1
|
Sun B, da Costa KAS, Alrubayyi A, Kokici J, Fisher-Pearson N, Hussain N, D'Anna S, Piermatteo L, Salpini R, Svicher V, Kucykowicz S, Ghosh I, Burns F, Kinloch S, Simoes P, Bhagani S, Kennedy PTF, Maini MK, Bashford-Rogers R, Gill US, Peppa D. HIV/HBV coinfection remodels the immune landscape and natural killer cell ADCC functional responses. Hepatology 2024; 80:649-663. [PMID: 38687604 DOI: 10.1097/hep.0000000000000877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/23/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND AND AIMS HBV and HIV coinfection is a common occurrence globally, with significant morbidity and mortality. Both viruses lead to immune dysregulation including changes in natural killer (NK) cells, a key component of antiviral defense and a promising target for HBV cure strategies. Here we used high-throughput single-cell analysis to explore the immune cell landscape in people with HBV mono-infection and HIV/HBV coinfection, on antiviral therapy, with emphasis on identifying the distinctive characteristics of NK cell subsets that can be therapeutically harnessed. APPROACH AND RESULTS Our data show striking differences in the transcriptional programs of NK cells. HIV/HBV coinfection was characterized by an over-representation of adaptive, KLRC2 -expressing NK cells, including a higher abundance of a chemokine-enriched ( CCL3/CCL4 ) adaptive cluster. The NK cell remodeling in HIV/HBV coinfection was reflected in enriched activation pathways, including CD3ζ phosphorylation and ZAP-70 translocation that can mediate stronger antibody-dependent cellular cytotoxicity responses and a bias toward chemokine/cytokine signaling. By contrast, HBV mono-infection imposed a stronger cytotoxic profile on NK cells and a more prominent signature of "exhaustion" with higher circulating levels of HBsAg. Phenotypic alterations in the NK cell pool in coinfection were consistent with increased "adaptiveness" and better capacity for antibody-dependent cellular cytotoxicity compared to HBV mono-infection. Overall, an adaptive NK cell signature correlated inversely with circulating levels of HBsAg and HBV-RNA in our cohort. CONCLUSIONS This study provides new insights into the differential signature and functional profile of NK cells in HBV and HIV/HBV coinfection, highlighting pathways that can be manipulated to tailor NK cell-focused approaches to advance HBV cure strategies in different patient groups.
Collapse
Affiliation(s)
- Bo Sun
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Kelly A S da Costa
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, UK
| | | | - Jonida Kokici
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, UK
| | | | - Noshin Hussain
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, UK
| | - Stefano D'Anna
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | | | - Romina Salpini
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | | | - Stephanie Kucykowicz
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, UK
| | - Indrajit Ghosh
- Department of HIV, Mortimer Market Centre, CNWL NHS Trust, London, UK
| | - Fiona Burns
- The Ian Charleson Day Centre, Royal Free Hospital NHS Foundation Trust, London, UK
- UCL Faculty of Population Health Sciences, Institute for Global Health, University College London, London, UK
| | - Sabine Kinloch
- The Ian Charleson Day Centre, Royal Free Hospital NHS Foundation Trust, London, UK
| | - Pedro Simoes
- The Ian Charleson Day Centre, Royal Free Hospital NHS Foundation Trust, London, UK
| | - Sanjay Bhagani
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, UK
- Department of HIV Medicine, Royal Free Hospital NHS Foundation Trust, London, UK
| | - Patrick T F Kennedy
- Centre for Immunobiology, Barts Liver Centre, Barts & The London School of Medicine & Dentistry, QMUL, London, UK
| | - Mala K Maini
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, UK
| | | | - Upkar S Gill
- Centre for Immunobiology, Barts Liver Centre, Barts & The London School of Medicine & Dentistry, QMUL, London, UK
| | - Dimitra Peppa
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, UK
- Department of HIV, Mortimer Market Centre, CNWL NHS Trust, London, UK
- The Ian Charleson Day Centre, Royal Free Hospital NHS Foundation Trust, London, UK
| |
Collapse
|
2
|
Netskar H, Pfefferle A, Goodridge JP, Sohlberg E, Dufva O, Teichmann SA, Brownlie D, Michaëlsson J, Marquardt N, Clancy T, Horowitz A, Malmberg KJ. Pan-cancer profiling of tumor-infiltrating natural killer cells through transcriptional reference mapping. Nat Immunol 2024; 25:1445-1459. [PMID: 38956379 PMCID: PMC11291284 DOI: 10.1038/s41590-024-01884-z] [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: 10/25/2023] [Accepted: 05/30/2024] [Indexed: 07/04/2024]
Abstract
The functional diversity of natural killer (NK) cell repertoires stems from differentiation, homeostatic, receptor-ligand interactions and adaptive-like responses to viral infections. In the present study, we generated a single-cell transcriptional reference map of healthy human blood- and tissue-derived NK cells, with temporal resolution and fate-specific expression of gene-regulatory networks defining NK cell differentiation. Transfer learning facilitated incorporation of tumor-infiltrating NK cell transcriptomes (39 datasets, 7 solid tumors, 427 patients) into the reference map to analyze tumor microenvironment (TME)-induced perturbations. Of the six functionally distinct NK cell states identified, a dysfunctional stressed CD56bright state susceptible to TME-induced immunosuppression and a cytotoxic TME-resistant effector CD56dim state were commonly enriched across tumor types, the ratio of which was predictive of patient outcome in malignant melanoma and osteosarcoma. This resource may inform the design of new NK cell therapies and can be extended through transfer learning to interrogate new datasets from experimental perturbations or disease conditions.
Collapse
Affiliation(s)
- Herman Netskar
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
| | - Aline Pfefferle
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
| | | | - Ebba Sohlberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Olli Dufva
- Wellcome Sanger Institute, Wellcome Genome Clymphoid cells (ILCs)ampus, Hinxton, Cambridge, UK
| | - Sarah A Teichmann
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Demi Brownlie
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Sweden
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Nicole Marquardt
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Sweden
| | - Trevor Clancy
- Oslo Cancer Cluster, NEC OncoImmunity AS, Oslo, Norway
- Department of Vaccine Informatics, Institute for Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Amir Horowitz
- Department of Immunology & Immunotherapy, Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Karl-Johan Malmberg
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway.
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
3
|
Rebuffet L, Melsen JE, Escalière B, Basurto-Lozada D, Bhandoola A, Björkström NK, Bryceson YT, Castriconi R, Cichocki F, Colonna M, Davis DM, Diefenbach A, Ding Y, Haniffa M, Horowitz A, Lanier LL, Malmberg KJ, Miller JS, Moretta L, Narni-Mancinelli E, O'Neill LAJ, Romagnani C, Ryan DG, Sivori S, Sun D, Vagne C, Vivier E. High-dimensional single-cell analysis of human natural killer cell heterogeneity. Nat Immunol 2024; 25:1474-1488. [PMID: 38956378 PMCID: PMC11291291 DOI: 10.1038/s41590-024-01883-0] [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: 01/16/2024] [Accepted: 05/23/2024] [Indexed: 07/04/2024]
Abstract
Natural killer (NK) cells are innate lymphoid cells (ILCs) contributing to immune responses to microbes and tumors. Historically, their classification hinged on a limited array of surface protein markers. Here, we used single-cell RNA sequencing (scRNA-seq) and cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) to dissect the heterogeneity of NK cells. We identified three prominent NK cell subsets in healthy human blood: NK1, NK2 and NK3, further differentiated into six distinct subgroups. Our findings delineate the molecular characteristics, key transcription factors, biological functions, metabolic traits and cytokine responses of each subgroup. These data also suggest two separate ontogenetic origins for NK cells, leading to divergent transcriptional trajectories. Furthermore, we analyzed the distribution of NK cell subsets in the lung, tonsils and intraepithelial lymphocytes isolated from healthy individuals and in 22 tumor types. This standardized terminology aims at fostering clarity and consistency in future research, thereby improving cross-study comparisons.
