H, Seitz V, Hammer R, Adam PJ, Eggeling S, Wölfel C, Wölfel T, Hennig S. T-cell receptors identified by a personalized antigen-agnostic screening approach target shared neoantigen KRAS Q61H. Front Immunol 2025; 16:1509855. [PMID: 40165973 PMCID: PMC11955635 DOI: 10.3389/fimmu.2025.1509855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Accepted: 02/27/2025] [Indexed: 04/02/2025] Open
Abstract
Adoptive cell therapy (ACT) with TCR-engineered T-cells represents a promising alternative to TIL- or CAR-T therapies for patients with advanced solid cancers. Currently, selection of therapeutic TCRs critically depends on knowing the target antigens, a condition excluding most patients from treatment. Direct antigen-agnostic identification of tumor-specific T-cell clonotypes and TCR-T manufacturing using their TCRs can advance ACT for patients with aggressive solid cancers. We present a method to identify tumor-specific clonotypes from surgical specimens by comparing TCRβ-chain repertoires of TILs and adjacent tissue-resident lymphocytes. In six out of seven NSCLC-patients analyzed, our selection of tumor-specific clonotypes based on TIL-abundance and high tumor-to-nontumor frequency ratios was confirmed by gene expression signatures determined by scRNA-Seq. In three patients, we demonstrated that predicted tumor-specific clonotypes reacted against autologous tumors. For one of these patients, we engineered TCR-T cells with four candidate tumor-specific TCRs that showed reactivity against the patient's tumor and HLA-matched NSCLC cell lines. The TCR-T cells were then used to screen for candidate neoantigens and aberrantly expressed antigens. Three TCRs recognized recurrent driver-mutation KRAS Q61H-peptide ILDTAGHEEY presented by HLA-A*01:01. The TCRs were also dominant in a tumor relapse, one was found in cell free DNA. The finding of homologous TCRs in independent KRAS Q61H-positive cancers suggests a therapeutic opportunity for HLA-matched patients with KRAS Q61H-expressing tumors.
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MESH Headings
- Humans
- Antigens, Neoplasm/immunology
- Antigens, Neoplasm/genetics
- Proto-Oncogene Proteins p21(ras)/genetics
- Proto-Oncogene Proteins p21(ras)/immunology
- Lung Neoplasms/immunology
- Lung Neoplasms/genetics
- Lung Neoplasms/therapy
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/genetics
- Immunotherapy, Adoptive/methods
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Carcinoma, Non-Small-Cell Lung/immunology
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/therapy
- Precision Medicine
- Mutation
- Female
- Male
- Middle Aged
- T-Lymphocytes/immunology
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Affiliation(s)
- Volker Lennerz
- Internal Medicine III, University Medical Center (UMC) of the Johannes Gutenberg University Mainz, Mainz, Germany
- HSDiagnomics GmbH, Berlin, Germany
- TheryCell GmbH, Berlin, Germany
| | - Christoph Doppler
- Internal Medicine III, University Medical Center (UMC) of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Martina Fatho
- Internal Medicine III, University Medical Center (UMC) of the Johannes Gutenberg University Mainz, Mainz, Germany
| | | | | | | | | | | | - David Weismann
- Boehringer Ingelheim RCV, GmbH & Co KG., Cancer Immunology & Immune Modulation, Vienna, Austria
| | - Samuel W. Lukowski
- Boehringer Ingelheim RCV, GmbH & Co KG., Cancer Immunology & Immune Modulation, Vienna, Austria
| | | | | | - Karen Kriese
- Vivantes Pathology, Vivantes Clinic Neukölln, Berlin, Germany
| | - Hermann Herbst
- Vivantes Pathology, Vivantes Clinic Neukölln, Berlin, Germany
| | | | - Rudolf Hammer
- HSDiagnomics GmbH, Berlin, Germany
- TheryCell GmbH, Berlin, Germany
| | - Paul J. Adam
- Boehringer Ingelheim RCV, GmbH & Co KG., Cancer Immunology & Immune Modulation, Vienna, Austria
| | - Stephan Eggeling
- Vivantes Clinic Neukölln, Vivantes Thoracic Surgery, Berlin, Germany
| | - Catherine Wölfel
- Internal Medicine III, University Medical Center (UMC) of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Thomas Wölfel
- Internal Medicine III, University Medical Center (UMC) of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Steffen Hennig
- HSDiagnomics GmbH, Berlin, Germany
- TheryCell GmbH, Berlin, Germany
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22
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Xia X, He C, Xue Z, Wang Y, Qin Y, Ren Z, Huang Y, Luo H, Chen HN, Zhang WH, Huang LB, Shi Y, Bai Y, Cai B, Wang L, Zhang F, Qian M, Zhang W, Shu Y, Yin G, Xu H, Xie Q. Single cell immunoprofile of synovial fluid in rheumatoid arthritis with TNF/JAK inhibitor treatment. Nat Commun 2025; 16:2152. [PMID: 40038288 PMCID: PMC11880340 DOI: 10.1038/s41467-025-57361-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 02/20/2025] [Indexed: 03/06/2025] Open
Abstract
Numerous patients with rheumatoid arthritis (RA) manifest severe syndromes, including elevated synovial fluid volumes (SF) with abundant immune cells, which can be controlled by TNF/JAK inhibitors. Here, we apply single-cell RNA sequencing (scRNA-seq) and subsequent validations in SF from RA patients. These analyses of synovial tissue show reduced density of SF-derived pathogenic cells (e.g., SPP1+ macrophages and CXCL13+CD4+ T cells), altered gene expression (e.g., SPP1 and STAT1), molecular pathway changes (e.g., JAK/STAT), and cell-cell communications in drug-specific manners in samples from patients pre-/post-treated with adalimumab/tofacitinib. Particularly, SPP1+ macrophages exhibit pronounced communication with CXCL13+CD4+ T cells, which are abolished after treatment and correlate with treatment efficacy. These pathogenic cell types alone or in combination can augment inflammation of fibroblast-like synoviocytes in vitro, while conditional Spp1 knocking-out reduces RA-related cytokine expression in collagen-induced arthritis mice models. Our study shows the functional role of SF-derived pathogenic cells in progression and drug-specific treatment outcomes in RA.
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Affiliation(s)
- Xuyang Xia
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Laboratory Medicine/Research Centre of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Division of Gastrointestinal Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chenjia He
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhinan Xue
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yuelan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yun Qin
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhixiang Ren
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yupeng Huang
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Han Luo
- Division of Thyroid Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hai-Ning Chen
- Colorectal Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Institute of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wei-Han Zhang
- Institute of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Gastric Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Li-Bin Huang
- Division of Gastrointestinal Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Institute of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yunying Shi
- Department of Nephrology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yangjuan Bai
- Department of Laboratory Medicine/Research Centre of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Bei Cai
- Department of Laboratory Medicine/Research Centre of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lanlan Wang
- Department of Laboratory Medicine/Research Centre of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Feng Zhang
- Center for Precision Medicine, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, Zhejiang, China
| | - Maoxiang Qian
- Institute of Pediatrics and Department of Hematology and Oncology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Wei Zhang
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yang Shu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Institute of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Gastric Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Geng Yin
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
- Department of General Practice, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Heng Xu
- Department of Laboratory Medicine/Research Centre of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
- Institute of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
- Tianfu Jincheng Laboratory, Chengdu, Sichuan, China.
| | - Qibing Xie
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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23
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Liang Z, Li S, Pan Z, Duan Y, Ouyang Q, Zhu L, Song E, Chen K. Profiling Multiple CD8+ T-cell Functional Dimensions Enhances Breast Cancer Immune Assessment. Cancer Immunol Res 2025; 13:337-352. [PMID: 39715293 DOI: 10.1158/2326-6066.cir-24-0235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 08/19/2024] [Accepted: 12/20/2024] [Indexed: 12/25/2024]
Abstract
CD8+ T-cell abundance is insufficient to assess antitumor immunity and shows poor performance in predicting breast cancer prognosis and immunotherapy response, presumably owing to the complexity of CD8+ T-cell functionalities. Although single-cell RNA sequencing can dissect the multifaceted functions of CD8+ T cells for better immune assessment, its clinical application is limited. In this study, we developed bulk RNA sequencing-based FuncDimen models from integrative analysis of single-cell RNA sequencing and matched bulk RNA sequencing data to evaluate CD8+ T-cell functionalities across five dimensions: tumor reactivity, cytotoxicity, IFNγ secretion, proliferation, and apoptosis. The FuncDimen models quantifying different functional dimensions of CD8+ T cells were validated in our breast cancer cohort and external databases using immunofluorescence and imaging mass cytometry. We calculated the FuncAggre score by weighted aggregation of all five FuncDimen models to encapsulate the overall antitumor immunity. In our breast cancer cohort and external databases, the FuncAggre score demonstrated superior predictive performance for breast cancer prognosis (time-dependent AUC: 0.56-0.70) and immunotherapy response (AUC: 0.71-0.83) over other immune biomarkers, regardless of the breast cancer molecular subtype. Together, the FuncDimen models offer a refined assessment of antitumor immunity mediated by CD8+ T cells in the clinic, enhancing prognostic prediction and aiding personalized immunotherapy in breast cancer.
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Affiliation(s)
- Zhuozhi Liang
- School of Basic Medical Science, Southern Medical University, Guangzhou, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Zenith Institute of Medical Sciences, Guangzhou, China
| | - Shunrong Li
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Zhilong Pan
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yuanqiang Duan
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Qian Ouyang
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Liling Zhu
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Erwei Song
- School of Basic Medical Science, Southern Medical University, Guangzhou, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Zenith Institute of Medical Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Kai Chen
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Artificial Intelligence Lab, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Shenshan Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Shanwei, Guangdong, China
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24
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Pétremand R, Chiffelle J, Bobisse S, Perez MAS, Schmidt J, Arnaud M, Barras D, Lozano-Rabella M, Genolet R, Sauvage C, Saugy D, Michel A, Huguenin-Bergenat AL, Capt C, Moore JS, De Vito C, Labidi-Galy SI, Kandalaft LE, Dangaj Laniti D, Bassani-Sternberg M, Oliveira G, Wu CJ, Coukos G, Zoete V, Harari A. Identification of clinically relevant T cell receptors for personalized T cell therapy using combinatorial algorithms. Nat Biotechnol 2025; 43:323-328. [PMID: 38714897 PMCID: PMC11919687 DOI: 10.1038/s41587-024-02232-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/02/2024] [Indexed: 06/27/2024]
Abstract
A central challenge in developing personalized cancer cell immunotherapy is the identification of tumor-reactive T cell receptors (TCRs). By exploiting the distinct transcriptomic profile of tumor-reactive T cells relative to bystander cells, we build and benchmark TRTpred, an antigen-agnostic in silico predictor of tumor-reactive TCRs. We integrate TRTpred with an avidity predictor to derive a combinatorial algorithm of clinically relevant TCRs for personalized T cell therapy and benchmark it in patient-derived xenografts.
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Affiliation(s)
- Rémy Pétremand
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Johanna Chiffelle
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Sara Bobisse
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Marta A S Perez
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Molecular Modelling Group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Julien Schmidt
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
- Center of Experimental Therapeutics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Marion Arnaud
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - David Barras
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Maria Lozano-Rabella
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Raphael Genolet
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Christophe Sauvage
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Damien Saugy
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Alexandra Michel
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Anne-Laure Huguenin-Bergenat
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Charlotte Capt
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Jonathan S Moore
- Department of Medicine and Center of Translational Research in Onco-Hematology, Faculty of Medicine, University of Geneva, Swiss Cancer Center Leman, Geneva, Switzerland
| | - Claudio De Vito
- Division of Clinical Pathology, Department of Diagnostics, Hôpitaux Universitaires de Genève, Geneva, Switzerland
| | - S Intidhar Labidi-Galy
- Department of Medicine and Center of Translational Research in Onco-Hematology, Faculty of Medicine, University of Geneva, Swiss Cancer Center Leman, Geneva, Switzerland
- Department of Oncology, Hôpitaux Universitaires de Genève, Geneva, Switzerland
| | - Lana E Kandalaft
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
- Center of Experimental Therapeutics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Denarda Dangaj Laniti
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
- Center of Experimental Therapeutics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Giacomo Oliveira
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Catherine J Wu
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - George Coukos
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
- Immuno-oncology Service, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Vincent Zoete
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Molecular Modelling Group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Alexandre Harari
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland.
