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Rathgeber AC, Ludwig LS, Penter L. Single-cell genomics-based immune and disease monitoring in blood malignancies. Clin Hematol Int 2024; 6:62-84. [PMID: 38884110 PMCID: PMC11180218 DOI: 10.46989/001c.117961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 12/25/2023] [Indexed: 06/18/2024] Open
Abstract
Achieving long-term disease control using therapeutic immunomodulation is a long-standing concept with a strong tradition in blood malignancies. Besides allogeneic hematopoietic stem cell transplantation that continues to provide potentially curative treatment for otherwise challenging diagnoses, recent years have seen impressive progress in immunotherapies for leukemias and lymphomas with immune checkpoint blockade, bispecific monoclonal antibodies, and CAR T cell therapies. Despite their success, non-response, relapse, and immune toxicities remain frequent, thus prioritizing the elucidation of the underlying mechanisms and identifying predictive biomarkers. The increasing availability of single-cell genomic tools now provides a system's immunology view to resolve the molecular and cellular mechanisms of immunotherapies at unprecedented resolution. Here, we review recent studies that leverage these technological advancements for tracking immune responses, the emergence of immune resistance, and toxicities. As single-cell immune monitoring tools evolve and become more accessible, we expect their wide adoption for routine clinical applications to catalyze more precise therapeutic steering of personal immune responses.
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Affiliation(s)
- Anja C Rathgeber
- Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine
- Department of Hematology, Oncology, and Tumorimmunology Charité - Universitätsmedizin Berlin
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin
| | - Leif S Ludwig
- Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin
| | - Livius Penter
- Department of Hematology, Oncology, and Tumorimmunology Charité - Universitätsmedizin Berlin
- BIH Biomedical Innovation Academy Berlin Institute of Health at Charité - Universitätsmedizin Berlin
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2
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Penter L, Borji M, Nagler A, Lyu H, Lu WS, Cieri N, Maurer K, Oliveira G, Al'Khafaji AM, Garimella KV, Li S, Neuberg DS, Ritz J, Soiffer RJ, Garcia JS, Livak KJ, Wu CJ. Integrative genotyping of cancer and immune phenotypes by long-read sequencing. Nat Commun 2024; 15:32. [PMID: 38167262 PMCID: PMC10762175 DOI: 10.1038/s41467-023-44137-7] [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: 03/11/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
Single-cell transcriptomics has become the definitive method for classifying cell types and states, and can be augmented with genotype information to improve cell lineage identification. Due to constraints of short-read sequencing, current methods to detect natural genetic barcodes often require cumbersome primer panels and early commitment to targets. Here we devise a flexible long-read sequencing workflow and analysis pipeline, termed nanoranger, that starts from intermediate single-cell cDNA libraries to detect cell lineage-defining features, including single-nucleotide variants, fusion genes, isoforms, sequences of chimeric antigen and TCRs. Through systematic analysis of these classes of natural 'barcodes', we define the optimal targets for nanoranger, namely those loci close to the 5' end of highly expressed genes with transcript lengths shorter than 4 kB. As proof-of-concept, we apply nanoranger to longitudinal tracking of subclones of acute myeloid leukemia (AML) and describe the heterogeneous isoform landscape of thousands of marrow-infiltrating immune cells. We propose that enhanced cellular genotyping using nanoranger can improve the tracking of single-cell tumor and immune cell co-evolution.