Collapse
Grants
- Wellcome Trust
- P01 CA111412 NCI NIH HHS
- E.V laboratory at CIML and Assistance-Publique des Hôpitaux de Marseille is supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (TILC, grant agreement No. 694502 and MInfla-TILC, grand agreement No. 875102), the Agence Nationale de la Recherche including the PIONEER Project (ANR-17-RHUS-0007), MSDAvenir, Innate Pharma and institutional grants awarded to the CIML (INSERM, CNRS and Aix-Marseille University) and Marseille Immunopole.
- D.M.D laboratory is funded by the Medical Research Council (MR/W031698/1) and the Wellcome Trust (110091/Z/15/Z).
- A.D. laboratory is supported by the European Research Council (ERC AdG ILCAdapt, 101055309 to A.D.) and by the German Research Foundation (DFG) (SFB 1444/427826188 and TRR 241/375876048 to A.D., SPP1937/Di764 /9-2 to A.D.). We are grateful to the Benjamin Franklin Flow Cytometry Facility (BFFC) for support in cell sorting. BFFC is supported by DFG Instrument Grants INST 335/597-1 FUGG und INST 335/777-1 FUGG.
- KJM was supported by the Research Council of Norway, Center of Excellence: Precision Immunotherapy Alliance (332727), the US National Cancer Institute (P01 CA111412, P009500901).
- L.M. is funded by Associazione Italiana contro il Cancro (AIRC), 5xmille project n. 21147.
- C.R. laboratory is supported by the ERC Advanced Grant ‘MEM-CLONK’ (101055157) and the Deutsche Forschungsgemeinschaft (DFG) grants SFB TRR241 B02 and RO 3565/7-1.
- D.G.R is supported by funding from the Medical Research Council (MRC) (MC_UU_00028) and Wellcome Trust-Academy of Medical Sciences (WT-AMS) (SBF009\1119).
- S.S. is funded by Ministero dell’Istruzione, dell’Università e della Ricerca: PRIN 2017WC8499_004 and Fondazione AIRC: AIRC 5×1000 project id. 21147.
Collapse
Affiliation(s)
- Lucas Rebuffet
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Janine E Melsen
- Leiden University Medical Center, Willem-Alexander Children's Hospital, Laboratory for Pediatric Immunology, Leiden, the Netherlands
- Leiden University Medical Center, Department of Immunology, Leiden, the Netherlands
| | - Bertrand Escalière
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Daniela Basurto-Lozada
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Avinash Bhandoola
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Yenan T Bryceson
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
- Sweden Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Roberta Castriconi
- Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy
- Laboratory of Clinical and Experimental Immunology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Frank Cichocki
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel M Davis
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, South Kensington, London, UK
| | - Andreas Diefenbach
- Laboratory of Innate Immunity, Institute of Microbiology, Infectious Diseases and Immunology (I-MIDI), Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Mucosal and Developmental Immunology, Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Yi Ding
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Dermatology and NIHR Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Amir Horowitz
- Department of Immunology & Immunotherapy, The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lewis L Lanier
- Department of Microbiology and Immunology and the Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, USA
| | - Karl-Johan Malmberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Precision Immunotherapy Alliance, The University of Oslo, Oslo, Norway
- The Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Jeffrey S Miller
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Lorenzo Moretta
- Tumor Immunology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Emilie Narni-Mancinelli
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Luke A J O'Neill
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Chiara Romagnani
- Institute of Medical Immunology, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Innate Immunity, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), ein Leibniz Institut, Berlin, Germany
- Berlin University Alliance, Berlin, Germany
| | - Dylan G Ryan
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Simona Sivori
- Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Dan Sun
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Constance Vagne
- Innate Pharma Research Laboratories, Innate Pharma, Marseille, France
| | - Eric Vivier
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France.
- Innate Pharma Research Laboratories, Innate Pharma, Marseille, France.
- APHM, Hôpital de la Timone, Marseille-Immunopôle, Marseille, France.
- Paris-Saclay Cancer Cluster, Le Kremlin-Bicêtre, France.
| |
Collapse
|
4
|
Nath PR, Maclean M, Nagarajan V, Lee JW, Yakin M, Kumar A, Nadali H, Schmidt B, Kaya KD, Kodati S, Young A, Caspi RR, Kuiper JJW, Sen HN. Single-cell profiling identifies a CD8 bright CD244 bright Natural Killer cell subset that reflects disease activity in HLA-A29-positive birdshot chorioretinopathy. Nat Commun 2024; 15:6443. [PMID: 39085199 PMCID: PMC11291632 DOI: 10.1038/s41467-024-50472-0] [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: 11/14/2022] [Accepted: 07/12/2024] [Indexed: 08/02/2024] Open
Abstract
Birdshot chorioretinopathy is an inflammatory eye condition strongly associated with MHC-I allele HLA-A29. The striking association with MHC-I suggests involvement of T cells, whereas natural killer (NK) cell involvement remains largely unstudied. Here we show that HLA-A29-positive birdshot chorioretinopathy patients have a skewed NK cell pool containing expanded CD16 positive NK cells which produce more proinflammatory cytokines. These NK cells contain populations that express CD8A which is involved in MHC-I recognition on target cells, display gene signatures indicative of high cytotoxic activity (GZMB, PRF1 and ISG15), and signaling through NK cell receptor CD244 (SH2D1B). Long-term monitoring of a cohort of birdshot chorioretinopathy patients with active disease identifies a population of CD8bright CD244bright NK cells, which rapidly declines to normal levels upon clinical remission following successful treatment. Collectively, these studies implicate CD8bright CD244bright NK cells in birdshot chorioretinopathy.
Collapse
Affiliation(s)
- Pulak R Nath
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA.
- Lentigen Technology Inc., A Miltenyi Biotec Company, 910 Clopper Road, Gaithersburg, MD, 20878, USA.
| | - Mary Maclean
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
- Translational Immunology Section, Office of Science and Technology, NIAMS, Bethesda, NIH, USA
| | - Vijay Nagarajan
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
- Immunoregulation Section, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Jung Wha Lee
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Mehmet Yakin
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Aman Kumar
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Hadi Nadali
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Brian Schmidt
- NIH Intramural Sequencing Center, NIH, Rockville, USA
| | - Koray D Kaya
- Medical Genetics and Ophthalmic Genomics Unit, NEI, NIH, Bethesda, USA
| | - Shilpa Kodati
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Alice Young
- NIH Intramural Sequencing Center, NIH, Rockville, USA
| | - Rachel R Caspi
- Immunoregulation Section, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Jonas J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands.