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland.
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25
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Lopez de Rodas M, Villalba-Esparza M, Sanmamed MF, Chen L, Rimm DL, Schalper KA. Biological and clinical significance of tumour-infiltrating lymphocytes in the era of immunotherapy: a multidimensional approach. Nat Rev Clin Oncol 2025; 22:163-181. [PMID: 39820025 DOI: 10.1038/s41571-024-00984-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2024] [Indexed: 01/19/2025]
Abstract
Immune-checkpoint inhibitors (ICIs) have improved clinical outcomes across several solid tumour types. Prominent efforts have focused on understanding the anticancer mechanisms of these agents, identifying biomarkers of response and uncovering resistance mechanisms to develop new immunotherapeutic approaches. This research has underscored the crucial roles of the tumour microenvironment and, particularly, tumour-infiltrating lymphocytes (TILs) in immune-mediated tumour elimination. Numerous studies have evaluated the prognostic and predictive value of TILs and the mechanisms that govern T cell dysfunction, fuelled by technical developments in single-cell transcriptomics, proteomics, high-dimensional spatial platforms and advanced computational models. However, questions remain regarding the definition of TILs, optimal strategies to study them, specific roles of different TIL subpopulations and their clinical implications in different treatment contexts. Additionally, most studies have focused on the abundance of major TIL subpopulations but have not developed standardized quantification strategies or analysed other crucial aspects such as their functional profile, spatial distribution and/or arrangement, tumour antigen-reactivity, clonal diversity and heterogeneity. In this Review, we discuss a conceptual framework for the systematic study of TILs and summarize the evidence regarding their biological properties and biomarker potential for ICI therapy. We also highlight opportunities, challenges and strategies to support future developments in this field.
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Affiliation(s)
- Miguel Lopez de Rodas
- Department of Pathology and Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Cancer Center Clinica Universidad de Navarra, Pamplona, Navarra, Spain
| | - Maria Villalba-Esparza
- Department of Pathology and Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Miguel F Sanmamed
- Department of Immunology and Immunotherapy, Centro de Investigación Médica Aplicada and Clínica Universidad de Navarra, Pamplona, Navarra, Spain
| | - Lieping Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - David L Rimm
- Department of Pathology and Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Kurt A Schalper
- Department of Pathology and Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA.
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26
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Afeyan AB, Wu CJ, Oliveira G. Rapid parallel reconstruction and specificity screening of hundreds of T cell receptors. Nat Protoc 2025; 20:539-586. [PMID: 39516267 PMCID: PMC11896752 DOI: 10.1038/s41596-024-01061-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 08/06/2024] [Indexed: 11/16/2024]
Abstract
The ability to screen the reactivity of T cell receptors (TCRs) is essential to understanding how antigen-specific T cells drive productive or dysfunctional immune responses during infections, cancer and autoimmune diseases. Methods to profile large numbers of TCRs are critical for characterizing immune responses sustained by diverse T cell clones. Here we provide a medium-throughput approach to reconstruct dozens to hundreds of TCRs in parallel, which can be simultaneously screened against primary human tissues and broad curated panels of antigenic targets. Using Gibson assembly and miniaturized lentiviral transduction, individual TCRs are rapidly cloned and expressed in T cells; before screening, TCR cell lines undergo combinatorial labeling with dilutions of three fluorescent dyes, which allows retrieval of the identity of individual T cell effectors when they are organized and tested in pools using flow cytometry. Upon incubation with target cells, we measure the upregulation of CD137 on T cells as a readout of TCR activation. This approach is scalable and simultaneously captures the reactivity of pooled TCR cell lines, whose activation can be deconvoluted in real time, thus providing a path for screening the reactivity of dozens of TCRs against broad panels of synthetic antigens or against cellular targets, such as human tumor cells. We applied this pipeline to systematically deconvolute the antitumoral and antiviral reactivity and antigenic specificity of TCRs from human tumor-infiltrating lymphocytes. This protocol takes ~2 months, from experimental design to data analysis, and requires standard expertise in cloning, cell culture and flow cytometry.
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Affiliation(s)
- Alexander B Afeyan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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27
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Shoushtari AN, Powell DJ. Tumor-Infiltrating Lymphocyte Therapy for Melanoma and Other Solid Tumors: Looking Back, Yet Moving Forward. Transplant Cell Ther 2025; 31:S581-S590. [PMID: 40089327 DOI: 10.1016/j.jtct.2024.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Accepted: 11/24/2024] [Indexed: 03/17/2025]
Abstract
Lifileucel, the first solid tumor adoptive tumor infiltrating lymphocyte (TIL) therapy product to receive regulatory approval in advanced melanoma, represents a critical achievement in the pursuit of improving outcomes using cellular therapies in patients with solid tumors. This review traces the development of adoptive TIL therapy from the initial human studies in melanoma, through recent advances in studies of other solid tumors, and previews ongoing and future areas for preclinical and clinical advances to improve upon this novel therapeutic strategy.
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Affiliation(s)
- Alexander N Shoushtari
- Memorial Sloan Kettering Cancer Center, New York, New York; Weill Cornell Medical College, New York, New York.
| | - Daniel J Powell
- University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
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28
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Echchannaoui H, Legscha KJ, Theobald M. Tumor-Infiltrating Lymphocytes, CAR-, and T-Cell Receptor-Modified T Cells in Solid Cancer Oncology. Oncol Res Treat 2025; 48:294-304. [PMID: 39938499 DOI: 10.1159/000543998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Accepted: 11/18/2024] [Indexed: 02/14/2025]
Abstract
BACKGROUND Adoptive cellular therapy (ACT) is a promising treatment approach aiming at enhancing T-cell antitumor immune response. ACT includes tumor-infiltrating lymphocytes, chimeric antigen receptor (CAR) and T-cell receptor gene-modified T cells. Despite a milestone achievement with CAR-T cells in hematopoietic malignancies, ACT has shown modest clinical responses in refractory solid cancers and durable responses remain limited to a minor fraction of patients. SUMMARY In this review, we highlight major advances, limitations and current developments of T-cell therapies for solid cancers. We discuss emerging promising strategies as next-generation ACT, exploring local delivery routes to maximize efficacy and improve safety, integrating predictive biomarkers to optimize selection of patients who most likely would benefit from ACT, using combination therapy to overcome the immunosuppressive tumor microenvironment, targeting multiple tumor antigen to avoid tumor antigen escape, selection of the most potent T-cell product to overcome T-cell dysfunction, and incorporating cutting-edge new technologies, such as gene-editing to further improve antitumor T-cell functions and reduce therapy-related toxicity. KEY MESSAGES Advances made in ACT trials have move the field of immunotherapy for refractory solid cancers to a new stage, by constantly incorporating new strategies to develop next-generation therapies designed to enhance efficacy and improve safety and to allow a broaden access to a large numbers of patients.
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Affiliation(s)
- Hakim Echchannaoui
- Department of Hematology and Medical Oncology, University Cancer Center (UCT), University Medical Center (UMC) of the Johannes Gutenberg University, Mainz, Germany
- German Cancer Consortium (DKTK), Partner site Frankfurt/Mainz, Mainz, Germany
- Institute for Immunology and Research Center for Immunotherapy, UMC of the Johannes Gutenberg University, Mainz, Germany
| | - Kevin Jan Legscha
- Department of Hematology and Medical Oncology, University Cancer Center (UCT), University Medical Center (UMC) of the Johannes Gutenberg University, Mainz, Germany
- German Cancer Consortium (DKTK), Partner site Frankfurt/Mainz, Mainz, Germany
| | - Matthias Theobald
- Department of Hematology and Medical Oncology, University Cancer Center (UCT), University Medical Center (UMC) of the Johannes Gutenberg University, Mainz, Germany
- German Cancer Consortium (DKTK), Partner site Frankfurt/Mainz, Mainz, Germany
- Institute for Immunology and Research Center for Immunotherapy, UMC of the Johannes Gutenberg University, Mainz, Germany
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29
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Lutz R, Poos AM, Solé-Boldo L, John L, Wagner J, Prokoph N, Baertsch MA, Vonficht D, Palit S, Brobeil A, Mechtersheimer G, Hildenbrand N, Hemmer S, Steiger S, Horn S, Pepke W, Spranz DM, Rehnitz C, Sant P, Mallm JP, Friedrich MJ, Reichert P, Huhn S, Trumpp A, Rippe K, Haghverdi L, Fröhling S, Müller-Tidow C, Hübschmann D, Goldschmidt H, Willimsky G, Sauer S, Raab MS, Haas S, Weinhold N. Bone marrow breakout lesions act as key sites for tumor-immune cell diversification in multiple myeloma. Sci Immunol 2025; 10:eadp6667. [PMID: 39919199 DOI: 10.1126/sciimmunol.adp6667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 01/03/2025] [Indexed: 02/09/2025]
Abstract
The bone marrow microenvironment plays a crucial role in the development of multiple myeloma. As the disease progresses, malignant myeloma cells can evolve to survive outside the bone marrow. However, the processes underlying bone marrow independence and their consequences for immune control remain poorly understood. Here, we conducted single-cell and spatial multiomics analyses of bone marrow-confined intramedullary disease and paired breakout lesions that disrupt the cortical bone. These analyses revealed a distinct cellular microenvironment and architectural features of breakout lesions, characterized by extensive areas of malignant plasma cells interspersed with lesion-specific solitary natural killer and macrophage populations, as well as focal accumulations of immune cell agglomerates. Within these agglomerates, spatially confined T cell clones expanded alongside various immune cells, coinciding with the local genomic evolution of tumor cells. These analyses identify breakout lesions as a hotspot for tumor-immune cell interactions and diversification, representing a key event in myeloma pathogenesis.