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Grants
- P01 CA229092 NCI NIH HHS
- P50 CA101942 NCI NIH HHS
- UM1 CA186709 NCI NIH HHS
- U24 CA224316 NCI NIH HHS
- U24 CA224331 NCI NIH HHS
- U24 CA224285 NCI NIH HHS
- R50 CA251956 NCI NIH HHS
- U24 CA224309 NCI NIH HHS
- U24 CA224319 NCI NIH HHS
- K08 CA245209 NCI NIH HHS
- This work was supported by National Institutes of Health, National Cancer Institute grant P01CA229092 (CJW), UM1CA186709 (Principal Investigator: Geoffrey Shapiro), National Cancer Institute Cancer Therapy Evaluation Program, Bristol-Myers Squibb, and LLS Therapy Accelerator Program. L.P. was supported by a research fellowship from the German Research Foundation (DFG, PE 3127/1-1) and is a Scholar of the American Society of Hematology, participant in the BIH Charité Digital Clinician Scientist Program funded by the DFG, the Charité – Universitätsmedizin Berlin, and the Berlin Institute of Health at Charité (BIH) and is supported by the Max-Eder program of the German Cancer Aid. A.A. is supported by the Broad Institute IGNITE award. K.M. is suppored by the ASCO YIA award. G.O. was supported by the Claudia Adams Barr Program for Innovative Cancer Research and by DF/HCC Kidney Cancer SPORE P50 CA101942. S.L. is supported by the National Institutes of Health, National Cancer Institute Research Specialist Award (R50CA251956). JSG is supported by the Conquer Cancer Foundation Career Development Award, Leukemia and Lymphoma Society Translational Research Program Award, and NIH K08CA245209. NCI CTEP provided study drug (Ipilimumab) support. This work was further supported by the CIMAC-CIDC Network. Scientific and financial support for the CIMAC-CIDC Network is provided through National Institutes of Health, National Cancer Institute Cooperative Agreements U24CA224319 (to the Icahn School of Medicine at Mount Sinai CIMAC), U24CA224331 (to the Dana-Farber Cancer Institute CIMAC), U24CA224285 (to the MD Anderson Cancer Center CIMAC), U24CA224309 (to the Stanford University CIMAC), and U24CA224316 (to the CIDC at Dana-Farber Cancer Institute). The CIMAC-CIDC website is found at https://cimac-network.org/.
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Affiliation(s)
- Livius Penter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Hematology, Oncology, and Tumorimmunology, Campus Virchow Klinikum, Berlin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Digital Clinician Scientist Program, Charitéplatz 1, 10117, Berlin, Germany
| | - Mehdi Borji
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adi Nagler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Haoxiang Lyu
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wesley S Lu
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicoletta Cieri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Katie Maurer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Aziz M Al'Khafaji
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Kiran V Garimella
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Shuqiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Robert J Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jacqueline S Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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3
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Sauerer T, Velázquez GF, Schmid C. Relapse of acute myeloid leukemia after allogeneic stem cell transplantation: immune escape mechanisms and current implications for therapy. Mol Cancer 2023; 22:180. [PMID: 37951964 PMCID: PMC10640763 DOI: 10.1186/s12943-023-01889-6] [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: 08/11/2023] [Accepted: 10/24/2023] [Indexed: 11/14/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease characterized by the expansion of immature myeloid cells in the bone marrow (BM) and peripheral blood (PB) resulting in failure of normal hematopoiesis and life-threating cytopenia. Allogeneic hematopoietic stem cell transplantation (allo-HCT) is an established therapy with curative potential. Nevertheless, post-transplant relapse is common and associated with poor prognosis, representing the major cause of death after allo-HCT. The occurrence of relapse after initially successful allo-HCT indicates that the donor immune system is first able to control the leukemia, which at a later stage develops evasion strategies to escape from immune surveillance. In this review we first provide a comprehensive overview of current knowledge regarding immune escape in AML after allo-HCT, including dysregulated HLA, alterations in immune checkpoints and changes leading to an immunosuppressive tumor microenvironment. In the second part, we draw the line from bench to bedside and elucidate to what extend immune escape mechanisms of relapsed AML are yet exploited in treatment strategies. Finally, we give an outlook how new emerging technologies could help to improve the therapy for these patients, and elucidate potential new treatment options.