| | - H Nida Sen
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| |
Collapse
|
5
|
Schlenker R, Schwalie PC, Dettling S, Huesser T, Irmisch A, Mariani M, Martínez Gómez JM, Ribeiro A, Limani F, Herter S, Yángüez E, Hoves S, Somandin J, Siebourg-Polster J, Kam-Thong T, de Matos IG, Umana P, Dummer R, Levesque MP, Bacac M. Myeloid-T cell interplay and cell state transitions associated with checkpoint inhibitor response in melanoma. MED 2024; 5:759-779.e7. [PMID: 38593812 DOI: 10.1016/j.medj.2024.03.015] [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: 06/14/2023] [Revised: 11/23/2023] [Accepted: 03/17/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND The treatment of melanoma, the deadliest form of skin cancer, has greatly benefited from immunotherapy. However, many patients do not show a durable response, which is only partially explained by known resistance mechanisms. METHODS We performed single-cell RNA sequencing of tumor immune infiltrates and matched peripheral blood mononuclear cells of 22 checkpoint inhibitor (CPI)-naive stage III-IV metastatic melanoma patients. After sample collection, the same patients received CPI treatment, and their response was assessed. FINDINGS CPI responders showed high levels of classical monocytes in peripheral blood, which preferentially transitioned toward CXCL9-expressing macrophages in tumors. Trajectories of tumor-infiltrating CD8+ T cells diverged at the level of effector memory/stem-like T cells, with non-responder cells progressing into a state characterized by cellular stress and apoptosis-related gene expression. Consistently, predicted non-responder-enriched myeloid-T/natural killer cell interactions were primarily immunosuppressive, while responder-enriched interactions were supportive of T cell priming and effector function. CONCLUSIONS Our study illustrates that the tumor immune microenvironment prior to CPI treatment can be indicative of response. In perspective, modulating the myeloid and/or effector cell compartment by altering the described cell interactions and transitions could improve immunotherapy response. FUNDING This research was funded by Roche Pharma Research and Early Development.
Collapse
Affiliation(s)
- Ramona Schlenker
- Roche Innovation Center Munich, Roche Pharma Research and Early Development (pRED), Penzberg, Germany.
| | | | - Steffen Dettling
- Roche Innovation Center Munich, Roche Pharma Research and Early Development (pRED), Penzberg, Germany
| | - Tamara Huesser
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Anja Irmisch
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Marisa Mariani
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Julia M Martínez Gómez
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Alison Ribeiro
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Florian Limani
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Sylvia Herter
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Emilio Yángüez
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Sabine Hoves
- Roche Innovation Center Munich, Roche Pharma Research and Early Development (pRED), Penzberg, Germany
| | - Jitka Somandin
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | | | | | | | - Pablo Umana
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Reinhard Dummer
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Marina Bacac
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| |
Collapse
|
6
|
Ruoss S, Nasamran CA, Ball ST, Chen JL, Halter KN, Bruno KA, Whisenant TC, Parekh JN, Dorn SN, Esparza MC, Bremner SN, Fisch KM, Engler AJ, Ward SR. Comparative single-cell transcriptional and proteomic atlas of clinical-grade injectable mesenchymal source tissues. SCIENCE ADVANCES 2024; 10:eadn2831. [PMID: 38996032 PMCID: PMC11244553 DOI: 10.1126/sciadv.adn2831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 06/06/2024] [Indexed: 07/14/2024]
Abstract
Bone marrow aspirate concentrate (BMAC) and adipose-derived stromal vascular fraction (ADSVF) are the most marketed stem cell therapies to treat a variety of conditions in the general population and elite athletes. Both tissues have been used interchangeably clinically even though their detailed composition, heterogeneity, and mechanisms of action have neither been rigorously inventoried nor compared. This lack of information has prevented investigations into ideal dosages and has facilitated anecdata and misinformation. Here, we analyzed single-cell transcriptomes, proteomes, and flow cytometry profiles from paired clinical-grade BMAC and ADSVF. This comparative transcriptional atlas challenges the prevalent notion that there is one therapeutic cell type present in both tissues. We also provide data of surface markers that may enable isolation and investigation of cell (sub)populations. Furthermore, the proteome atlas highlights intertissue and interpatient heterogeneity of injected proteins with potentially regenerative or immunomodulatory capacities. An interactive webtool is available online.
Collapse
Affiliation(s)
- Severin Ruoss
- Department of Orthopaedic Surgery, UC San Diego, La Jolla, CA, USA
| | - Chanond A. Nasamran
- Center for Computational Biology and Bioinformatics, UC San Diego, La Jolla, CA, USA
| | - Scott T. Ball
- Department of Orthopaedic Surgery, UC San Diego, La Jolla, CA, USA
| | - Jeffrey L. Chen
- Department of Anesthesiology, Center for Pain, UC San Diego, La Jolla, CA, USA
| | - Kenneth N. Halter
- Department of Anesthesiology, Center for Pain, UC San Diego, La Jolla, CA, USA
| | - Kelly A. Bruno
- Department of Anesthesiology, Center for Pain, UC San Diego, La Jolla, CA, USA
| | - Thomas C. Whisenant
- Center for Computational Biology and Bioinformatics, UC San Diego, La Jolla, CA, USA
| | - Jesal N. Parekh
- Department of Orthopaedic Surgery, UC San Diego, La Jolla, CA, USA
| | - Shanelle N. Dorn
- Department of Orthopaedic Surgery, UC San Diego, La Jolla, CA, USA
| | - Mary C. Esparza
- Department of Orthopaedic Surgery, UC San Diego, La Jolla, CA, USA
| | | | - Kathleen M. Fisch
- Center for Computational Biology and Bioinformatics, UC San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, UC San Diego, La Jolla, CA, USA
| | - Adam J. Engler
- Chien-Lay Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Samuel R. Ward
- Department of Orthopaedic Surgery, UC San Diego, La Jolla, CA, USA
- Chien-Lay Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Department of Radiology, UC San Diego, La Jolla, CA, USA
| |
Collapse
|
7
|
Peris Sempere V, Luo G, Muñiz-Castrillo S, Pinto AL, Picard G, Rogemond V, Titulaer MJ, Finke C, Leypoldt F, Kuhlenbäumer G, Jones HF, Dale RC, Binks S, Irani SR, Bastiaansen AE, de Vries JM, de Bruijn MAAM, Roelen DL, Kim TJ, Chu K, Lee ST, Kanbayashi T, Pollock NR, Kichula KM, Mumme-Monheit A, Honnorat J, Norman PJ, Mignot E. HLA and KIR genetic association and NK cells in anti-NMDAR encephalitis. Front Immunol 2024; 15:1423149. [PMID: 39050850 PMCID: PMC11266021 DOI: 10.3389/fimmu.2024.1423149] [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: 04/25/2024] [Accepted: 06/06/2024] [Indexed: 07/27/2024] Open
Abstract
Introduction Genetic predisposition to autoimmune encephalitis with antibodies against N-methyl-D-aspartate receptor (NMDAR) is poorly understood. Given the diversity of associated environmental factors (tumors, infections), we hypothesized that human leukocyte antigen (HLA) and killer-cell immunoglobulin-like receptors (KIR), two extremely polymorphic gene complexes key to the immune system, might be relevant for the genetic predisposition to anti-NMDAR encephalitis. Notably, KIR are chiefly expressed by Natural Killer (NK) cells, recognize distinct HLA class I allotypes and play a major role in anti-tumor and anti-infection responses. Methods We conducted a Genome Wide Association Study (GWAS) with subsequent control-matching using Principal Component Analysis (PCA) and HLA imputation, in a multi-ethnic cohort of anti-NMDAR encephalitis (n=479); KIR and HLA were further sequenced in a large subsample (n=323). PCA-controlled logistic regression was then conducted for carrier frequencies (HLA and KIR) and copy number variation (KIR). HLA-KIR interaction associations were also modeled. Additionally, single cell sequencing was conducted in peripheral blood mononuclear cells from 16 cases and 16 controls, NK cells were sorted and phenotyped. Results Anti-NMDAR encephalitis showed a weak HLA association with DRB1*01:01~DQA1*01:01~DQB1*05:01 (OR=1.57, 1.51, 1.45; respectively), and DRB1*11:01 (OR=1.60); these effects were stronger in European descendants and in patients without an underlying ovarian teratoma. More interestingly, we found increased copy number variation of KIR2DL5B (OR=1.72), principally due to an overrepresentation of KIR2DL5B*00201. Further, we identified two allele associations in framework genes, KIR2DL4*00103 (25.4% vs. 12.5% in controls, OR=1.98) and KIR3DL3*00302 (5.3% vs. 1.3%, OR=4.44). Notably, the ligands of these KIR2DL4 and KIR3DL3, respectively, HLA-G and HHLA2, are known to act as immune checkpoint with immunosuppressive functions. However, we did not find differences in specific KIR-HLA ligand interactions or HLA-G polymorphisms between cases and controls. Similarly, gene expression of CD56dim or CD56bright NK cells did not differ between cases and controls. Discussion Our observations for the first time suggest that the HLA-KIR axis might be involved in anti-NMDAR encephalitis. While the genetic risk conferred by the identified polymorphisms appears small, a role of this axis in the pathophysiology of this disease appears highly plausible and should be analyzed in future studies.