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Affiliation(s)
- Raphael Lutz
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexandra M Poos
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Llorenç Solé-Boldo
- Berlin Institute of Health (BIH) at Charité Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine, Berlin, Germany
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
| | - Lukas John
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johanna Wagner
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
| | - Nina Prokoph
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marc A Baertsch
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominik Vonficht
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Subarna Palit
- Berlin Institute of Health (BIH) at Charité Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine, Berlin, Germany
| | - Alexander Brobeil
- Department of Pathology, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
- Tissue Bank of the National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Gunhild Mechtersheimer
- Department of Pathology, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Nina Hildenbrand
- Department of Orthopaedics, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Stefan Hemmer
- Department of Orthopaedics, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Simon Steiger
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Sabrina Horn
- Berlin Institute of Health (BIH) at Charité Universitätsmedizin Berlin, Berlin, Germany
- Institute of Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Wojciech Pepke
- Department of Orthopaedics, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - David M Spranz
- Department of Orthopaedics, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Christoph Rehnitz
- Department of Radiology, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Pooja Sant
- Single Cell Open Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan-Philipp Mallm
- Single Cell Open Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mirco J Friedrich
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Philipp Reichert
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Stefanie Huhn
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Andreas Trumpp
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Laleh Haghverdi
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Carsten Müller-Tidow
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Daniel Hübschmann
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Computational Oncology, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hartmut Goldschmidt
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
- GMMG-Study Group at Heidelberg University Hospital, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Gerald Willimsky
- Berlin Institute of Health (BIH) at Charité Universitätsmedizin Berlin, Berlin, Germany
- Institute of Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sandra Sauer
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Marc S Raab
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simon Haas
- Berlin Institute of Health (BIH) at Charité Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine, Berlin, Germany
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany
| | - Niels Weinhold
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
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30
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Zeng Z, Zhang T, Zhang J, Li S, Connor S, Zhang B, Zhao Y, Wilson J, Singh D, Kulikauskas R, Church CD, Pulliam TH, Jani S, Nghiem P, Topalian SL, Forde PM, Pardoll DM, Ji H, Smith KN. A minimal gene set characterizes TIL specific for diverse tumor antigens across different cancer types. Nat Commun 2025; 16:1070. [PMID: 39900903 PMCID: PMC11791090 DOI: 10.1038/s41467-024-55059-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 11/27/2024] [Indexed: 02/05/2025] Open
Abstract
Identifying tumor-specific T cell clones that mediate immunotherapy responses remains challenging. Mutation-associated neoantigen (MANA) -specific CD8+ tumor-infiltrating lymphocytes (TIL) have been shown to express high levels of CXCL13 and CD39 (ENTPD1), and low IL-7 receptor (IL7R) levels in many cancer types, but their collective relevance to T cell functionality has not been established. Here we present an integrative tool to identify MANA-specific TIL using weighted expression levels of these three genes in lung cancer and melanoma single-cell RNAseq datasets. Our three-gene "MANAscore" algorithm outperforms other RNAseq-based algorithms in identifying validated neoantigen-specific CD8+ clones, and accurately identifies TILs that recognize other classes of tumor antigens, including cancer testis antigens, endogenous retroviruses and viral oncogenes. Most of these TIL are characterized by a tissue resident memory gene expression program. Putative tumor-reactive cells (pTRC) identified via MANAscore in anti-PD-1-treated lung tumors had higher expression of checkpoint and cytotoxicity-related genes relative to putative non-tumor-reactive cells. pTRC in pathologically responding tumors showed distinguished gene expression patterns and trajectories. Collectively, we show that MANAscore is a robust tool that can greatly enrich candidate tumor-specific T cells and be used to understand the functional programming of tumor-reactive TIL.
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Affiliation(s)
- Zhen Zeng
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, MD, US
- Mark Center for Advanced Genomics and Imaging, Baltimore, MD, US
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, US
| | - Tianbei Zhang
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, MD, US
- Mark Center for Advanced Genomics and Imaging, Baltimore, MD, US
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, US
| | - Jiajia Zhang
- David Geffen School of Medicine, University of California, Los Angeles, CA, US
| | - Shuai Li
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, US
| | - Sydney Connor
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, MD, US
- Mark Center for Advanced Genomics and Imaging, Baltimore, MD, US
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, US
| | - Boyang Zhang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, US
| | - Yimin Zhao
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, US
- Department of Biostatistics, University of Washington, Seattle, WA, US
| | - Jordan Wilson
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, US
| | - Dipika Singh
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, MD, US
- Mark Center for Advanced Genomics and Imaging, Baltimore, MD, US
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, US
| | - Rima Kulikauskas
- Fred Hutchinson Cancer Center, Seattle, WA, US
- Department of Medicine, University of Washington, Seattle, WA, US
| | - Candice D Church
- Fred Hutchinson Cancer Center, Seattle, WA, US
- Department of Medicine, University of Washington, Seattle, WA, US
| | - Thomas H Pulliam
- Fred Hutchinson Cancer Center, Seattle, WA, US
- Department of Medicine, University of Washington, Seattle, WA, US
| | - Saumya Jani
- Fred Hutchinson Cancer Center, Seattle, WA, US
- Department of Medicine, University of Washington, Seattle, WA, US
| | - Paul Nghiem
- Fred Hutchinson Cancer Center, Seattle, WA, US
- Department of Medicine, University of Washington, Seattle, WA, US
| | - Suzanne L Topalian
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, MD, US
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, US
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, US
| | - Patrick M Forde
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, MD, US
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, US
| | - Drew M Pardoll
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, MD, US
- Mark Center for Advanced Genomics and Imaging, Baltimore, MD, US
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, US
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, US
| | - Kellie N Smith
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, MD, US.
- Mark Center for Advanced Genomics and Imaging, Baltimore, MD, US.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, US.
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31
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Moravec Z, Zhao Y, Voogd R, Cook DR, Kinrot S, Capra B, Yang H, Raud B, Ou J, Xuan J, Wei T, Ren L, Hu D, Wang J, Haanen JBAG, Schumacher TN, Chen X, Porter E, Scheper W. Discovery of tumor-reactive T cell receptors by massively parallel library synthesis and screening. Nat Biotechnol 2025; 43:214-222. [PMID: 38653798 DOI: 10.1038/s41587-024-02210-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 03/18/2024] [Indexed: 04/25/2024]
Abstract
T cell receptor (TCR) gene therapy is a potent form of cellular immunotherapy in which patient T cells are genetically engineered to express TCRs with defined tumor reactivity. However, the isolation of therapeutic TCRs is complicated by both the general scarcity of tumor-specific T cells among patient T cell repertoires and the patient-specific nature of T cell epitopes expressed on tumors. Here we describe a high-throughput, personalized TCR discovery pipeline that enables the assembly of complex synthetic TCR libraries in a one-pot reaction, followed by pooled expression in reporter T cells and functional genetic screening against patient-derived tumor or antigen-presenting cells. We applied the method to screen thousands of tumor-infiltrating lymphocyte (TIL)-derived TCRs from multiple patients and identified dozens of CD4+ and CD8+ T-cell-derived TCRs with potent tumor reactivity, including TCRs that recognized patient-specific neoantigens.
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Affiliation(s)
- Ziva Moravec
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Yue Zhao
- RootPath, Inc. (Guangzhou), Guangzhou, China
| | - Rhianne Voogd
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | - Haiyan Yang
- RootPath, Inc. (Guangzhou), Guangzhou, China
| | - Brenda Raud
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jiayu Ou
- RootPath, Inc. (Guangzhou), Guangzhou, China
| | - Jiekun Xuan
- RootPath, Inc. (US), Watertown, MA, USA
- RootPath, Inc. (Hangzhou), Hangzhou, China
| | - Teng Wei
- Cytotherapy Laboratory, People's Hospital, Shenzhen, Guangdong, China
| | - Lili Ren
- Cytotherapy Laboratory, People's Hospital, Shenzhen, Guangdong, China
| | - Dandan Hu
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jun Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - John B A G Haanen
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ton N Schumacher
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Xi Chen
- RootPath, Inc. (Guangzhou), Guangzhou, China.
- RootPath, Inc. (US), Watertown, MA, USA.
- RootPath, Inc. (Hangzhou), Hangzhou, China.
| | - Ely Porter
- RootPath, Inc. (US), Watertown, MA, USA.
| | - Wouter Scheper
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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32
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Ceraolo MG, Leccese M, Cassotta A, Triolo S, Bombaci M, Coluccio E, Prati D, Ungaro R, Abrignani S, Bandera A, Sallusto F, Lanzavecchia A, Notarbartolo S. Dual Activation-Induced Marker Combinations Efficiently Identify and Discern Antigen-Specific and Bystander-Activated Human CD4 + T Cells. Eur J Immunol 2025; 55:e202451404. [PMID: 39663678 PMCID: PMC11830384 DOI: 10.1002/eji.202451404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 11/29/2024] [Accepted: 12/02/2024] [Indexed: 12/13/2024]
Abstract
Identifying activated T lymphocytes and differentiating antigen-specific from bystander T cells is crucial for understanding adaptive immune responses. This study investigates the efficacy of activation-induced markers (AIMs) in distinguishing these cell populations. We measured the expression of commonly used AIMs (CD25, CD38, CD40L, CD69, CD137, HLA-DR, ICOS, and OX40) in an in vitro T-cell activation system and evaluated their sensitivity, specificity, and positive predictive value. We demonstrated that individual AIMs, while specific in detecting activated CD4+ T cells, poorly discriminate between antigen-specific and bystander activation, as assessed by a discriminative capacity (DC) score we developed. Our analysis revealed that dual AIM combinations significantly enhanced the ability to distinguish antigen-specific from bystander-activated T cells, achieving DC scores above 90%. These combinations also improved positive predictive value and specificity with a modest reduction in sensitivity. The CD25hi/ICOShi combination emerged as the most efficient, with an average sensitivity of 84.35%, specificity of 99.7%, and DC score of 90.12%. Validation through T-cell cloning and antigen re-stimulation confirmed the robustness of our predictions. This study provides a practical framework for researchers to optimize strategies for identifying and isolating antigen-specific human CD4+ T lymphocytes and studying their phenotype, function, and T-cell receptor repertoire.
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Affiliation(s)
- Maria Grazia Ceraolo
- INGM, Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”MilanItaly
| | - Maristella Leccese
- INGM, Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”MilanItaly
| | - Antonino Cassotta
- Institute for Research in BiomedicineUniversità della Svizzera italianaBellinzonaSwitzerland
| | - Sara Triolo
- INGM, Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”MilanItaly
| | - Mauro Bombaci
- INGM, Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”MilanItaly
| | - Elena Coluccio
- Department of Transfusion Medicine and HematologyFondazione IRCCS Ca' Granda Ospedale Maggiore PoliclinicoMilanItaly
| | - Daniele Prati
- Department of Transfusion Medicine and HematologyFondazione IRCCS Ca' Granda Ospedale Maggiore PoliclinicoMilanItaly
| | - Riccardo Ungaro
- Infectious Diseases UnitFondazione IRCCS Ca’ Granda Ospedale Maggiore PoliclinicoMilanItaly
| | - Sergio Abrignani
- INGM, Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”MilanItaly
- Department of Clinical Sciences and Community HealthUniversità degli Studi di MilanoMilanItaly
| | - Alessandra Bandera
- Infectious Diseases UnitFondazione IRCCS Ca’ Granda Ospedale Maggiore PoliclinicoMilanItaly
- Department of Pathophysiology and TransplantationUniversità degli Studi di MilanoMilanItaly
- Centre for Multidisciplinary Research in Health Science (MACH)Università degli Studi di MilanoMilanItaly
| | - Federica Sallusto
- Institute for Research in BiomedicineUniversità della Svizzera italianaBellinzonaSwitzerland
- Institute of Microbiology, ETH ZurichZurichSwitzerland
| | - Antonio Lanzavecchia
- INGM, Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”MilanItaly
| | - Samuele Notarbartolo
- Infectious Diseases UnitFondazione IRCCS Ca’ Granda Ospedale Maggiore PoliclinicoMilanItaly
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33
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Huang Y, Du Z, Lai Z, Wen D, Huang L, He M, Wu Z, Li H, OuYang H, Wu W, Kan A, Shi M. Single-Nucleus and Spatial Transcriptome Profiling Delineates the Multicellular Ecosystem in Hepatocellular Carcinoma After Hepatic Arterial Infusion Chemotherapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025; 12:e2405749. [PMID: 39686623 PMCID: PMC11791974 DOI: 10.1002/advs.202405749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 11/08/2024] [Indexed: 12/18/2024]
Abstract
Hepatic arterial infusion chemotherapy (HAIC) has emerged as a promising treatment strategy for hepatocellular carcinoma (HCC), but a detailed understanding of the multicellular ecosystem after HAIC treatment is lacking. Here, we collected tumor samples from treatment-naïve primary and post-HAIC HCC, and integrated single-nucleus RNA sequencing with spatial transcriptomics to characterize the tumor ecosystem in the post-HAIC HCC. Increased fractions and enhanced cellular communication of CD4+ T, CD20+ B, and dendritic cell subtypes were identified in post-HAIC tumors. Moreover, it is substantiated that HAIC promoted tertiary lymphoid structures (TLS) formation, and addressed the roles of TLSs as spatial niches of cellular communication. Specifically, intermediate exhausted CD8+ T cells expressing Granzyme-K and PD-1 (PD-1+CD8+ Tex-int) expanded following HAIC and exhibited a functionally antitumor phenotype. PD-1+CD8+ Tex-int accumulated in the TLS vicinity and disseminated throughout the tumor microenvironment, demonstrating potential as an effective biomarker for HAIC-based treatment in HCC. This study provides valuable resources and biological insights in the cellular underpinnings of HAIC treatment.