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Affiliation(s)
- Tatjana Sauerer
- Department of Hematology and Oncology, Augsburg University Hospital and Medical Faculty, Bavarian Cancer Research Center (BZKF) and Comprehensive Cancer Center Augsburg, Augsburg, Germany
| | - Giuliano Filippini Velázquez
- Department of Hematology and Oncology, Augsburg University Hospital and Medical Faculty, Bavarian Cancer Research Center (BZKF) and Comprehensive Cancer Center Augsburg, Augsburg, Germany
| | - Christoph Schmid
- Department of Hematology and Oncology, Augsburg University Hospital and Medical Faculty, Bavarian Cancer Research Center (BZKF) and Comprehensive Cancer Center Augsburg, Augsburg, Germany.
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4
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Apostolova P, Kreutmair S, Toffalori C, Punta M, Unger S, Burk AC, Wehr C, Maas-Bauer K, Melchinger W, Haring E, Hoefflin R, Shoumariyeh K, Hupfer V, Lauer EM, Duquesne S, Lowinus T, Gonzalo Núñez N, Alberti C, da Costa Pereira S, Merten CH, Power L, Weiss M, Böke C, Pfeifer D, Marks R, Bertz H, Wäsch R, Ihorst G, Gentner B, Duyster J, Boerries M, Andrieux G, Finke J, Becher B, Vago L, Zeiser R. Phase II trial of hypomethylating agent combined with nivolumab for acute myeloid leukaemia relapse after allogeneic haematopoietic cell transplantation-Immune signature correlates with response. Br J Haematol 2023; 203:264-281. [PMID: 37539479 DOI: 10.1111/bjh.19007] [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: 06/03/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023]
Abstract
Acute myeloid leukaemia (AML) relapse after allogeneic haematopoietic cell transplantation (allo-HCT) is often driven by immune-related mechanisms and associated with poor prognosis. Immune checkpoint inhibitors combined with hypomethylating agents (HMA) may restore or enhance the graft-versus-leukaemia effect. Still, data about using this combination regimen after allo-HCT are limited. We conducted a prospective, phase II, open-label, single-arm study in which we treated patients with haematological AML relapse after allo-HCT with HMA plus the anti-PD-1 antibody nivolumab. The response was correlated with DNA-, RNA- and protein-based single-cell technology assessments to identify biomarkers associated with therapeutic efficacy. Sixteen patients received a median number of 2 (range 1-7) nivolumab applications. The overall response rate (CR/PR) at day 42 was 25%, and another 25% of the patients achieved stable disease. The median overall survival was 15.6 months. High-parametric cytometry documented a higher frequency of activated (ICOS+ , HLA-DR+ ), low senescence (KLRG1- , CD57- ) CD8+ effector T cells in responders. We confirmed these findings in a preclinical model. Single-cell transcriptomics revealed a pro-inflammatory rewiring of the expression profile of T and myeloid cells in responders. In summary, the study indicates that the post-allo-HCT HMA/nivolumab combination induces anti-AML immune responses in selected patients and could be considered as a bridging approach to a second allo-HCT. Trial-registration: EudraCT-No. 2017-002194-18.