Collapse
Affiliation(s)
- Vicente Peris Sempere
- Stanford Center for Sleep Science and Medicine, Stanford University, Palo Alto, CA, United States
| | - Guo Luo
- Stanford Center for Sleep Science and Medicine, Stanford University, Palo Alto, CA, United States
| | - Sergio Muñiz-Castrillo
- Stanford Center for Sleep Science and Medicine, Stanford University, Palo Alto, CA, United States
| | - Anne-Laurie Pinto
- French Reference Center on Paraneoplastic Neurological Syndrome and Autoimmune Encephalitis, Hospices Civils de Lyon, Lyon, France
- Institut MeLiS INSERM U1314/CNRS UMR 5284, Université Claude Bernard Lyon 1, Lyon, France
| | - Géraldine Picard
- French Reference Center on Paraneoplastic Neurological Syndrome and Autoimmune Encephalitis, Hospices Civils de Lyon, Lyon, France
- Institut MeLiS INSERM U1314/CNRS UMR 5284, Université Claude Bernard Lyon 1, Lyon, France
| | - Véronique Rogemond
- French Reference Center on Paraneoplastic Neurological Syndrome and Autoimmune Encephalitis, Hospices Civils de Lyon, Lyon, France
- Institut MeLiS INSERM U1314/CNRS UMR 5284, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Carsten Finke
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin School of Mind and Brain, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Frank Leypoldt
- Department of Neurology, Christian-Albrechts-University/University Hospital Schleswig-Holstein, Kiel, Germany
- Neuroimmunology, Institute of Clinical Chemistry, University Hospital Schleswig-Holstein Kiel/Lübeck, Kiel, Germany
| | - Gregor Kuhlenbäumer
- Department of Neurology, Christian-Albrechts-University/University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Hannah F. Jones
- Starship Hospital, Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Russell C. Dale
- Kids Neuroscience Centre, Children’s Hospital at Westmead clinical school, University of Sydney, Sydney, NSW, Australia
| | - Sophie Binks
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Department of Neurology, John Radcliffe Hospital, Oxford, United Kingdom
| | - Sarosh R. Irani
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Departments of Neurology and Neurosciences, Mayo Clinic, Jacksonville, FL, United States
| | | | - Juna M. de Vries
- Department of Neurology, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Dave L. Roelen
- Department of Immunogenetics and Transplantation Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Tae-Joon Kim
- Department of Neurology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Kon Chu
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Soon-Tae Lee
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | | | - Nicholas R. Pollock
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Katherine M. Kichula
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Abigail Mumme-Monheit
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Jérôme Honnorat
- French Reference Center on Paraneoplastic Neurological Syndrome and Autoimmune Encephalitis, Hospices Civils de Lyon, Lyon, France
- Institut MeLiS INSERM U1314/CNRS UMR 5284, Université Claude Bernard Lyon 1, Lyon, France
| | - Paul J. Norman
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Emmanuel Mignot
- Stanford Center for Sleep Science and Medicine, Stanford University, Palo Alto, CA, United States
| |
Collapse
|
8
|
Hmiel L, Zhang S, Obare LM, Santana MADO, Wanjalla CN, Titanji BK, Hileman CO, Bagchi S. Inflammatory and Immune Mechanisms for Atherosclerotic Cardiovascular Disease in HIV. Int J Mol Sci 2024; 25:7266. [PMID: 39000373 PMCID: PMC11242562 DOI: 10.3390/ijms25137266] [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: 06/01/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Atherosclerotic vascular disease disproportionately affects persons living with HIV (PLWH) compared to those without. The reasons for the excess risk include dysregulated immune response and inflammation related to HIV infection itself, comorbid conditions, and co-infections. Here, we review an updated understanding of immune and inflammatory pathways underlying atherosclerosis in PLWH, including effects of viral products, soluble mediators and chemokines, innate and adaptive immune cells, and important co-infections. We also present potential therapeutic targets which may reduce cardiovascular risk in PLWH.
Collapse
Affiliation(s)
- Laura Hmiel
- Department of Medicine, Division of Infectious Disease, MetroHealth Medical Center and Case Western Reserve University, Cleveland, OH 44109, USA
| | - Suyu Zhang
- Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Laventa M. Obare
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Celestine N. Wanjalla
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Boghuma K. Titanji
- Division of Infectious Diseases, Emory University, Atlanta, GA 30322, USA
| | - Corrilynn O. Hileman
- Department of Medicine, Division of Infectious Disease, MetroHealth Medical Center and Case Western Reserve University, Cleveland, OH 44109, USA
| | - Shashwatee Bagchi
- Division of Infectious Diseases, Washington University in St. Louis, St. Louis, MO 63110, USA
| |
Collapse
|
9
|
Ding Y, Lavaert M, Grassmann S, Band VI, Chi L, Das A, Das S, Harly C, Shissler SC, Malin J, Peng D, Zhao Y, Zhu J, Belkaid Y, Sun JC, Bhandoola A. Distinct developmental pathways generate functionally distinct populations of natural killer cells. Nat Immunol 2024; 25:1183-1192. [PMID: 38872000 DOI: 10.1038/s41590-024-01865-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 05/08/2024] [Indexed: 06/15/2024]
Abstract
Natural killer (NK) cells function by eliminating virus-infected or tumor cells. Here we identified an NK-lineage-biased progenitor population, referred to as early NK progenitors (ENKPs), which developed into NK cells independently of common precursors for innate lymphoid cells (ILCPs). ENKP-derived NK cells (ENKP_NK cells) and ILCP-derived NK cells (ILCP_NK cells) were transcriptionally different. We devised combinations of surface markers that identified highly enriched ENKP_NK and ILCP_NK cell populations in wild-type mice. Furthermore, Ly49H+ NK cells that responded to mouse cytomegalovirus infection primarily developed from ENKPs, whereas ILCP_NK cells were better IFNγ producers after infection with Salmonella and herpes simplex virus. Human CD56dim and CD56bright NK cells were transcriptionally similar to ENKP_NK cells and ILCP_NK cells, respectively. Our findings establish the existence of two pathways of NK cell development that generate functionally distinct NK cell subsets in mice and further suggest these pathways may be conserved in humans.