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Affiliation(s)
- YeXing Huang
- Department of Hepatobiliary OncologySun Yat‐sen University Cancer CenterGuangdong Provincial Clinical Research Center for CancerState Key Laboratory of Oncology in South ChinaGuangzhou510060P. R. China
| | - ZeFeng Du
- Department of Hepatobiliary OncologySun Yat‐sen University Cancer CenterGuangdong Provincial Clinical Research Center for CancerState Key Laboratory of Oncology in South ChinaGuangzhou510060P. R. China
| | - ZhiCheng Lai
- Department of Hepatobiliary OncologySun Yat‐sen University Cancer CenterGuangdong Provincial Clinical Research Center for CancerState Key Laboratory of Oncology in South ChinaGuangzhou510060P. R. China
| | - DongSheng Wen
- Department of Hepatobiliary OncologySun Yat‐sen University Cancer CenterGuangdong Provincial Clinical Research Center for CancerState Key Laboratory of Oncology in South ChinaGuangzhou510060P. R. China
| | - LiChang Huang
- Department of Hepatobiliary OncologySun Yat‐sen University Cancer CenterGuangdong Provincial Clinical Research Center for CancerState Key Laboratory of Oncology in South ChinaGuangzhou510060P. R. China
| | - MinKe He
- Department of Hepatobiliary OncologySun Yat‐sen University Cancer CenterGuangdong Provincial Clinical Research Center for CancerState Key Laboratory of Oncology in South ChinaGuangzhou510060P. R. China
| | - ZiChao Wu
- Department of Hepatobiliary OncologySun Yat‐sen University Cancer CenterGuangdong Provincial Clinical Research Center for CancerState Key Laboratory of Oncology in South ChinaGuangzhou510060P. R. China
| | - HuiFang Li
- Department of Hepatobiliary OncologySun Yat‐sen University Cancer CenterGuangdong Provincial Clinical Research Center for CancerState Key Laboratory of Oncology in South ChinaGuangzhou510060P. R. China
| | - HanYue OuYang
- Department of Hepatobiliary OncologySun Yat‐sen University Cancer CenterGuangdong Provincial Clinical Research Center for CancerState Key Laboratory of Oncology in South ChinaGuangzhou510060P. R. China
| | - WenChao Wu
- Department of Hepatobiliary OncologySun Yat‐sen University Cancer CenterGuangdong Provincial Clinical Research Center for CancerState Key Laboratory of Oncology in South ChinaGuangzhou510060P. R. China
| | - Anna Kan
- Department of Hepatobiliary OncologySun Yat‐sen University Cancer CenterGuangdong Provincial Clinical Research Center for CancerState Key Laboratory of Oncology in South ChinaGuangzhou510060P. R. China
| | - Ming Shi
- Department of Hepatobiliary OncologySun Yat‐sen University Cancer CenterGuangdong Provincial Clinical Research Center for CancerState Key Laboratory of Oncology in South ChinaGuangzhou510060P. R. China
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34
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Lin J, Jiang S, Chen B, Du Y, Qin C, Song Y, Peng Y, Ding M, Wu J, Lin Y, Xu T. Tertiary Lymphoid Structures are Linked to Enhanced Antitumor Immunity and Better Prognosis in Muscle-Invasive Bladder Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025; 12:e2410998. [PMID: 39739621 PMCID: PMC11831474 DOI: 10.1002/advs.202410998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Revised: 12/02/2024] [Indexed: 01/02/2025]
Abstract
The prognosis for muscle-invasive bladder cancer (MIBC) remains poor, and reliable prognostic markers have yet to be identified. Tertiary lymphoid structures (TLS) have been associated with favorable outcomes in certain cancers. However, the relationship between TLS and MIBC remains unclear. A multi-omics approach is utilized, leveraging single-cell RNA sequencing, spatial transcriptomics, bulk RNA sequencing, and immunohistochemistry, to investigate the roles of B cells and TLS in MIBC. These findings indicate that elevated levels of B cells and TLS correlate with improved prognoses in patients with MIBC, aligning with the robust antitumor immune responses observed in the TLS region. From a mechanistic perspective, CXCL13 serves as a critical cytokine for TLS formation in MIBC, primarily secreted by clonally expanded CXCL13+ T cells. This cytokine interacts with the CXCR5 receptor on NR4A2+ B cells, promoting TLS development. Plasma cells arising within the TLS microenvironment predominantly produce the IGHG antibody, potentially enhancing the phagocytic capabilities of C1QC+ macrophages. From an application standpoint, a TLS-specific gene signature is developed that effectively predicts outcomes in MIBC and other cancers. This study highlights the prognostic potential of TLS in MIBC and reveals immune mechanisms, offering insights for personalized treatment strategies.
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Affiliation(s)
- Jiaxing Lin
- Department of UrologyPeking University People's HospitalBeijing100044China
- Center for Quantitative Biology and Peking‐Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary Studies, Peking UniversityBeijing100871China
| | - Shan Jiang
- Department of UrologyPeking University People's HospitalBeijing100044China
- Center for Quantitative Biology and Peking‐Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary Studies, Peking UniversityBeijing100871China
| | - Baoqiang Chen
- Center for Quantitative Biology and Peking‐Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary Studies, Peking UniversityBeijing100871China
| | - Yiqing Du
- Department of UrologyPeking University People's HospitalBeijing100044China
| | - Caipeng Qin
- Department of UrologyPeking University People's HospitalBeijing100044China
| | - Yuxuan Song
- Department of UrologyPeking University People's HospitalBeijing100044China
| | - Yun Peng
- Department of UrologyPeking University People's HospitalBeijing100044China
| | - Mengting Ding
- Department of UrologyPeking University People's HospitalBeijing100044China
| | - Jilin Wu
- Department of UrologyPeking University People's HospitalBeijing100044China
| | - Yihan Lin
- Center for Quantitative Biology and Peking‐Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary Studies, Peking UniversityBeijing100871China
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life SciencesPeking UniversityBeijing100871China
- Peking University Chengdu Academy for Advanced Interdisciplinary BiotechnologiesChengduSichuan610213China
| | - Tao Xu
- Department of UrologyPeking University People's HospitalBeijing100044China
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35
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Schultheiss PJ, Pulkundwar A, Li W, Kam LC. Taming Variability in T-Cell Mechanosensing. Cells 2025; 14:203. [PMID: 39936994 PMCID: PMC11817355 DOI: 10.3390/cells14030203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2024] [Revised: 01/23/2025] [Accepted: 01/28/2025] [Indexed: 02/13/2025] Open
Abstract
A central step in T-cell immunotherapy is the expansion of a starting population into therapeutically potent numbers of these "living drugs". This process can be enhanced by replacing the mechanically stiff materials used for activation with softer counterparts. However, this mechanosensitive expansion response varies between individuals, impeding the full deployment of potential cell immunotherapy. This report identifies the sources of this variability, ultimately improving the reliability of T-cell expansion. T cells from a cohort of healthy donors were phenotypically characterized, activated, and expanded in vitro on soft and hard substrates, capturing and quantifying a wide range of mechanosensing responses. An analysis of expansion against demographic and phenotypic features correlated mechanosensing with the percentage of effector T cells (TEffs) in the starting population. Depletion experiments confirmed that TEffs mediate mechanosensitive expansion but also suggest that these cells are not responsible for large-scale cell production. Instead, population-level expansion results from interactions between T-cell subtypes. By providing a framework and experimental approach to understanding donor variability, the results of this study will improve the success and reliability of T-cell immunotherapy.
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Affiliation(s)
- Paula J. Schultheiss
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; (P.J.S.); (A.P.)
| | - Aarya Pulkundwar
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; (P.J.S.); (A.P.)
| | - Wangqi Li
- Department of Computer Science, Columbia University, New York, NY 10027, USA;
| | - Lance C. Kam
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; (P.J.S.); (A.P.)
- Department of Medicine, Columbia University, New York, NY 10027, USA
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36
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Cardon A, Guinebretière T, Dong C, Gil L, Ado S, Gavlovsky PJ, Braud M, Danger R, Schultheiß C, Doméné A, Paul-Gilloteaux P, Chevalier C, Bernier L, Judor JP, Fourgeux C, Imbert A, Khaldi M, Bardou-Jacquet E, Elkrief L, Lannes A, Silvain C, Schnee M, Tanne F, Vavasseur F, Brusselle L, Brouard S, Kwok WW, Mosnier JF, Lohse AW, Poschmann J, Binder M, Gournay J, Conchon S, Milpied P, Renand A. Single cell profiling of circulating autoreactive CD4 T cells from patients with autoimmune liver diseases suggests tissue imprinting. Nat Commun 2025; 16:1161. [PMID: 39880819 PMCID: PMC11779892 DOI: 10.1038/s41467-025-56363-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 01/15/2025] [Indexed: 01/31/2025] Open
Abstract
Autoimmune liver diseases (AILD) involve dysregulated CD4 T cell responses against liver self-antigens, but how these autoreactive T cells relate to liver tissue pathology remains unclear. Here we perform single-cell transcriptomic and T cell receptor analyses of circulating, self-antigen-specific CD4 T cells from patients with AILD and identify a subset of liver-autoreactive CD4 T cells with a distinct B-helper transcriptional profile characterized by PD-1, TIGIT and HLA-DR expression. These cells share clonal relationships with expanded intrahepatic T cells and exhibit transcriptional signatures overlapping with tissue-resident T cells in chronically inflamed environments. Using a mouse model, we demonstrate that, following antigen recognition in the liver, CD4 T cells acquire an exhausted phenotype, play a crucial role in liver damage, and are controlled by immune checkpoint pathways. Our findings thus suggest that circulating autoreactive CD4 T cells in AILD are imprinted by chronic antigen exposure to promote liver inflammation, thereby serving as a potential target for developing biomarkers and therapies for AILD.
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Affiliation(s)
- Anaïs Cardon
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes, France
| | - Thomas Guinebretière
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes, France
| | - Chuang Dong
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, CIML, Marseille, France
| | - Laurine Gil
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, CIML, Marseille, France
| | - Sakina Ado
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, CIML, Marseille, France
| | - Pierre-Jean Gavlovsky
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes, France
| | - Martin Braud
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes, France
| | - Richard Danger
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes, France
| | - Christoph Schultheiß
- Laboratory of Translational Immuno-Oncology, Department of Biomedicine, University and University Hospital Basel, Division of Oncology, University Hospital Basel, Basel, Switzerland
| | - Aurélie Doméné
- Nantes Université, CHU Nantes, CNRS, Inserm, BioCore, US16, SFR Bonamy, Nantes, France
| | | | | | - Laura Bernier
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes, France
| | - Jean-Paul Judor
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes, France
| | - Cynthia Fourgeux
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes, France
| | - Astrid Imbert
- Service Hepato-gastro-entérologie et Assistance Nutritionnelle, CHU Nantes, Nantes, France
| | - Marion Khaldi
- Service Hepato-gastro-entérologie et Assistance Nutritionnelle, CHU Nantes, Nantes, France
- Institut des Maladies de l'Appareil Digestif, IMAD, CHU Nantes, Nantes, France
| | - Edouard Bardou-Jacquet
- CHU Rennes, Service des maladies du foie, Université Rennes, INSERM, INRAE, Institut NUMECAN, Rennes, France
| | - Laure Elkrief
- CHRU Tours, Service Hépato-Gastroentérologie, Tours, France
| | - Adrien Lannes
- CHU Angers, Service Hépato-Gastroentérologie et Oncologie Digestive, Université d'Angers, Laboratoire HIFIH, UPRES EA3859, SFR 4208, Angers, France
| | | | - Matthieu Schnee
- CHD Vendée-La Roche sur Yon, Service Hépato-Gastroentérologie, F- 85000, la Roche sur Yon, France
| | - Florence Tanne
- CHU Brest, Service Hépato-Gastroentérologie, Brest, France
| | | | - Lucas Brusselle
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes, France
| | - Sophie Brouard
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes, France
| | - William W Kwok
- Center for Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Jean-François Mosnier
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes, France
- Service Anatomie et Cytologie Pathologiques, CHU Nantes, Nantes, France
| | - Ansgar W Lohse
- First Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jeremie Poschmann
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes, France
| | - Mascha Binder
- Laboratory of Translational Immuno-Oncology, Department of Biomedicine, University and University Hospital Basel, Division of Oncology, University Hospital Basel, Basel, Switzerland
| | - Jérôme Gournay
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes, France
- Service Hepato-gastro-entérologie et Assistance Nutritionnelle, CHU Nantes, Nantes, France
- Institut des Maladies de l'Appareil Digestif, IMAD, CHU Nantes, Nantes, France
| | - Sophie Conchon
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes, France.
| | - Pierre Milpied
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, CIML, Marseille, France.
| | - Amédée Renand
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes, France.