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Affiliation(s)
- Petya Apostolova
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefanie Kreutmair
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Cristina Toffalori
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Division of Immunology, Transplantation and Infectious Disease, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marco Punta
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Division of Immunology, Transplantation and Infectious Disease, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Center for OMICS Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Susanne Unger
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Ann-Cathrin Burk
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claudia Wehr
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kristina Maas-Bauer
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Wolfgang Melchinger
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eileen Haring
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rouven Hoefflin
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Khalid Shoumariyeh
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Valerie Hupfer
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eliza Maria Lauer
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sandra Duquesne
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Theresa Lowinus
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Chiara Alberti
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | | | - Carla Helena Merten
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Laura Power
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Matthias Weiss
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Caroline Böke
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dietmar Pfeifer
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Reinhard Marks
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hartmut Bertz
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ralph Wäsch
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gabriele Ihorst
- Clinical Trials Unit, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bernhard Gentner
- Translational Stem Cell and Leukemia Unit, San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Justus Duyster
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Juergen Finke
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Luca Vago
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Division of Immunology, Transplantation and Infectious Disease, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Robert Zeiser
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Signalling Research Centres BIOSS and CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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5
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Cao H, Wu T, Zhou X, Xie S, Sun H, Sun Y, Li Y. Progress of research on PD-1/PD-L1 in leukemia. Front Immunol 2023; 14:1265299. [PMID: 37822924 PMCID: PMC10562551 DOI: 10.3389/fimmu.2023.1265299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 09/13/2023] [Indexed: 10/13/2023] Open
Abstract
Leukemia cells prevent immune system from clearing tumor cells by inducing the immunosuppression of the bone marrow (BM) microenvironment. In recent years, further understanding of the BM microenvironment and immune landscape of leukemia has resulted in the introduction of several immunotherapies, including checkpoint inhibitors, T-cell engager, antibody drug conjugates, and cellular therapies in clinical trials. Among them, the programmed cell death protein 1 (PD-1)/programmed death-ligand 1 (PD-L1) axis is a significant checkpoint for controlling immune responses, the PD-1 receptor on tumor-infiltrating T cells is bound by PD-L1 on leukemia cells. Consequently, the activation of tumor reactive T cells is inhibited and their apoptosis is promoted, preventing the rejection of the tumor by immune system and thus resulting in the occurrence of immune tolerance. The PD-1/PD-L1 axis serves as a significant mechanism by which tumor cells evade immune surveillance, and PD-1/PD-L1 checkpoint inhibitors have been approved for the treatment of lymphomas and varieties of solid tumors. However, the development of drugs targeting PD-1/PD-L1 in leukemia remains in the clinical-trial stage. In this review, we tally up the basic research and clinical trials on PD-1/PD-L1 inhibitors in leukemia, as well as discuss the relevant toxicity and impacts of PD-1/PD-L1 on other immunotherapies such as hematopoietic stem cell transplantation, bi-specific T-cell engager, chimeric antigen receptor T-cell immunotherapy.
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Affiliation(s)
- Huizhen Cao
- Department of Pediatrics, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Tianyu Wu
- Department of Gastrointestinal Surgery, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Xue Zhou
- Department of Pediatrics, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Shuyang Xie
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai, China
| | - Hongfang Sun
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai, China
| | - Yunxiao Sun
- Department of Pediatrics, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Youjie Li
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai, China
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6
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Penter L, Liu Y, Wolff JO, Yang L, Taing L, Jhaveri A, Southard J, Patel M, Cullen NM, Pfaff KL, Cieri N, Oliveira G, Kim-Schulze S, Ranasinghe S, Leonard R, Robertson T, Morgan EA, Chen HX, Song MH, Thurin M, Li S, Rodig SJ, Cibulskis C, Gabriel S, Bachireddy P, Ritz J, Streicher H, Neuberg DS, Hodi FS, Davids MS, Gnjatic S, Livak KJ, Altreuter J, Michor F, Soiffer RJ, Garcia JS, Wu CJ. Mechanisms of response and resistance to combined decitabine and ipilimumab for advanced myeloid disease. Blood 2023; 141:1817-1830. [PMID: 36706355 PMCID: PMC10122106 DOI: 10.1182/blood.2022018246] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/29/2023] Open
Abstract
The challenge of eradicating leukemia in patients with acute myelogenous leukemia (AML) after initial cytoreduction has motivated modern efforts to combine synergistic active modalities including immunotherapy. Recently, the ETCTN/CTEP 10026 study tested the combination of the DNA methyltransferase inhibitor decitabine together with the immune checkpoint inhibitor ipilimumab for AML/myelodysplastic syndrome (MDS) either after allogeneic hematopoietic stem cell transplantation (HSCT) or in the HSCT-naïve setting. Integrative transcriptome-based analysis of 304 961 individual marrow-infiltrating cells for 18 of 48 subjects treated on study revealed the strong association of response with a high baseline ratio of T to AML cells. Clinical responses were predominantly driven by decitabine-induced cytoreduction. Evidence of immune activation was only apparent after ipilimumab exposure, which altered CD4+ T-cell gene expression, in line with ongoing T-cell differentiation and increased frequency of marrow-infiltrating regulatory T cells. For post-HSCT samples, relapse could be attributed to insufficient clearing of malignant clones in progenitor cell populations. In contrast to AML/MDS bone marrow, the transcriptomes of leukemia cutis samples from patients with durable remission after ipilimumab monotherapy showed evidence of increased infiltration with antigen-experienced resident memory T cells and higher expression of CTLA-4 and FOXP3. Altogether, activity of combined decitabine and ipilimumab is impacted by cellular expression states within the microenvironmental niche of leukemic cells. The inadequate elimination of leukemic progenitors mandates urgent development of novel approaches for targeting these cell populations to generate long-lasting responses. This trial was registered at www.clinicaltrials.gov as #NCT02890329.