Collapse
Affiliation(s)
- Yi Ding
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marieke Lavaert
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Simon Grassmann
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Victor I Band
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Liang Chi
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Arundhoti Das
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sumit Das
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christelle Harly
- Nantes Université, Inserm UMR 1307, CNRS UMR 6075, Université d'Angers, Nantes, France
- LabEx IGO "Immunotherapy, Graft Oncology", Nantes, France
| | - Susannah C Shissler
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Justin Malin
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dingkang Peng
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yongge Zhao
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jinfang Zhu
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Avinash Bhandoola
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
10
|
Hashemi E, McCarthy C, Rao S, Malarkannan S. Transcriptomic diversity of innate lymphoid cells in human lymph nodes compared to BM and spleen. Commun Biol 2024; 7:769. [PMID: 38918571 PMCID: PMC11199704 DOI: 10.1038/s42003-024-06450-9] [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: 10/27/2023] [Accepted: 06/12/2024] [Indexed: 06/27/2024] Open
Abstract
Innate lymphoid cells (ILCs) are largely tissue-resident, mostly described within the mucosal tissues. However, their presence and functions in the human draining lymph nodes (LNs) are unknown. Our study unravels the tissue-specific transcriptional profiles of 47,287 CD127+ ILCs within the human abdominal and thoracic LNs. LNs contain a higher frequency of CD127+ ILCs than in BM or spleen. We define independent stages of ILC development, including EILP and pILC in the BM. These progenitors exist in LNs in addition to naïve ILCs (nILCs) that can differentiate into mature ILCs. We define three ILC1 and four ILC3 sub-clusters in the LNs. ILC1 and ILC3 subsets have clusters with high heat shock protein-encoding genes. We identify previously unrecognized regulons, including the BACH2 family for ILC1 and the ATF family for ILC3. Our study is the comprehensive characterization of ILCs in LNs, providing an in-depth understanding of ILC-mediated immunity in humans.
Collapse
Affiliation(s)
- Elaheh Hashemi
- Blood Research Institute, Versiti, Milwaukee, WI, USA
- Department of Microbiology and Immunology, Medical College of Wisconsin (MCW), Milwaukee, WI, USA
| | | | - Sridhar Rao
- Blood Research Institute, Versiti, Milwaukee, WI, USA
- Division of Hematology, Oncology, and Bone Marrow Transplantation, Department of Pediatrics, MCW, Milwaukee, WI, USA
- Department of Cell Biology, Neurobiology, and Anatomy, MCW, Milwaukee, WI, USA
| | - Subramaniam Malarkannan
- Blood Research Institute, Versiti, Milwaukee, WI, USA.
- Department of Microbiology and Immunology, Medical College of Wisconsin (MCW), Milwaukee, WI, USA.
- Division of Hematology, Oncology, and Bone Marrow Transplantation, Department of Pediatrics, MCW, Milwaukee, WI, USA.
- Division of Hematology and Oncology, Department of Medicine, MCW, Milwaukee, WI, USA.
| |
Collapse
|
11
|
Wang Y, Huang B, Liang T, Jiang L, Wu M, Liu X, Zhu M, Song X, Zhao N, Wei H, Zheng C, Ni F. Venetoclax acts as an immunometabolic modulator to potentiate adoptive NK cell immunotherapy against leukemia. Cell Rep Med 2024; 5:101580. [PMID: 38776913 PMCID: PMC11228450 DOI: 10.1016/j.xcrm.2024.101580] [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: 12/20/2023] [Revised: 03/27/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
Natural killer (NK) cell-based immunotherapy holds promise for cancer treatment; however, its efficacy remains limited, necessitating the development of alternative strategies. Here, we report that venetoclax, an FDA-approved BCL-2 inhibitor, directly activates NK cells, enhancing their cytotoxicity against acute myeloid leukemia (AML) both in vitro and in vivo, likely independent of BCL-2 inhibition. Through comprehensive approaches, including bulk and single-cell RNA sequencing, avidity measurement, and functional assays, we demonstrate that venetoclax increases the avidity of NK cells to AML cells and promotes lytic granule polarization during immunological synapse (IS) formation. Notably, we identify a distinct CD161lowCD218b+ NK cell subpopulation that exhibits remarkable sensitivity to venetoclax treatment. Furthermore, venetoclax promotes mitochondrial respiration and ATP synthesis via the NF-κB pathway, thereby facilitating IS formation in NK cells. Collectively, our findings establish venetoclax as a multifaceted immunometabolic modulator of NK cell function and provide a promising strategy for augmenting NK cell-based cancer immunotherapy.
Collapse
MESH Headings
- Bridged Bicyclo Compounds, Heterocyclic/pharmacology
- Bridged Bicyclo Compounds, Heterocyclic/therapeutic use
- Killer Cells, Natural/immunology
- Killer Cells, Natural/drug effects
- Humans
- Sulfonamides/pharmacology
- Animals
- Leukemia, Myeloid, Acute/therapy
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/pathology
- Mice
- Immunotherapy, Adoptive/methods
- Cell Line, Tumor
- NF-kappa B/metabolism
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Mice, Inbred NOD
Collapse
Affiliation(s)
- Yan Wang
- Department of Hematology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; Institute of Immunology, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Beibei Huang
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Tingting Liang
- Department of Hematology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; Institute of Immunology, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Lai Jiang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Mingming Wu
- Department of Hematology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; Institute of Immunology, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Xinru Liu
- Department of Hematology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; Institute of Immunology, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Mingming Zhu
- Department of Hematology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; Institute of Immunology, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Xian Song
- Department of Hematology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; Institute of Immunology, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Na Zhao
- Department of Hematology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Haiming Wei
- Department of Hematology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; Institute of Immunology, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
| | - Changcheng Zheng
- Department of Hematology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
| | - Fang Ni
- Department of Hematology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; Institute of Immunology, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
| |
Collapse
|
12
|
Decker JT, Hall MS, Nanua D, Orbach SM, Roy J, Angadi A, Caton J, Hesse L, Jeruss JS, Shea LD. Dynamic Transcriptional Programs During Single NK Cell Killing: Connecting Form to Function in Cellular Immunotherapy. Cell Mol Bioeng 2024; 17:177-188. [PMID: 39050513 PMCID: PMC11263395 DOI: 10.1007/s12195-024-00812-3] [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: 09/12/2023] [Accepted: 07/03/2024] [Indexed: 07/27/2024] Open
Abstract
Introduction Natural killer (NK) cell-based therapies are a promising new method for treating indolent cancer, however engineering new therapies is complex and progress towards therapy for solid tumors is slow. New methods for determining the underlying intracellular signaling driving the killing phenotype would significantly improve this progress. Methods We combined single-cell RNA sequencing with live cell imaging of a model system of NK cell killing to correlate transcriptomic data with functional output. A model of NK cell activity, the NK-92 cell line killing of HeLa cervical cancer cells, was used for these studies. NK cell killing activity was observed by microscopy during co-culture with target HeLa cells and killing activity subsequently manually mapped based on NK cell location and Annexin V expression. NK cells from this culture system were profiled by single-cell RNA sequencing using the 10× Genomics platform, and transcription factor activity inferred using the Viper and DoRothEA R packages. Luminescent microscopy of reporter constructs in the NK cells was then used to correlate activity of inferred transcriptional activity with killing activity. Results NK cells had heterogeneous killing activity during 10 h of culture with target HeLa cells. Analysis of the single cell sequencing data identified Nuclear Factor Kappa B (NF-κB), Signal Transducer and Activator of Transcription 1 (STAT1) and MYC activity as potential drivers of NK cell functional phenotype in our model system. Live cell imaging of the transcription factor activity found NF-κB activity was significantly correlated with past killing activity. No correlation was observed between STAT1 or MYC activity and NK cell killing. Conclusions Combining luminescent microscopy of transcription factor activity with single-cell RNA sequencing is an effective means of assigning functional phenotypes to inferred transcriptomics data. Supplementary Information The online version contains supplementary material available at 10.1007/s12195-024-00812-3.