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37
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Kuilman T, Schrikkema DS, Gadiot J, Gomez-Eerland R, Bies L, Walker J, Spaapen RM, Kok H, Houg D, Viyacheva M, Claassen YB, Saornil M, Krijgsman O, Stringer B, Ding H, Geleijnse A, Meinema AC, Weissbrich B, Lancee M, Engele CG, Sabatino M, Chen PL, Tsai KY, Mulé JJ, Sondak VK, van den Bulk J, de Miranda NF, Jedema I, Haanen JG, van Heijst JWJ, Schumacher TN, Linnemann C, Bendle GM. Enabling next-generation engineered TCR-T therapies based on high-throughput TCR discovery from diagnostic tumor biopsies. Nat Commun 2025; 16:649. [PMID: 39809767 PMCID: PMC11733228 DOI: 10.1038/s41467-024-55420-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Accepted: 12/10/2024] [Indexed: 01/16/2025] Open
Abstract
Adoptive cell therapy with tumor-infiltrating lymphocytes (TIL) can mediate tumor regression, including complete and durable responses, in a range of solid cancers, most notably in melanoma. However, its wider application and efficacy has been restricted by the limited accessibility, proliferative capacity and effector function of tumor-specific TIL. Here, we develop a platform for the efficient identification of tumor-specific TCR genes from diagnostic tumor biopsies, including core-needle biopsies frozen in a non-viable format, to enable engineered T cell therapy. Using a genetic screening approach that detects antigen-reactive TCRs with high sensitivity and specificity based on T cell activation, we show that high complexity TCR libraries can be efficiently screened against multiplexed antigen libraries to identify both HLA class I and II restricted TCRs. Through the identification of neoantigen-specific TCRs directly from melanoma as well as low tumor mutational burden microsatellite-stable colorectal carcinoma samples, we demonstrate the pan-cancer potential of this platform.
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Affiliation(s)
- Thomas Kuilman
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands.
| | - Deborah S Schrikkema
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Jules Gadiot
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Raquel Gomez-Eerland
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Laura Bies
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Julia Walker
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Robbert M Spaapen
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Hanna Kok
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Demi Houg
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Milena Viyacheva
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Yvonne B Claassen
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Manuel Saornil
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Oscar Krijgsman
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Bas Stringer
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Huiwen Ding
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Anou Geleijnse
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Anne C Meinema
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Bianca Weissbrich
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Melissa Lancee
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Carmen G Engele
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Marianna Sabatino
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Pei-Ling Chen
- Department of Pathology, Moffitt Cancer Center, Tampa, FL, USA
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Kenneth Y Tsai
- Department of Pathology, Moffitt Cancer Center, Tampa, FL, USA
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - James J Mulé
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, FL, USA
- Department of Immunology and Radiation Oncology Program, Moffitt Cancer Center, Tampa, FL, USA
| | - Vernon K Sondak
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Jitske van den Bulk
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Noel F de Miranda
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Inge Jedema
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - John G Haanen
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Clinical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Ton N Schumacher
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Carsten Linnemann
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands
| | - Gavin M Bendle
- Neogene Therapeutics, A member of the AstraZeneca Group, Amsterdam, The Netherlands.
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38
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Leko V, Groh E, Levi ST, Copeland AR, White BS, Gasmi B, Li Y, Hill V, Gurusamy D, Levin N, Kim SP, Sindiri S, Gartner JJ, Prickett TD, Parkhust M, Lowery FJ, Goff SL, Rosenberg SA, Robbins P. Utilization of primary tumor samples for cancer neoantigen discovery. J Immunother Cancer 2025; 13:e010993. [PMID: 39800378 PMCID: PMC11748769 DOI: 10.1136/jitc-2024-010993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2024] [Accepted: 12/11/2024] [Indexed: 01/23/2025] Open
Abstract
BACKGROUND The use of tumor-infiltrating T lymphocytes (TIL) that recognize cancer neoantigens has led to lasting remissions in metastatic melanoma and certain cases of metastatic epithelial cancer. For the treatment of the latter, selecting cells for therapy typically involves laborious screening of TIL for recognition of autologous tumor-specific mutations, detected through next-generation sequencing of freshly resected metastatic tumors. Our study explored the feasibility of using archived formalin-fixed, paraffin-embedded (FFPE) primary tumor samples for cancer neoantigen discovery, to potentially expedite this process and reduce the need for resections normally required for tumor sequencing. METHOD Whole-exome sequencing was conducted on matched primary and metastatic colorectal cancer samples from 22 patients. The distribution of metastatic tumor mutations that were confirmed as neoantigens through cognate TIL screening was evaluated in the corresponding primary tumors. Mutations unique to primary tumors were screened for recognition by metastasis-derived TIL and circulating T lymphocytes. RESULTS We found that 25 (65.8%) of the 38 validated neoantigens identified in metastatic tumors from 18 patients with colorectal cancer were also present in matched primary tumor samples. This included all 12 neoantigens encoded by putative cancer driver genes, which are generally regarded as superior targets for adoptive cell therapy. The detection rate for other neoantigens, representing mutations without an established role in cancer biology, was 50% (13/26). Gene products encoding neoantigens detected in the primary tumors were not more likely to be clonal or broadly distributed among the analyzed metastatic lesions compared with those undetected in the primary tumors. Additionally, we found that mutations detected only in primary tumor samples did not elicit recognition by metastatic tumor-derived TIL but could elicit specific recognition by the autologous circulating memory T cells. CONCLUSIONS Our findings indicate that primary FFPE tumor-derived screening libraries could be used to discover most neoantigens present in metastatic tumors requiring treatment. Furthermore, this approach can reveal additional neoantigens not present in resected metastatic tumors, prompting further research to understand their clinical relevance as potential therapeutic targets.
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Affiliation(s)
- Vid Leko
- Immune Deficiency Cellular Therapy Program, National Cancer Institute, Bethesda, Maryland, USA
| | - Eric Groh
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Shoshana T Levi
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Amy R Copeland
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | | | - Billel Gasmi
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
- Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland, USA
| | - Yong Li
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Victoria Hill
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | | | - Noam Levin
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | | | - Sivasish Sindiri
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Jared J Gartner
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Todd D Prickett
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Maria Parkhust
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Frank J Lowery
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Stephanie L Goff
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | | | - Paul Robbins
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
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39
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Wu B, Luo D, Wang X, Qiao C, Li R, Liu J. The global trends and distribution in tumor-infiltrating lymphocytes over the past 49 years: bibliometric and visualized analysis. Front Immunol 2025; 15:1511866. [PMID: 39835135 PMCID: PMC11743541 DOI: 10.3389/fimmu.2024.1511866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Accepted: 12/11/2024] [Indexed: 01/22/2025] Open
Abstract
Background The body of research on tumor-infiltrating lymphocytes (TILs) is expanding rapidly; yet, a comprehensive analysis of related publications has been notably absent. Objective This study utilizes bibliometric methodologies to identify emerging research hotspots and to map the distribution of tumor-infiltrating lymphocyte research. Methods Literature from the Web of Science database was analyzed and visualized using VOSviewer, CiteSpace, Scimago Graphica, R-bibliometrix, and R packages. Results Research on tumor-infiltrating lymphocytes began in 1975 and has experienced significant growth, particularly after 2015. Leading contributors include the United States, the National Cancer Institute, the journal Cancer Immunology Immunotherapy, and researcher Steven A. Rosenberg. Other prominent contributors include China, the National Institutes of Health, researcher Roberto Salgado, and the Journal of Immunology. Prominent institutions in the USA and Europe occupy central roles within collaborative networks. Financial support plays a pivotal role in driving research advancements. Keyword clustering analysis reveals four primary knowledge domains: adoptive cell therapy; the prognostic value of TILs; PD-1/PD-L1 and TILs; and prognostic studies of TILs across various cancers. Keyword and reference analyses further indicate that "adoptive cell therapy," "the prognostic value of TILs," and "immune checkpoint inhibitors and TILs" are central themes in current and future research. Combination therapies; tumor neoantigens; gene editing; dominant population selection of TILs therapy; TILs in Tumor microenvironment; emerging predictive biomarkers; TILs in predicting the efficacy of neoadjuvant chemotherapy and immunotherapy; the relationship between TILs and PD-L1; TIL-based patient stratification; tertiary lymphoid structures; and TIL evaluation through digital pathology and artificial intelligence are identified as key areas of interest. Conclusions This analysis highlights the increasing academic focus on tumor-infiltrating lymphocyte research and identifies key recent themes in the field such as prognostic value of TILs, personalized treatments, and combination therapies.
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Affiliation(s)
- Beibei Wu
- Beijing Traditional Chinese Medicine Office for Cancer Prevention and Control, Xiyuan Hospital, China Academy of Chinese Medical Science, Beijing, China
- Department of Information, Xiyuan Hospital, China Academy of Chinese Medical Science, Beijing, China
- Department of Oncology, Xiyuan Hospital, China Academy of Chinese Medical Science, Beijing, China
| | - Ding Luo
- Beijing Traditional Chinese Medicine Office for Cancer Prevention and Control, Xiyuan Hospital, China Academy of Chinese Medical Science, Beijing, China
- Department of Information, Xiyuan Hospital, China Academy of Chinese Medical Science, Beijing, China
| | - Xuejie Wang
- Beijing Traditional Chinese Medicine Office for Cancer Prevention and Control, Xiyuan Hospital, China Academy of Chinese Medical Science, Beijing, China
- Department of Information, Xiyuan Hospital, China Academy of Chinese Medical Science, Beijing, China
| | - Chen Qiao
- Beijing Traditional Chinese Medicine Office for Cancer Prevention and Control, Xiyuan Hospital, China Academy of Chinese Medical Science, Beijing, China
- Department of Information, Xiyuan Hospital, China Academy of Chinese Medical Science, Beijing, China
| | - Rui Li
- Department of Oncology, Xiyuan Hospital, China Academy of Chinese Medical Science, Beijing, China
| | - Jian Liu
- Beijing Traditional Chinese Medicine Office for Cancer Prevention and Control, Xiyuan Hospital, China Academy of Chinese Medical Science, Beijing, China
- Department of Information, Xiyuan Hospital, China Academy of Chinese Medical Science, Beijing, China
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40
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Tan CL, Lindner K, Boschert T, Meng Z, Rodriguez Ehrenfried A, De Roia A, Haltenhof G, Faenza A, Imperatore F, Bunse L, Lindner JM, Harbottle RP, Ratliff M, Offringa R, Poschke I, Platten M, Green EW. Prediction of tumor-reactive T cell receptors from scRNA-seq data for personalized T cell therapy. Nat Biotechnol 2025; 43:134-142. [PMID: 38454173 PMCID: PMC11738991 DOI: 10.1038/s41587-024-02161-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 02/01/2024] [Indexed: 03/09/2024]
Abstract
The identification of patient-derived, tumor-reactive T cell receptors (TCRs) as a basis for personalized transgenic T cell therapies remains a time- and cost-intensive endeavor. Current approaches to identify tumor-reactive TCRs analyze tumor mutations to predict T cell activating (neo)antigens and use these to either enrich tumor infiltrating lymphocyte (TIL) cultures or validate individual TCRs for transgenic autologous therapies. Here we combined high-throughput TCR cloning and reactivity validation to train predicTCR, a machine learning classifier that identifies individual tumor-reactive TILs in an antigen-agnostic manner based on single-TIL RNA sequencing. PredicTCR identifies tumor-reactive TCRs in TILs from diverse cancers better than previous gene set enrichment-based approaches, increasing specificity and sensitivity (geometric mean) from 0.38 to 0.74. By predicting tumor-reactive TCRs in a matter of days, TCR clonotypes can be prioritized to accelerate the manufacture of personalized T cell therapies.