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Affiliation(s)
- Livius Penter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
- Harvard Medical School, Boston, MA
- Department of Hematology, Oncology, and Tumorimmunology, Campus Virchow Klinikum, Berlin, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Yang Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | | | - Lin Yang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Len Taing
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Aashna Jhaveri
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Jackson Southard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA
| | - Manishkumar Patel
- Human Immune Monitoring Center at the Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nicole M. Cullen
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Kathleen L. Pfaff
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Nicoletta Cieri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
- Harvard Medical School, Boston, MA
| | - Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
- Harvard Medical School, Boston, MA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center at the Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Rebecca Leonard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Taylor Robertson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Elizabeth A. Morgan
- Harvard Medical School, Boston, MA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Helen X. Chen
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD
| | - Minkyung H. Song
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD
| | - Magdalena Thurin
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD
| | - Shuqiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA
| | - Scott J. Rodig
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Carrie Cibulskis
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Stacey Gabriel
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | | | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Howard Streicher
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD
| | - Donna S. Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - F. Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Matthew S. Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Sacha Gnjatic
- Human Immune Monitoring Center at the Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kenneth J. Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA
| | | | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Robert J. Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Jacqueline S. Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
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7
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Ho JNHG, Schmidt D, Lowinus T, Ryoo J, Dopfer EP, Gonzalo Núñez N, Costa-Pereira S, Toffalori C, Punta M, Fetsch V, Wertheimer T, Rittmann MC, Braun LM, Follo M, Briere C, Vinnakota JM, Langenbach M, Koppers F, Shoumariyeh K, Engel H, Rückert T, Märklin M, Holzmayer S, Illert AL, Magon F, Andrieux G, Duquesne S, Pfeifer D, Staniek J, Rizzi M, Miething C, Köhler N, Duyster J, Menssen HD, Boerries M, Buescher JM, Cabezas-Wallscheid N, Blazar BR, Apostolova P, Vago L, Pearce EL, Becher B, Zeiser R. Targeting MDM2 enhances antileukemia immunity after allogeneic transplantation via MHC-II and TRAIL-R1/2 upregulation. Blood 2022; 140:1167-1181. [PMID: 35853161 PMCID: PMC9461473 DOI: 10.1182/blood.2022016082] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 07/01/2022] [Indexed: 11/20/2022] Open
Abstract
Patients with acute myeloid leukemia (AML) often achieve remission after allogeneic hematopoietic cell transplantation (allo-HCT) but subsequently die of relapse driven by leukemia cells resistant to elimination by allogeneic T cells based on decreased major histocompatibility complex II (MHC-II) expression and apoptosis resistance. Here we demonstrate that mouse-double-minute-2 (MDM2) inhibition can counteract immune evasion of AML. MDM2 inhibition induced MHC class I and II expression in murine and human AML cells. Using xenografts of human AML and syngeneic mouse models of leukemia, we show that MDM2 inhibition enhanced cytotoxicity against leukemia cells and improved survival. MDM2 inhibition also led to increases in tumor necrosis factor-related apoptosis-inducing ligand receptor-1 and -2 (TRAIL-R1/2) on leukemia cells and higher frequencies of CD8+CD27lowPD-1lowTIM-3low T cells, with features of cytotoxicity (perforin+CD107a+TRAIL+) and longevity (bcl-2+IL-7R+). CD8+ T cells isolated from leukemia-bearing MDM2 inhibitor-treated allo-HCT recipients exhibited higher glycolytic activity and enrichment for nucleotides and their precursors compared with vehicle control subjects. T cells isolated from MDM2 inhibitor-treated AML-bearing mice eradicated leukemia in secondary AML-bearing recipients. Mechanistically, the MDM2 inhibitor-mediated effects were p53-dependent because p53 knockdown abolished TRAIL-R1/2 and MHC-II upregulation, whereas p53 binding to TRAILR1/2 promotors increased upon MDM2 inhibition. The observations in the mouse models were complemented by data from human individuals. Patient-derived AML cells exhibited increased TRAIL-R1/2 and MHC-II expression on MDM2 inhibition. In summary, we identified a targetable vulnerability of AML cells to allogeneic T-cell-mediated cytotoxicity through the restoration of p53-dependent TRAIL-R1/2 and MHC-II production via MDM2 inhibition.