Collapse
Affiliation(s)
- Joseph T. Decker
- Department of Biomedical Engineering, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109 USA
- Department of Cariology, Restorative Sciences, and Endodontics, University of Michigan School of Dentistry, Ann Arbor, MI 48109 USA
| | - Matthew S. Hall
- Department of Biomedical Engineering, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109 USA
| | - Devak Nanua
- Department of Biomedical Engineering, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109 USA
| | - Sophia M. Orbach
- Department of Biomedical Engineering, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109 USA
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028 USA
| | - Jyotirmoy Roy
- Department of Biomedical Engineering, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109 USA
| | - Amogh Angadi
- Department of Biomedical Engineering, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109 USA
| | - Julianna Caton
- Department of Biomedical Engineering, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109 USA
| | - Lauren Hesse
- Department of Biomedical Engineering, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109 USA
| | - Jacqueline S. Jeruss
- Department of Biomedical Engineering, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109 USA
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Lonnie D. Shea
- Department of Biomedical Engineering, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109 USA
| |
Collapse
|
13
|
Lee EJ, Suh M, Choi H, Choi Y, Hwang DW, Bae S, Lee DS. Spatial transcriptomic brain imaging reveals the effects of immunomodulation therapy on specific regional brain cells in a mouse dementia model. BMC Genomics 2024; 25:516. [PMID: 38796425 PMCID: PMC11128132 DOI: 10.1186/s12864-024-10434-8] [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: 02/18/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024] Open
Abstract
Increasing evidence of brain-immune crosstalk raises expectations for the efficacy of novel immunotherapies in Alzheimer's disease (AD), but the lack of methods to examine brain tissues makes it difficult to evaluate therapeutics. Here, we investigated the changes in spatial transcriptomic signatures and brain cell types using the 10x Genomics Visium platform in immune-modulated AD models after various treatments. To proceed with an analysis suitable for barcode-based spatial transcriptomics, we first organized a workflow for segmentation of neuroanatomical regions, establishment of appropriate gene combinations, and comprehensive review of altered brain cell signatures. Ultimately, we investigated spatial transcriptomic changes following administration of immunomodulators, NK cell supplements and an anti-CD4 antibody, which ameliorated behavior impairment, and designated brain cells and regions showing probable associations with behavior changes. We provided the customized analytic pipeline into an application named STquantool. Thus, we anticipate that our approach can help researchers interpret the real action of drug candidates by simultaneously investigating the dynamics of all transcripts for the development of novel AD therapeutics.
Collapse
Affiliation(s)
- Eun Ji Lee
- Department of Nuclear Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Minseok Suh
- Department of Nuclear Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Institute of Radiation Medicine, Medical Research Center, Seoul National University, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Hongyoon Choi
- Department of Nuclear Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Yoori Choi
- Department of Nuclear Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Cliniclal Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Do Won Hwang
- Research and Development Center, THERABEST Inc., Seocho-daero 40-gil, Seoul, 06657, Republic of Korea
| | - Sungwoo Bae
- Department of Nuclear Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
- Institute of Radiation Medicine, Medical Research Center, Seoul National University, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
| | - Dong Soo Lee
- Department of Nuclear Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea.
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
- Institute of Radiation Medicine, Medical Research Center, Seoul National University, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Medical Science and Engineering, School of Convergence Science and Technology, POSTECH, Pohang, Republic of Korea.
| |
Collapse
|
14
|
Xu L, Saunders K, Huang SP, Knutsdottir H, Martinez-Algarin K, Terrazas I, Chen K, McArthur HM, Maués J, Hodgdon C, Reddy SM, Roussos Torres ET, Xu L, Chan IS. A comprehensive single-cell breast tumor atlas defines epithelial and immune heterogeneity and interactions predicting anti-PD-1 therapy response. Cell Rep Med 2024; 5:101511. [PMID: 38614094 PMCID: PMC11148512 DOI: 10.1016/j.xcrm.2024.101511] [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: 03/09/2023] [Revised: 02/20/2024] [Accepted: 03/20/2024] [Indexed: 04/15/2024]
Abstract
We present an integrated single-cell RNA sequencing atlas of the primary breast tumor microenvironment (TME) containing 236,363 cells from 119 biopsy samples across eight datasets. In this study, we leverage this resource for multiple analyses of immune and cancer epithelial cell heterogeneity. We define natural killer (NK) cell heterogeneity through six subsets in the breast TME. Because NK cell heterogeneity correlates with epithelial cell heterogeneity, we characterize epithelial cells at the level of single-gene expression, molecular subtype, and 10 categories reflecting intratumoral transcriptional heterogeneity. We develop InteractPrint, which considers how cancer epithelial cell heterogeneity influences cancer-immune interactions. We use T cell InteractPrint to predict response to immune checkpoint inhibition (ICI) in two breast cancer clinical trials testing neoadjuvant anti-PD-1 therapy. T cell InteractPrint was predictive of response in both trials versus PD-L1 (AUC = 0.82, 0.83 vs. 0.50, 0.72). This resource enables additional high-resolution investigations of the breast TME.
Collapse
Affiliation(s)
- Lily Xu
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kaitlyn Saunders
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shao-Po Huang
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hildur Knutsdottir
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD, USA
| | - Kenneth Martinez-Algarin
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Isabella Terrazas
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Heather M McArthur
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | | | - Sangeetha M Reddy
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Evanthia T Roussos Torres
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Isaac S Chan
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
15
|
Anderko RR, DePuyt AE, Bronson R, Bullotta AC, Aga E, Bosch RJ, Jones RB, Eron JJ, Mellors JW, Gandhi RT, McMahon DK, Macatangay BJ, Rinaldo CR, Mailliard RB. Persistence of a Skewed Repertoire of NK Cells in People with HIV-1 on Long-Term Antiretroviral Therapy. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1564-1578. [PMID: 38551350 PMCID: PMC11073922 DOI: 10.4049/jimmunol.2300672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
Abstract
HIV-1 infection greatly alters the NK cell phenotypic and functional repertoire. This is highlighted by the expansion of a rare population of FcRγ- NK cells exhibiting characteristics of traditional immunologic memory in people with HIV (PWH). Although current antiretroviral therapy (ART) effectively controls HIV-1 viremia and disease progression, its impact on HIV-1-associated NK cell abnormalities remains unclear. To address this, we performed a longitudinal analysis detailing conventional and memory-like NK cell characteristics in n = 60 PWH during the first 4 y of ART. Throughout this regimen, a skewed repertoire of cytokine unresponsive FcRγ- memory-like NK cells persisted and accompanied an overall increase in NK surface expression of CD57 and KLRG1, suggestive of progression toward immune senescence. These traits were linked to elevated serum inflammatory biomarkers and increasing Ab titers to human CMV, with human CMV viremia detected in approximately one-third of PWH at years 1-4 of ART. Interestingly, 40% of PWH displayed atypical NK cell subsets, representing intermediate stages of NK-poiesis based on single-cell multiomic trajectory analysis. Our findings indicate that NK cell irregularities persist in PWH despite long-term ART, underscoring the need to better understand the causative mechanisms that prevent full restoration of immune health in PWH.