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Affiliation(s)
- C L Tan
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - K Lindner
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany
- Immune Monitoring Unit, National Center for Tumor Diseases, Heidelberg, Germany
| | - T Boschert
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Helmholtz Institute for Translational Oncology, Mainz, Germany
| | - Z Meng
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, Heidelberg, Germany
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - A Rodriguez Ehrenfried
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Helmholtz Institute for Translational Oncology, Mainz, Germany
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, Heidelberg, Germany
| | - A De Roia
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- DNA Vector Laboratory, German Cancer Research Center, Heidelberg, Germany
| | - G Haltenhof
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany
| | | | | | - L Bunse
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany
| | | | - R P Harbottle
- DNA Vector Laboratory, German Cancer Research Center, Heidelberg, Germany
| | - M Ratliff
- Department of Neurosurgery, University Hospital Mannheim, Mannheim, Germany
| | - R Offringa
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, Heidelberg, Germany
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - I Poschke
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany
- Immune Monitoring Unit, National Center for Tumor Diseases, Heidelberg, Germany
| | - M Platten
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany.
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany.
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany.
- Immune Monitoring Unit, National Center for Tumor Diseases, Heidelberg, Germany.
- Helmholtz Institute for Translational Oncology, Mainz, Germany.
- German Cancer Research Center-Hector Cancer Institute at the Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.
| | - E W Green
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany.
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany.
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany.
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41
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Link JM, Eng JR, Pelz C, MacPherson-Hawthorne K, Worth PJ, Sivagnanam S, Keith DJ, Owen S, Langer EM, Grossblatt-Wait A, Salgado-Garza G, Creason AL, Protzek S, Egger J, Holly H, Heskett MB, Chin K, Kirchberger N, Betre K, Bucher E, Kilburn D, Hu Z, Munks MW, English IA, Tsuda M, Goecks J, Demir E, Adey AC, Kardosh A, Lopez CD, Sheppard BC, Guimaraes A, Brinkerhoff B, Morgan TK, Mills GB, Coussens LM, Brody JR, Sears RC. Ongoing replication stress tolerance and clonal T cell responses distinguish liver and lung recurrence and outcomes in pancreatic cancer. NATURE CANCER 2025; 6:123-144. [PMID: 39789181 PMCID: PMC11779630 DOI: 10.1038/s43018-024-00881-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 11/15/2024] [Indexed: 01/12/2025]
Abstract
Patients with metastatic pancreatic ductal adenocarcinoma survive longer if disease spreads to the lung but not the liver. Here we generated overlapping, multi-omic datasets to identify molecular and cellular features that distinguish patients whose disease develops liver metastasis (liver cohort) from those whose disease develops lung metastasis without liver metastases (lung cohort). Lung cohort patients survived longer than liver cohort patients, despite sharing the same tumor subtype. We developed a primary organotropism (pORG) gene set enriched in liver cohort versus lung cohort primary tumors. We identified ongoing replication stress response pathways in high pORG/liver cohort tumors, whereas low pORG/lung cohort tumors had greater densities of lymphocytes and shared T cell clonal responses. Our study demonstrates that liver-avid pancreatic ductal adenocarcinoma is associated with tolerance to ongoing replication stress, limited tumor immunity and less-favorable outcomes, whereas low replication stress, lung-avid/liver-averse tumors are associated with active tumor immunity that may account for favorable outcomes.
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Affiliation(s)
- Jason M Link
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA.
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA.
| | - Jennifer R Eng
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Carl Pelz
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
| | | | - Patrick J Worth
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Portland, OR, USA
- Department of Surgery, Oregon Health and Science University, Portland, OR, USA
| | - Shamaline Sivagnanam
- Department of Cell, Development and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Dove J Keith
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
| | - Sydney Owen
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
| | - Ellen M Langer
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Portland, OR, USA
- Center for Early Detection Advanced Research, Oregon Health and Science University, Portland, OR, USA
| | - Alison Grossblatt-Wait
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
- Center for Early Detection Advanced Research, Oregon Health and Science University, Portland, OR, USA
| | | | - Allison L Creason
- Knight Cancer Institute, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Sara Protzek
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
| | - Julian Egger
- Knight Cancer Institute, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Hannah Holly
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | | | - Koei Chin
- Knight Cancer Institute, Portland, OR, USA
- Center for Early Detection Advanced Research, Oregon Health and Science University, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Nell Kirchberger
- Department of Cell, Development and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Konjit Betre
- Department of Cell, Development and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Elmar Bucher
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - David Kilburn
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Zhi Hu
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Michael W Munks
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
| | - Isabel A English
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Motoyuki Tsuda
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Jeremy Goecks
- Knight Cancer Institute, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Emek Demir
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Andrew C Adey
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Portland, OR, USA
| | - Adel Kardosh
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Portland, OR, USA
- Department of Hematology and Oncology, Oregon Health and Science University, Portland, OR, USA
| | - Charles D Lopez
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Portland, OR, USA
- Department of Hematology and Oncology, Oregon Health and Science University, Portland, OR, USA
| | - Brett C Sheppard
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Portland, OR, USA
- Department of Surgery, Oregon Health and Science University, Portland, OR, USA
| | - Alex Guimaraes
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Portland, OR, USA
- Department of Radiology, Oregon Health and Science University, Portland, OR, USA
| | - Brian Brinkerhoff
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
- Department of Pathology and Laboratory Medicine, Oregon Health and Science University, Portland, OR, USA
| | - Terry K Morgan
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Portland, OR, USA
- Center for Early Detection Advanced Research, Oregon Health and Science University, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
- Department of Pathology and Laboratory Medicine, Oregon Health and Science University, Portland, OR, USA
| | - Gordon B Mills
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Portland, OR, USA
- Department of Oncological Sciences, Oregon Health and Science University, Portland, OR, USA
| | - Lisa M Coussens
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Portland, OR, USA
- Department of Cell, Development and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Jonathan R Brody
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Portland, OR, USA
- Department of Surgery, Oregon Health and Science University, Portland, OR, USA
- Department of Cell, Development and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Rosalie C Sears
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA.
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA.
- Knight Cancer Institute, Portland, OR, USA.
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42
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Lu BY, Lucca LE, Lewis W, Wang J, Nogueira CV, Heer S, Rayon-Estrada V, Axisa PP, Reeves SM, Buitrago-Pocasangre NC, Pham GH, Kojima ML, Wei W, Aizenbud L, Bacchiocchi A, Zhang L, Walewski JJ, Chiang V, Olino K, Clune J, Halaban R, Kluger Y, Coyle AJ, Kisielow J, Obermair FJ, Kluger HM, Hafler DA. Circulating tumor-reactive KIR +CD8 + T cells suppress anti-tumor immunity in patients with melanoma. Nat Immunol 2025; 26:82-91. [PMID: 39609626 DOI: 10.1038/s41590-024-02023-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 10/24/2024] [Indexed: 11/30/2024]
Abstract
Effective anti-tumor immunity is driven by cytotoxic CD8+ T cells with specificity for tumor antigens. However, the factors that control successful tumor rejection are not well understood. Here we identify a subpopulation of CD8+ T cells that are tumor-antigen-specific and can be identified by KIR expression but paradoxically impair anti-tumor immunity in patients with melanoma. These tumor-antigen-specific KIR+CD8+ regulatory T cells target other tumor-antigen-specific CD8+ T cells, can be detected in both the tumor and the blood, have a conserved transcriptional program and are associated with a poor overall survival. These findings broaden our understanding of the transcriptional and functional heterogeneity of human CD8+ T cells and implicate KIR+CD8+ regulatory T cells as a cellular mediator of immune evasion in human cancer.
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Affiliation(s)
- Benjamin Y Lu
- Department of Medicine (Medical Oncology), Yale School of Medicine, New Haven, CT, USA.
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA.
| | - Liliana E Lucca
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- University of Toulouse, Inserm, CNRS, University Toulouse III-Paul Sabatier, Cancer Research Center of Toulouse, Toulouse, France
| | - Wesley Lewis
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Jiping Wang
- Applied Mathematics Program, Yale University, New Haven, CT, USA
| | | | | | | | - Pierre-Paul Axisa
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- University of Toulouse, Inserm, CNRS, University Toulouse III-Paul Sabatier, Cancer Research Center of Toulouse, Toulouse, France
| | - Sarah M Reeves
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | | | - Giang H Pham
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Mina L Kojima
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Wei Wei
- Department of Medicine (Medical Oncology), Yale School of Medicine, New Haven, CT, USA
| | - Lilach Aizenbud
- Department of Medicine (Medical Oncology), Yale School of Medicine, New Haven, CT, USA
| | | | - Lin Zhang
- Department of Medicine (Medical Oncology), Yale School of Medicine, New Haven, CT, USA
| | - Joseph J Walewski
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Veronica Chiang
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Kelly Olino
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - James Clune
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Ruth Halaban
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA
| | - Yuval Kluger
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Applied Mathematics Program, Yale University, New Haven, CT, USA
| | | | - Jan Kisielow
- Repertoire Immune Medicines, Schlieren, Switzerland
| | | | - Harriet M Kluger
- Department of Medicine (Medical Oncology), Yale School of Medicine, New Haven, CT, USA
| | - David A Hafler
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA.
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA.
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Erickson SM, Manning BM, Kumar A, Patel MR. Engineered Cellular Therapies for the Treatment of Thoracic Cancers. Cancers (Basel) 2024; 17:35. [PMID: 39796666 PMCID: PMC11718842 DOI: 10.3390/cancers17010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Revised: 12/16/2024] [Accepted: 12/23/2024] [Indexed: 01/13/2025] Open
Abstract
Thoracic malignancies (lung cancers and malignant pleural mesothelioma) are prevalent worldwide and are associated with high morbidity and mortality. Effective treatments are needed for patients with advanced disease. Cell therapies are a promising approach to the treatment of advanced cancers that make use of immune effector cells that have the ability to mediate antitumor immune responses. In this review, we discuss the prospect of chimeric antigen receptor-T (CAR-T) cells, natural killer (NK) cells, T cell receptor-engineered (TCR-T) cells, and tumor-infiltrating lymphocytes (TILs) as treatments for thoracic malignancies. CAR-T cells and TILs have proven successful in several hematologic cancers and advanced melanoma, respectively, but outside of melanoma, results have thus far been unsuccessful in most other solid tumors. NK cells and TCR-T cells are additional cell therapy platforms with their own unique advantages and challenges. Obstacles that must be overcome to develop effective cell therapy for these malignancies include selecting an appropriate target antigen, combating immunosuppressive cells and signaling molecules present in the tumor microenvironment, persistence, and delivering a sufficient quantity of antitumor immune cells to the tumor. Induced pluripotent stem cells (iPSCs) offer great promise as a source for both NK and T cell-based therapies due to their unlimited expansion potential. Here, we review clinical trial data, as well as recent basic scientific advances that offer insight into how we may overcome these obstacles, and provide an overview of ongoing trials testing novel strategies to overcome these obstacles.