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Affiliation(s)
- Jenny N H G Ho
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Dominik Schmidt
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Theresa Lowinus
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Jeongmin Ryoo
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Elaine-Pashupati Dopfer
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | | | - Sara Costa-Pereira
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Cristina Toffalori
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Division of Immunology, Transplantation and Infectious Disease, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milano, Italy
| | - Marco Punta
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Division of Immunology, Transplantation and Infectious Disease, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milano, Italy
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy
| | - Viktor Fetsch
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Tobias Wertheimer
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Marie-Claire Rittmann
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Lukas M Braun
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Marie Follo
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Christelle Briere
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Janaki Manoja Vinnakota
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Marlene Langenbach
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Felicitas Koppers
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Khalid Shoumariyeh
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
| | - Helena Engel
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Tamina Rückert
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Melanie Märklin
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Tuebingen, Germany
- Deutsche Forschungsgemeinschaft Cluster of Excellence 2180 "Image-guided and Functional Instructed Tumor Therapy," University of Tuebingen, Tuebingen, Germany
| | - Samuel Holzmayer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Tuebingen, Germany
- Deutsche Forschungsgemeinschaft Cluster of Excellence 2180 "Image-guided and Functional Instructed Tumor Therapy," University of Tuebingen, Tuebingen, Germany
| | - Anna L Illert
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
| | - Federica Magon
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Geoffroy Andrieux
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sandra Duquesne
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Dietmar Pfeifer
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Julian Staniek
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, Medical Centre
| | - Marta Rizzi
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, Medical Centre
- Signalling Research Centres BIOSS and CIBSS - Centre for Integrative Biological, Signalling Studies, and
| | - Cornelius Miething
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
| | - Natalie Köhler
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Justus Duyster
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
| | | | - Melanie Boerries
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Joerg M Buescher
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Bruce R Blazar
- Division of Blood & Marrow Transplant and Cellular Therapy, Department of Pediatrics, University of Minnesota, Minneapolis, MN; and
| | - Petya Apostolova
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Johns Hopkins University, Baltimore, MD
| | - Luca Vago
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Division of Immunology, Transplantation and Infectious Disease, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milano, Italy
| | - Erika L Pearce
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Johns Hopkins University, Baltimore, MD
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Robert Zeiser
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