Collapse
Affiliation(s)
- Renee R. Anderko
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Allison E. DePuyt
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Rhianna Bronson
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Arlene C. Bullotta
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Evgenia Aga
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ronald J. Bosch
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - R. Brad Jones
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Joseph J. Eron
- Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - John W. Mellors
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Rajesh T. Gandhi
- Infectious Disease Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Deborah K. McMahon
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Bernard J. Macatangay
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Charles R. Rinaldo
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Robbie B. Mailliard
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| |
Collapse
|
16
|
Wang M, Wu H, Jiang W, Ren Y, Yuan X, Wang Y, Zhou J, Feng W, Wang Y, Xu T, Zhang D, Fang Y, He C, Li W. Differences in nature killer cell response and interference with mitochondrial DNA induced apoptosis in moxifloxacin environment. Int Immunopharmacol 2024; 132:111970. [PMID: 38608472 DOI: 10.1016/j.intimp.2024.111970] [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: 12/18/2023] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024]
Abstract
OBJECTIVES As antibiotics become more prevalent, accuracy and safety are critical. Moxifloxacin (MXF) have been reported to have immunomodulatory effects on a variety of immune cells and even anti-proliferative and pro-apoptotic effects, but the mechanism of action is not fully clear. METHODS Peripheral blood mononuclear cells (PBMC) from experimental groups of healthy adults (n = 3) were treated with MXF (10ug/ml) in vitro for 24 h. Single-cell sequencing was performed to investigate differences in the response of each immune cell to MXF. Flow cytometry determined differential gene expression in subsets of most damaged NK cells. Pseudo-time analysis identified drivers that influence MXF-stimulated cell differentiation. Detection of mitochondrial DNA and its involvement in the mitochondrial respiratory chain pathway clarifies the origin of MXF-induced stress injury. RESULTS Moxifloxacin-environmental NK cells are markedly reduced: a new subset of NK cells emerges, and immediate-early-response genes in this subset indicate the presence of an early activation response. The inhibitory receptor-dominant subset shows enhanced activation, leading to increased expression of cytokines and chemokines. The near-mature subset showed greater cytotoxicity and the most pronounced cellular damage. CD56bright cells responded by antagonizing the regulation of activation and inhibitory signals, demonstrating a strong cleavage capacity. The severe depletion of mitochondrial genes was focused on apoptosis induced by the mitochondrial respiratory chain complex. CONCLUSION NK cells exhibit heightened sensitivity to the MXF environment. Different NK subsets upregulate the expression of cytokines and chemokines through different activation pathways. Concurrently, MXF induces impairment of the mitochondrial oxidative phosphorylation system, culminating in apoptosis.
Collapse
Affiliation(s)
- Mengqing Wang
- Department of Emergency and Critical Care, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Hao Wu
- Department of Emergency and Critical Care, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Weiwei Jiang
- Department of Emergency and Critical Care, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Yunfei Ren
- Department of Emergency and Critical Care, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Xiaowei Yuan
- Department of Emergency and Critical Care, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Yanan Wang
- Department of Emergency and Critical Care, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Jian Zhou
- Department of Emergency and Critical Care, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Wei Feng
- Department of Emergency and Critical Care, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Yusen Wang
- Department of Emergency and Critical Care, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Tianpeng Xu
- Department of Emergency and Critical Care, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Danying Zhang
- Department of Emergency and Critical Care, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Yunhao Fang
- Department of Emergency and Critical Care, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Chao He
- Department of Emergency and Critical Care, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Wenfang Li
- Department of Emergency and Critical Care, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China.
| |
Collapse
|
17
|
Wang R, Peng X, Yuan Y, Shi B, Liu Y, Ni H, Guo W, Yang Q, Liu P, Wang J, Su Z, Yu S, Liu D, Zhang J, Xia J, Liu X, Li H, Yang Z, Peng Z. Dynamic immune recovery process after liver transplantation revealed by single-cell multi-omics analysis. Innovation (N Y) 2024; 5:100599. [PMID: 38510071 PMCID: PMC10952083 DOI: 10.1016/j.xinn.2024.100599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
Elucidating the temporal process of immune remodeling under immunosuppressive treatment after liver transplantation (LT) is critical for precise clinical management strategies. Here, we performed a single-cell multi-omics analysis of peripheral blood mononuclear cells (PBMCs) collected from LT patients (with and without acute cellular rejection [ACR]) at 13 time points. Validation was performed in two independent cohorts with additional LT patients and healthy controls. Our study revealed a four-phase recovery process after LT and delineated changes in immune cell composition, expression programs, and interactions along this process. The intensity of the immune response differs between the ACR and non-ACR patients. Notably, the newly identified inflamed NK cells, CD14+RNASE2+ monocytes, and FOS-expressing monocytes emerged as predictive indicators of ACR. This study illuminates the longitudinal evolution of the immune cell landscape under tacrolimus-based immunosuppressive treatment during LT recovery, providing a four-phase framework that aids the clinical management of LT patients.
Collapse
Affiliation(s)
- Rui Wang
- Organ Transplantation Clinical Medical Center of Xiamen University, Department of General Surgery, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361102, China
- Organ Transplantation Institute of Xiamen University, Xiamen Human Organ Transplantation Quality Control Center, Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen 361102, China
| | - Xiao Peng
- Organ Transplantation Clinical Medical Center of Xiamen University, Department of General Surgery, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361102, China
- Organ Transplantation Institute of Xiamen University, Xiamen Human Organ Transplantation Quality Control Center, Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen 361102, China
| | - Yixin Yuan
- Organ Transplantation Clinical Medical Center of Xiamen University, Department of General Surgery, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361102, China
- Organ Transplantation Institute of Xiamen University, Xiamen Human Organ Transplantation Quality Control Center, Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen 361102, China
| | - Baojie Shi
- Organ Transplantation Clinical Medical Center of Xiamen University, Department of General Surgery, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361102, China
- Organ Transplantation Institute of Xiamen University, Xiamen Human Organ Transplantation Quality Control Center, Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen 361102, China
| | - Yuan Liu
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Hengxiao Ni
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Qiwei Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China
| | - Pingguo Liu
- Department of Hepatobiliary & Pancreatic Surgery, The National Key Clinical Specialty, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361102, China
| | - Jie Wang
- Organ Transplantation Clinical Medical Center of Xiamen University, Department of General Surgery, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361102, China
- Organ Transplantation Institute of Xiamen University, Xiamen Human Organ Transplantation Quality Control Center, Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen 361102, China
| | - Zhaojie Su
- Organ Transplantation Clinical Medical Center of Xiamen University, Department of General Surgery, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361102, China
- Organ Transplantation Institute of Xiamen University, Xiamen Human Organ Transplantation Quality Control Center, Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen 361102, China
| | - Shengnan Yu
- Organ Transplantation Clinical Medical Center of Xiamen University, Department of General Surgery, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361102, China
- Organ Transplantation Institute of Xiamen University, Xiamen Human Organ Transplantation Quality Control Center, Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen 361102, China
| | - Dehua Liu
- Organ Transplantation Clinical Medical Center of Xiamen University, Department of General Surgery, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361102, China
- Organ Transplantation Institute of Xiamen University, Xiamen Human Organ Transplantation Quality Control Center, Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen 361102, China
| | - Jinyan Zhang
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Junjie Xia