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Affiliation(s)
- Spencer M. Erickson
- Internal Medicine Residency Program, Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Benjamin M. Manning
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 55455, USA (A.K.)
| | - Akhilesh Kumar
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 55455, USA (A.K.)
| | - Manish R. Patel
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 55455, USA (A.K.)
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Huang CX, Lao XM, Wang XY, Ren YZ, Lu YT, Shi W, Wang YZ, Wu CY, Xu L, Chen MS, Gao Q, Liu L, Wei Y, Kuang DM. Pericancerous cross-presentation to cytotoxic T lymphocytes impairs immunotherapeutic efficacy in hepatocellular carcinoma. Cancer Cell 2024; 42:2082-2097.e10. [PMID: 39547231 DOI: 10.1016/j.ccell.2024.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 09/09/2024] [Accepted: 10/21/2024] [Indexed: 11/17/2024]
Abstract
Hyperprogressive disease can occur in cancer patients receiving immune checkpoint blockade (ICB) therapy, but whether and how reactive cytotoxic T lymphocytes (CTLs) exert protumorigenic effects in this context remain elusive. Herein, our study reveals that pericancerous macrophages cross-present antigens to CD103+ CTLs in hepatocellular carcinoma (HCC) via the endoplasmic reticulum (ER)-associated degradation machinery-mediated cytosolic pathway. This process leads to the retention of CD103+ CTLs in the pericancerous area, whereby they activate NLRP3 inflammasome in macrophages, promoting hepatoma progression and resistance to immunotherapy. Our single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics analysis of HCC patients shows that despite their tissue-resident effector phenotype, the aggregation of CD103+ CTLs predicts unfavorable clinical outcomes for HCC patients receiving multiple types of treatment. Correspondingly, therapeutic strategies that redistribute CD103+ CTLs can disrupt this pathogenic interplay with macrophages, enhancing the efficacy of ICB treatment against HCC.
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MESH Headings
- Carcinoma, Hepatocellular/immunology
- Carcinoma, Hepatocellular/therapy
- Carcinoma, Hepatocellular/pathology
- Liver Neoplasms/immunology
- Liver Neoplasms/therapy
- Liver Neoplasms/pathology
- T-Lymphocytes, Cytotoxic/immunology
- Humans
- Immunotherapy/methods
- Macrophages/immunology
- Mice
- Animals
- Integrin alpha Chains/metabolism
- Integrin alpha Chains/immunology
- Cross-Priming/immunology
- Antigens, CD/metabolism
- Antigens, CD/immunology
- Immune Checkpoint Inhibitors/therapeutic use
- Immune Checkpoint Inhibitors/pharmacology
- NLR Family, Pyrin Domain-Containing 3 Protein/metabolism
- NLR Family, Pyrin Domain-Containing 3 Protein/immunology
- Inflammasomes/immunology
- Inflammasomes/metabolism
- Tumor Microenvironment/immunology
- Cell Line, Tumor
- Mice, Inbred C57BL
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Affiliation(s)
- Chun-Xiang Huang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xiang-Ming Lao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Xu-Yan Wang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yi-Zheng Ren
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yi-Tong Lu
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wei Shi
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ying-Zhe Wang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Cai-Yuan Wu
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Li Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Min-Shan Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Qiang Gao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Lianxin Liu
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Yuan Wei
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Innovation Center of the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510275, China.
| | - Dong-Ming Kuang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Innovation Center of the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510275, China.
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45
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Füchsl F, Untch J, Kavaka V, Zuleger G, Braun S, Schwanzer A, Jarosch S, Vogelsang C, de Andrade Krätzig N, Gosmann D, Öllinger R, Giansanti P, Hiltensperger M, Rad R, Busch DH, Beltrán E, Bräunlein E, Krackhardt AM. High-resolution profile of neoantigen-specific TCR activation links moderate stimulation to increased resilience of engineered TCR-T cells. Nat Commun 2024; 15:10520. [PMID: 39627205 PMCID: PMC11615276 DOI: 10.1038/s41467-024-53911-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 10/28/2024] [Indexed: 12/06/2024] Open
Abstract
Neoantigen-specific T cell receptors (neoTCRs) promise safe, personalized anti-tumor immunotherapy. However, detailed assessment of neoTCR-characteristics affecting therapeutic efficacy is mostly missing. Previously, we identified diverse neoTCRs restricted to different neoantigens in a melanoma patient. In this work, we now combine single-cell TCR-sequencing and RNA-sequencing after neoantigen-specific restimulation of peripheral blood-derived CD8+ T cells of this patient. We detect neoTCRs with specificity for the previously detected neoantigens and perform fine-characterization of neoTCR-transgenic (tg) T cells in vitro and in vivo. We describe a heterogeneous spectrum of TCR-intrinsic activation patterns in response to a shared neoepitope ranging from previously detected more highly frequent neoTCRs with moderate activation to rare ones with initially stronger activation. Experimental restimulation of adoptively transferred neoTCR-tg T cells in a xenogeneic rechallenge tumor model demonstrates superior anti-tumor responses of moderate neoTCR-tg T cells upon repeated tumor contact. These insights have significant implications for the selection of TCRs for therapeutic engineering of TCR-tg T cells.
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Affiliation(s)
- Franziska Füchsl
- Technical University of Munich, School of Medicine and Health, III Medical Department, TUM University Hospital, Ismaninger Str. 22, 81675, Munich, Germany
| | - Johannes Untch
- Technical University of Munich, School of Medicine and Health, III Medical Department, TUM University Hospital, Ismaninger Str. 22, 81675, Munich, Germany
| | - Vladyslav Kavaka
- Ludwig-Maximilians-Universität München, Institute of Clinical Neuroimmunology, University Hospital, Marchioninistr. 15, 81377, Munich, Germany
- Ludwig-Maximilians-Universität München, Faculty of Medicine, Biomedical Center (BMC), Großhaderner Str. 9, 82152, Martinsried, Germany
| | - Gabriela Zuleger
- Technical University of Munich, School of Medicine and Health, III Medical Department, TUM University Hospital, Ismaninger Str. 22, 81675, Munich, Germany
| | - Sarah Braun
- Technische Universität München, Institute for Medical Microbiology, Immunology and Hygiene, Trogerstr. 30, 81675, Munich, Germany
| | - Antonia Schwanzer
- Technical University of Munich, School of Medicine and Health, III Medical Department, TUM University Hospital, Ismaninger Str. 22, 81675, Munich, Germany
| | - Sebastian Jarosch
- Technische Universität München, Institute for Medical Microbiology, Immunology and Hygiene, Trogerstr. 30, 81675, Munich, Germany
| | - Carolin Vogelsang
- Technical University of Munich, School of Medicine and Health, III Medical Department, TUM University Hospital, Ismaninger Str. 22, 81675, Munich, Germany
| | - Niklas de Andrade Krätzig
- Technische Universität München, Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine and Health, Ismaninger Str. 22, 81675, Munich, Germany
- Technical University of Munich, Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine and Health, Einsteinstr. 25, 81675, Munich, Germany
| | - Dario Gosmann
- Technical University of Munich, School of Medicine and Health, III Medical Department, TUM University Hospital, Ismaninger Str. 22, 81675, Munich, Germany
| | - Rupert Öllinger
- Technische Universität München, Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine and Health, Ismaninger Str. 22, 81675, Munich, Germany
| | - Piero Giansanti
- Technical University of Munich, Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine and Health, Einsteinstr. 25, 81675, Munich, Germany
- Bavarian Center for Biomolecular Mass Spectrometry at Klinikum rechts der Isar, Technical University of Munich, Einsteinstr. 25, 81675, Munich, Germany
| | - Michael Hiltensperger
- Technical University of Munich, School of Medicine and Health, III Medical Department, TUM University Hospital, Ismaninger Str. 22, 81675, Munich, Germany
- German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Roland Rad
- Technische Universität München, Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine and Health, Ismaninger Str. 22, 81675, Munich, Germany
- Technical University of Munich, Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine and Health, Einsteinstr. 25, 81675, Munich, Germany
| | - Dirk H Busch
- Technische Universität München, Institute for Medical Microbiology, Immunology and Hygiene, Trogerstr. 30, 81675, Munich, Germany
- German Center for Infection Research (Deutsches Zentrum für Infektionsforschung, DZIF), Partner Site Munich, Munich, Germany
| | - Eduardo Beltrán
- Ludwig-Maximilians-Universität München, Institute of Clinical Neuroimmunology, University Hospital, Marchioninistr. 15, 81377, Munich, Germany
- Ludwig-Maximilians-Universität München, Faculty of Medicine, Biomedical Center (BMC), Großhaderner Str. 9, 82152, Martinsried, Germany
- Munich Cluster of Systems Neurology (SyNergy), Feodor-Lynen-Str. 17, 81377, Munich, Germany
| | - Eva Bräunlein
- Technical University of Munich, School of Medicine and Health, III Medical Department, TUM University Hospital, Ismaninger Str. 22, 81675, Munich, Germany
- German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Angela M Krackhardt
- Technical University of Munich, School of Medicine and Health, III Medical Department, TUM University Hospital, Ismaninger Str. 22, 81675, Munich, Germany.
- Technical University of Munich, Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine and Health, Einsteinstr. 25, 81675, Munich, Germany.
- German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
- Malteser Krankenhaus St. Franziskus-Hospital, Flensburg, Germany.
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46
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Hu W, Bian Y, Ji H. TIL Therapy in Lung Cancer: Current Progress and Perspectives. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2409356. [PMID: 39422665 PMCID: PMC11633538 DOI: 10.1002/advs.202409356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Revised: 10/03/2024] [Indexed: 10/19/2024]
Abstract
Lung cancer remains the most prevalent malignant tumor worldwide and is the leading cause of cancer-related mortality. Although immune checkpoint blockade has revolutionized the treatment of advanced lung cancer, many patients still do not respond well, often due to the lack of functional T cell infiltration. Adoptive cell therapy (ACT) using expanded immune cells has emerged as an important therapeutic modality. Tumor-infiltrating lymphocytes (TIL) therapy is one form of ACT involving the administration of expanded and activated autologous T cells derived from surgically resected cancer tissues and reinfusion into patients and holds great therapeutic potential for lung cancer. In this review, TIL therapy is introduced and its suitability for lung cancer is discussed. Then its historical and clinical developments are summarized, and the methods developed up-to-date to identify tumor-recognizing TILs and optimize TIL composition. Some perspectives toward future TIL therapy for lung cancer are also provided.