- Signalling Research Centres BIOSS and CIBSS - Centre for Integrative Biological, Signalling Studies, and
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8
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Ainciburu M, Morgan DM, DePasquale EAK, Love JC, Prósper F, van Galen P. WAT3R: Recovery of T Cell Receptor Variable Regions From 3' Single-Cell RNA-Sequencing. Bioinformatics 2022; 38:3645-3647. [PMID: 35674381 PMCID: PMC9272805 DOI: 10.1093/bioinformatics/btac382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/26/2022] [Accepted: 06/03/2022] [Indexed: 11/14/2022] Open
Abstract
SUMMARY Diversity of the T cell receptor (TCR) repertoire is central to adaptive immunity. The TCR is composed of α and β chains, encoded by the TRA and TRB genes, of which the variable regions determine antigen specificity. To generate novel biological insights into the complex functioning of immune cells, combined capture of variable regions and single-cell transcriptomes provides a compelling approach. Recent developments enable the enrichment of TRA and TRB variable regions from widely used technologies for 3'-based single-cell RNA-sequencing (scRNA-seq). However, a comprehensive computational pipeline to process TCR-enriched data from 3' scRNA-seq is not available. Here we present an analysis pipeline to process TCR variable regions enriched from 3' scRNA-seq cDNA. The tool reports TRA and TRB nucleotide and amino acid sequences linked to cell barcodes, enabling the reconstruction of T cell clonotypes with associated transcriptomes. We demonstrate the software using peripheral blood mononuclear cells (PBMCs) from a healthy donor and detect TCR sequences in a high proportion of single T cells. Detection of TCR sequences is low in non-T cell populations, demonstrating specificity. Finally, we show that TCR clones are larger in CD8 Memory T cells than in other T cell types, indicating an association between T cell clonotypes and differentiation states. AVAILABILITY AND IMPLEMENTATION The Workflow for Association of T cell receptors from 3' single-cell RNA-seq (WAT3R), including test data, is available on GitHub (https://github.com/mainciburu/WAT3R), Docker Hub (https://hub.docker.com/r/mainciburu/wat3r), and a workflow on the Terra platform (https://app.terra.bio). The test dataset is available on GEO (accession number GSE195956). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Marina Ainciburu
- Program of Hemato-Oncology, University of Navarra, Pamplona, 31008, Spain.,Division of Hematology, Brigham and Women's Hospital, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Duncan M Morgan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Koch Institute for Integrative Cancer Research,Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Erica A K DePasquale
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - J Christopher Love
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Koch Institute for Integrative Cancer Research,Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Felipe Prósper
- Program of Hemato-Oncology, University of Navarra, Pamplona, 31008, Spain
| | - Peter van Galen
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
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9
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Penter L, Gohil SH, Wu CJ. Natural Barcodes for Longitudinal Single Cell Tracking of Leukemic and Immune Cell Dynamics. Front Immunol 2022; 12:788891. [PMID: 35046946 PMCID: PMC8761982 DOI: 10.3389/fimmu.2021.788891] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022] Open
Abstract
Blood malignancies provide unique opportunities for longitudinal tracking of disease evolution following therapeutic bottlenecks and for the monitoring of changes in anti-tumor immunity. The expanding development of multi-modal single-cell sequencing technologies affords newer platforms to elucidate the mechanisms underlying these processes at unprecedented resolution. Furthermore, the identification of molecular events that can serve as in-vivo barcodes now facilitate the tracking of the trajectories of malignant and of immune cell populations over time within primary human samples, as these permit unambiguous identification of the clonal lineage of cell populations within heterogeneous phenotypes. Here, we provide an overview of the potential for chromosomal copy number changes, somatic nuclear and mitochondrial DNA mutations, single nucleotide polymorphisms, and T and B cell receptor sequences to serve as personal natural barcodes and review technical implementations in single-cell analysis workflows. Applications of these methodologies include the study of acquired therapeutic resistance and the dissection of donor- and host cellular interactions in the context of allogeneic hematopoietic stem cell transplantation.
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Affiliation(s)
- Livius Penter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States
- Harvard Medical School, Boston, MA, United States
- Department of Hematology, Oncology, and Tumorimmunology, Campus Virchow Klinikum, Berlin, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Satyen H. Gohil
- Department of Academic Haematology, University College London Cancer Institute, London, United Kingdom
- Department of Haematology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States
- Harvard Medical School, Boston, MA, United States
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
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10
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DePasquale EAK, Ssozi D, Ainciburu M, Good J, Noel J, Villanueva MA, Couturier CP, Shalek AK, Aranki SF, Mallidi HR, Griffin GK, Lane AA, van Galen P. Single-Cell Multiomics Reveals Clonal T-Cell Expansions and Exhaustion in Blastic Plasmacytoid Dendritic Cell Neoplasm. Front Immunol 2022; 13:809414. [PMID: 35359938 PMCID: PMC8960171 DOI: 10.3389/fimmu.2022.809414] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/16/2022] [Indexed: 12/18/2022] Open
Abstract
The immune system represents a major barrier to cancer progression, driving the evolution of immunoregulatory interactions between malignant cells and T-cells in the tumor environment. Blastic plasmacytoid dendritic cell neoplasm (BPDCN), a rare acute leukemia with plasmacytoid dendritic cell (pDC) differentiation, provides a unique opportunity to study these interactions. pDCs are key producers of interferon alpha (IFNA) that play an important role in T-cell activation at the interface between the innate and adaptive immune system. To assess how uncontrolled proliferation of malignant BPDCN cells affects the tumor environment, we catalog immune cell heterogeneity in the bone marrow (BM) of five healthy controls and five BPDCN patients by analyzing 52,803 single-cell transcriptomes, including 18,779 T-cells. We test computational techniques for robust cell type classification and find that T-cells in BPDCN patients consistently upregulate interferon alpha (IFNA) response and downregulate tumor necrosis factor alpha (TNFA) pathways. Integrating transcriptional data with T-cell receptor sequencing via shared barcodes reveals significant T-cell exhaustion in BPDCN that is positively correlated with T-cell clonotype expansion. By highlighting new mechanisms of T-cell exhaustion and immune evasion in BPDCN, our results demonstrate the value of single-cell multiomics to understand immune cell interactions in the tumor environment.
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Affiliation(s)
- Erica A. K. DePasquale
- Division of Hematology, Brigham and Women’s Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, United States
| | - Daniel Ssozi
- Division of Hematology, Brigham and Women’s Hospital, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Marina Ainciburu
- Hemato-Oncology Program, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Instituto de Investigación Sanitaria de Navarra (IDISNA), Pamplona, Spain
| | - Jonathan Good
- Division of Hematology, Brigham and Women’s Hospital, Boston, MA, United States
- Department of Human Biology, Sattler College, Boston, MA, United States
| | - Jenny Noel
- Division of Hematology, Brigham and Women’s Hospital, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Martin A. Villanueva
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Division of Health Science & Technology, Harvard Medical School, Cambridge, MA, United States
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, United States
- Ragon Institute, Harvard University, Massachusetts Institute of Technology, and Massachusetts General Hospital, Cambridge, MA, United States
| | - Charles P. Couturier
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Division of Health Science & Technology, Harvard Medical School, Cambridge, MA, United States
| | - Alex K. Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Division of Health Science & Technology, Harvard Medical School, Cambridge, MA, United States
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, United States
- Ragon Institute, Harvard University, Massachusetts Institute of Technology, and Massachusetts General Hospital, Cambridge, MA, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Sary F. Aranki
- Division of Thoracic and Cardiac Surgery, Brigham and Women’s Hospital, Boston, MA, United States
| | - Hari R. Mallidi
- Division of Thoracic and Cardiac Surgery, Brigham and Women’s Hospital, Boston, MA, United States
| | - Gabriel K. Griffin
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Andrew A. Lane
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Peter van Galen
- Division of Hematology, Brigham and Women’s Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, United States
- *Correspondence: Peter van Galen,
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