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Affiliation(s)
- Weilei Hu
- Key Laboratory of Systems Health Science of Zhejiang ProvinceSchool of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou310024China
- Key Laboratory of Multi‐Cell SystemsShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghai200031China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yifei Bian
- Key Laboratory of Multi‐Cell SystemsShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghai200031China
- University of Chinese Academy of SciencesBeijing100049China
| | - Hongbin Ji
- Key Laboratory of Systems Health Science of Zhejiang ProvinceSchool of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou310024China
- Key Laboratory of Multi‐Cell SystemsShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghai200031China
- University of Chinese Academy of SciencesBeijing100049China
- School of Life Science and TechnologyShanghai Tech UniversityShanghai200120China
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47
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Olivera I, Etxeberria I, Luri-Rey C, Molero-Glez P, Melero I. Regional and intratumoral adoptive T-cell therapy. IMMUNO-ONCOLOGY TECHNOLOGY 2024; 24:100715. [PMID: 39055165 PMCID: PMC11269935 DOI: 10.1016/j.iotech.2024.100715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Adoptive T-cell therapies (ACTs) including tumor-infiltrating lymphocytes and engineered T cells (transgenic T-cell receptor and chimeric antigen receptor T cells), have made an important impact in the field of cancer treatment over the past years. Most of these therapies are typically administered systemically in approaches that facilitate the elimination of hematologic malignancies. Therapeutical efficacy against solid tumors, however, with the exception of tumor-infiltrating lymphocytes against melanoma, remains limited due to several barriers preventing lymphocyte access to the tumor bed. Building upon the experience of regional administration in other immunotherapies, the regional administration of adoptive cell therapies is being assessed to overcome this challenge, granting a first round of access of the transferred T cells to the tumor niche and thereby ensuring their activation and expansion. Intralesional and intracavitary routes of delivery have been tested with promising antitumor objective responses in preclinical and clinical studies. Additionally, several strategies are being developed to further improve T-cell activity after reinfusing them back to the patient such as combinations with other immunotherapy agents or direct engineering of the transferred T cells, achieving long-term immune memory. Clinical trials testing different regional adoptive T-cell therapies are ongoing but some issues related to methodology of administration and correct selection of the target antigen to avoid on-target/off-tumor side-effects need to be further evaluated and improved. Herein, we discuss the current preclinical and clinical landscape of intratumoral and locoregional delivery of adoptive T-cell therapies.
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Affiliation(s)
- I. Olivera
- Program of Immunology and Immunotherapy, Cima Universidad de Navarra, Pamplona
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
| | - I. Etxeberria
- Human Oncology and Pathogenesis Program (HOPP), Immuno-Oncology Service, Memorial Sloan Kettering Cancer Center, New York
- Parker Institute for Cancer Immunotherapy, New York, USA
| | - C. Luri-Rey
- Program of Immunology and Immunotherapy, Cima Universidad de Navarra, Pamplona
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
| | - P. Molero-Glez
- Program of Immunology and Immunotherapy, Cima Universidad de Navarra, Pamplona
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
| | - I. Melero
- Program of Immunology and Immunotherapy, Cima Universidad de Navarra, Pamplona
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid
- Department of Immunology and Immunotherapy, Clínica Universidad de Navarra, Pamplona
- Department of Oncology, Clínica Universidad de Navarra, Madrid
- Centro del Cancer de la Universidad de Navarra (CCUN), Pamplona, Spain
- Nuffield Department of Medicine (NDM), University of Oxford, Oxford, UK
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Yang C, Qu J, Wu J, Cai S, Liu W, Deng Y, Meng Y, Zheng L, Zhang L, Wang L, Guo X. Single-cell dissection reveals immunosuppressive F13A1+ macrophage as a hallmark for multiple primary lung cancers. Clin Transl Med 2024; 14:e70091. [PMID: 39601163 PMCID: PMC11600049 DOI: 10.1002/ctm2.70091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 10/22/2024] [Accepted: 11/01/2024] [Indexed: 11/29/2024] Open
Abstract
BACKGROUND The increasing prevalence of multiple primarylung cancers (MPLCs) presents challenges to current diagnostic and clinicalmanagement approaches. However, the molecular mechanisms driving MPLCdevelopment and distinguishing it from solitary primary lung cancers (SPLCs)remain largely unexplored. METHODS We performed a comparative single-cell RNAsequencing (scRNA-seq) analysis on tumour and adjacent para-tumour tissues fromMPLC and SPLC patients to comparatively evaluate their immunological landscapes.Additionally, multiplex immunofluorescence (mIF) staining and independentvalidation datasets were used to confirm findings. RESULTS MPLCs and SPLCs share significant similarities in genetic, transcriptomic and immune profiles, suggesting common therapeutic strategies such as EGFR-TKIs andICIs. Notably, an immunosuppressive macrophage subtype, F13A1+ Macrophage (Mϕ), is specifically enriched in MPLCs. This subtype overexpresses M2 macrophagemarkers and exhibits up-regulation of SPP1-CD44/CCL13-ACKR1 interactions, indicatingits role in shaping the immunosuppressive tumour microenvironment and promotingtumour growth in MPLCs. CONCLUSIONS This study unveils shared molecular mechanismsbetween MPLCs and SPLCs, while identifying MPLC-specific cellular and molecularfeatures, such as the role of F13A1+ macrophages. The findings provide novelinsights into MPLC pathogenesis, supporting the development of targetedtherapeutic strategies. KEY POINTS Comparative scRNA-seq analysis reveals significant similarities in genetic, transcriptomicand immune profiles between MPLCs and SPLCs. Identification of a unique immunosuppressive F13A1+ macrophage subtype, preferentially enriched in MPLCs, linked to immune evasion and tumourprogression. SPP1-CD44/CCL13-ACKR1 interactions are crucial in MPLC tumour microenvironment, indicating potential targets for therapeutic intervention.
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Affiliation(s)
- Chenglin Yang
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeShenzhenChina
| | - Jiahao Qu
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeShenzhenChina
- Southern University of Science and TechnologyShenzhen CityGuangdong ProvinceChina
| | - Jingting Wu
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeShenzhenChina
| | - Songhua Cai
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeShenzhenChina
| | - Wenyi Liu
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeShenzhenChina
| | - Youjun Deng
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeShenzhenChina
| | - Yiran Meng
- Department of R&DHangzhou Repugene Technology Co., Ltd.HangzhouChina
| | - Liuqing Zheng
- Department of R&DHangzhou Repugene Technology Co., Ltd.HangzhouChina
| | - Lishen Zhang
- Department of R&DHangzhou Repugene Technology Co., Ltd.HangzhouChina
| | - Li Wang
- Department of R&DHangzhou Repugene Technology Co., Ltd.HangzhouChina
| | - Xiaotong Guo
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeShenzhenChina
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Keshari S, Shavkunov AS, Miao Q, Saha A, Minowa T, Molgora M, Williams CD, Chaib M, Highsmith AM, Pineda JE, Alekseev S, Alspach E, Hu KH, Colonna M, Pauken KE, Chen K, Gubin MM. Comparing neoantigen cancer vaccines and immune checkpoint therapy unveils an effective vaccine and anti-TREM2 macrophage-targeting dual therapy. Cell Rep 2024; 43:114875. [PMID: 39446585 PMCID: PMC11785356 DOI: 10.1016/j.celrep.2024.114875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 08/12/2024] [Accepted: 09/30/2024] [Indexed: 10/26/2024] Open
Abstract
The goal of therapeutic cancer vaccines and immune checkpoint therapy (ICT) is to promote T cells with anti-tumor capabilities. Here, we compared mutant neoantigen (neoAg) peptide-based vaccines with ICT in preclinical models. NeoAg vaccines induce the most robust expansion of proliferating and stem-like PD-1+TCF-1+ neoAg-specific CD8 T cells in tumors. Anti-CTLA-4 and/or anti-PD-1 ICT promotes intratumoral TCF-1- neoAg-specific CD8 T cells, although their phenotype depends in part on the specific ICT used. Anti-CTLA-4 also prompts substantial changes to CD4 T cells, including induction of ICOS+Bhlhe40+ T helper 1 (Th1)-like cells. Although neoAg vaccines or ICTs expand iNOS+ macrophages, neoAg vaccines maintain CX3CR1+CD206+ macrophages expressing the TREM2 receptor, unlike ICT, which suppresses them. TREM2 blockade enhances neoAg vaccine efficacy and is associated with fewer CX3CR1+CD206+ macrophages and induction of neoAg-specific CD8 T cells. Our findings highlight different mechanisms underlying neoAg vaccines and different forms of ICT and identify combinatorial therapies to enhance neoAg vaccine efficacy.
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Affiliation(s)
- Sunita Keshari
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander S Shavkunov
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Qi Miao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Akata Saha
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tomoyuki Minowa
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Martina Molgora
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA
| | - Charmelle D Williams
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mehdi Chaib
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anna M Highsmith
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Josué E Pineda
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sayan Alekseev
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Program of Biology, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Elise Alspach
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Kenneth H Hu
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; The Parker Institute for Cancer Immunotherapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; The James P. Allison Institute, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA
| | - Kristen E Pauken
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matthew M Gubin
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Li T, Guo S, Xu C, Zhang M, Lyu C, Xu H, Hou Z, Zhang M, Li X, Ren J, Liu C, Kong D, Hao D, Wang G. Integrated single-cell transcriptome and TCR profiles of hepatocellular carcinoma highlight the convergence on interferon signaling during immunotherapy. J Immunother Cancer 2024; 12:e010534. [PMID: 39581706 PMCID: PMC11590841 DOI: 10.1136/jitc-2024-010534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2024] [Accepted: 11/05/2024] [Indexed: 11/26/2024] Open
Abstract
BACKGROUND Despite the success of immune checkpoint inhibitor (ICI)-based combination therapies in hepatocellular carcinoma (HCC), its effectiveness remains confined to a subset of patients. The development of reliable, predictive markers is important for accurate patient stratification and further mechanistic understanding of therapy response. METHODS We comprehensively analyzed paired single-cell RNA transcriptome and T-cell repertoire profiles from 14 HCC ascites samples, collected from 7 patients before and after treatment with the combination of sintilimab (anti-PD-1) and bevacizumab (anti-VEGF). RESULTS We identify a widespread convergence on interferon (IFN) signaling across various immune cell lineages in treatment-responsive patients with HCC, indicating a common transcriptional state transition in the immune microenvironment linked to immunotherapy response in HCC. Strong IFN signaling marks CD8+ T cells with larger clonal expansion and enhanced cytotoxicity, macrophages toward M1-like polarization and strong T-cell recruitment ability, dendritic cells with increased antigen presentation capacity, as well as highly cytotoxic natural killer cells and activated B cells. By translating our finding to cohorts of patients with HCC, we demonstrate the specificity of IFN-signaling in the prognosis of patients with HCC and its ability to predict immunotherapy response. CONCLUSIONS This study provides a unique single-cell resource with clonal and longitudinal resolution during ICI therapy and reveals IFN signaling as a biomarker of immunotherapy response in HCC, suggesting a beneficial effect by combining IFN inducers with ICIs for patients with HCC.
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Affiliation(s)
- Tianhao Li
- Department of Phase 1 Trials Center, Harbin Medical University Cancer Hospital, Harbin, People's Republic of China
- School of Basic Medical Sciences, Harbin Medical University, Harbin, People's Republic of China
| | - Shengnan Guo
- School of Basic Medical Sciences, Harbin Medical University, Harbin, People's Republic of China
| | - Chang Xu
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, People's Republic of China
| | - Mingjie Zhang
- School of Basic Medical Sciences, Harbin Medical University, Harbin, People's Republic of China
| | - Cheng Lyu
- School of Basic Medical Sciences, Harbin Medical University, Harbin, People's Republic of China
| | - Huanhuan Xu
- School of Basic Medical Sciences, Harbin Medical University, Harbin, People's Republic of China
| | - Zepeng Hou
- School of Basic Medical Sciences, Harbin Medical University, Harbin, People's Republic of China
| | - Mingshuo Zhang
- School of Basic Medical Sciences, Harbin Medical University, Harbin, People's Republic of China
| | - Xiaobo Li
- School of Basic Medical Sciences, Harbin Medical University, Harbin, People's Republic of China
| | - Jing Ren
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, People's Republic of China
| | - Changqing Liu
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, People's Republic of China
| | - Dan Kong
- Department of Gynecologic Oncology, Harbin Medical University Cancer Hospital, Harbin, People's Republic of China
| | - Dapeng Hao
- Department of Phase 1 Trials Center, Harbin Medical University Cancer Hospital, Harbin, People's Republic of China
- School of Basic Medical Sciences, Harbin Medical University, Harbin, People's Republic of China
| | - Guangyu Wang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, People's Republic of China
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