- Organ Transplantation Clinical Medical Center of Xiamen University, Department of General Surgery, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361102, China
- Organ Transplantation Institute of Xiamen University, Xiamen Human Organ Transplantation Quality Control Center, Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen 361102, China
| | - Xueni Liu
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Hao Li
- Organ Transplantation Clinical Medical Center of Xiamen University, Department of General Surgery, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361102, China
- Organ Transplantation Institute of Xiamen University, Xiamen Human Organ Transplantation Quality Control Center, Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen 361102, China
| | - Zhengfeng Yang
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Zhihai Peng
- Organ Transplantation Clinical Medical Center of Xiamen University, Department of General Surgery, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361102, China
- Organ Transplantation Institute of Xiamen University, Xiamen Human Organ Transplantation Quality Control Center, Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen 361102, China
| |
Collapse
|
18
|
Andrews TS, Nakib D, Perciani CT, Ma XZ, Liu L, Winter E, Camat D, Chung SW, Lumanto P, Manuel J, Mangroo S, Hansen B, Arpinder B, Thoeni C, Sayed B, Feld J, Gehring A, Gulamhusein A, Hirschfield GM, Ricciuto A, Bader GD, McGilvray ID, MacParland S. Single-cell, single-nucleus, and spatial transcriptomics characterization of the immunological landscape in the healthy and PSC human liver. J Hepatol 2024; 80:730-743. [PMID: 38199298 DOI: 10.1016/j.jhep.2023.12.023] [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: 02/01/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024]
Abstract
BACKGROUND & AIMS Primary sclerosing cholangitis (PSC) is an immune-mediated cholestatic liver disease for which there is an unmet need to understand the cellular composition of the affected liver and how it underlies disease pathogenesis. We aimed to generate a comprehensive atlas of the PSC liver using multi-omic modalities and protein-based functional validation. METHODS We employed single-cell and single-nucleus RNA sequencing (47,156 cells and 23,000 nuclei) and spatial transcriptomics (one sample by 10x Visium and five samples with Nanostring GeoMx DSP) to profile the cellular ecosystem in 10 PSC livers. Transcriptomic profiles were compared to 24 neurologically deceased donor livers (107,542 cells) and spatial transcriptomics controls, as well as 18,240 cells and 20,202 nuclei from three PBC livers. Flow cytometry was performed to validate PSC-specific differences in immune cell phenotype and function. RESULTS PSC explants with parenchymal cirrhosis and prominent periductal fibrosis contained a population of cholangiocyte-like hepatocytes that were surrounded by diverse immune cell populations. PSC-associated biliary, mesenchymal, and endothelial populations expressed chemokine and cytokine transcripts involved in immune cell recruitment. Additionally, expanded CD4+ T cells and recruited myeloid populations in the PSC liver expressed the corresponding receptors to these chemokines and cytokines, suggesting potential recruitment. Tissue-resident macrophages, by contrast, were reduced in number and exhibited a dysfunctional and downregulated inflammatory response to lipopolysaccharide and interferon-γ stimulation. CONCLUSIONS We present a comprehensive atlas of the PSC liver and demonstrate an exhaustion-like phenotype of myeloid cells and markers of chronic cytokine expression in late-stage PSC lesions. This atlas expands our understanding of the cellular complexity of PSC and has potential to guide the development of novel treatments. IMPACT AND IMPLICATIONS Primary sclerosing cholangitis (PSC) is a rare liver disease characterized by chronic inflammation and irreparable damage to the bile ducts, which eventually results in liver failure. Due to a limited understanding of the underlying pathogenesis of disease, treatment options are limited. To address this, we sequenced healthy and diseased livers to compare the activity, interactions, and localization of immune and non-immune cells. This revealed that hepatocytes lining PSC scar regions co-express cholangiocyte markers, whereas immune cells infiltrate the scar lesions. Of these cells, macrophages, which typically contribute to tissue repair, were enriched in immunoregulatory genes and demonstrated a lack of responsiveness to stimulation. These cells may be involved in maintaining hepatic inflammation and could be a target for novel therapies.
Collapse
Affiliation(s)
- Tallulah S Andrews
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada; Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5C1, Canada; Department of Computer Science, University of Western Ontario, London, ON, N6A 3K7, Canada.
| | - Diana Nakib
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Catia T Perciani
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Xue Zhong Ma
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Lewis Liu
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Erin Winter
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Damra Camat
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Sai W Chung
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Patricia Lumanto
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Justin Manuel
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Shantel Mangroo
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Bettina Hansen
- Toronto Centre for Liver Disease, University Health Network, Toronto, ON, M5G 2C4, Canada; Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, M5T 3M6, Canada
| | - Bal Arpinder
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Cornelia Thoeni
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Blayne Sayed
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Jordan Feld
- Toronto Centre for Liver Disease, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Adam Gehring
- Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada; Toronto Centre for Liver Disease, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Aliya Gulamhusein
- Toronto Centre for Liver Disease, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Gideon M Hirschfield
- Toronto Centre for Liver Disease, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Amanda Ricciuto
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.
| | - Ian D McGilvray
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada.
| | - Sonya MacParland
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5G 1L7, Canada.
| |
Collapse
|
19
|
Kust SA, Ustiuzhanina MO, Streltsova MA, Shelyakin PV, Kryukov MA, Lutsenko GV, Sudarikova AV, Merzlyak EM, Britanova OV, Sapozhnikov AM, Kovalenko EI. HLA-DR Expression in Natural Killer Cells Marks Distinct Functional States, Depending on Cell Differentiation Stage. Int J Mol Sci 2024; 25:4609. [PMID: 38731828 PMCID: PMC11083986 DOI: 10.3390/ijms25094609] [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: 03/22/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
HLA-DR-positive NK cells, found in both healthy individuals and patients with different inflammatory diseases, are characterized as activated cells. However, data on their capacity for IFNγ production or cytotoxic response vary between studies. Thus, more precise investigation is needed of the mechanisms related to the induction of HLA-DR expression in NK cells, their associations with NK cell differentiation stage, and functional or metabolic state. In this work, HLA-DR-expressing NK cell subsets were investigated using transcriptomic analysis, metabolic activity assays, and analysis of intercellular signaling cascades. We demonstrated that HLA-DR+CD56bright NK cells were characterized by a proliferative phenotype, while HLA-DR+CD56dim NK cells exhibited features of adaptive cells and loss of inhibitory receptors with increased expression of MHC class II trans-activator CIITA. The activated state of HLA-DR-expressing NK cells was confirmed by higher levels of ATP and mitochondrial mass observed in this subset compared to HLA-DR- cells, both ex vivo and after stimulation in culture. We showed that HLA-DR expression in NK cells in vitro can be induced both through stimulation by exogenous IL-2 and IL-21, as well as through auto-stimulation by NK-cell-produced IFNγ. At the intracellular level, HLA-DR expression depended on the activation of STAT3- and ERK1/2-mediated pathways, with subsequent activation of isoform 3 of the transcription factor CIITA. The obtained results broaden the knowledge about HLA-DR-positive NK cell appearance, diversity, and functions, which might be useful in terms of understanding the role of this subset in innate immunity and assessing their possible implications in NK cell-based therapy.
Collapse
Affiliation(s)
- Sofya A. Kust
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (S.A.K.); (M.O.U.); (M.A.S.); (M.A.K.); (G.V.L.); (E.M.M.); (O.V.B.); (A.M.S.)
| | - Maria O. Ustiuzhanina
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (S.A.K.); (M.O.U.); (M.A.S.); (M.A.K.); (G.V.L.); (E.M.M.); (O.V.B.); (A.M.S.)
| | - Maria A. Streltsova
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (S.A.K.); (M.O.U.); (M.A.S.); (M.A.K.); (G.V.L.); (E.M.M.); (O.V.B.); (A.M.S.)
| | | | - Maxim A. Kryukov
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (S.A.K.); (M.O.U.); (M.A.S.); (M.A.K.); (G.V.L.); (E.M.M.); (O.V.B.); (A.M.S.)
- Federal State Autonomous Institution, N.N. Burdenko National Medical Research Center of Neurosurgery, the Ministry of Health of the Russian Federation, 125047 Moscow, Russia;
| | - Gennady V. Lutsenko
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (S.A.K.); (M.O.U.); (M.A.S.); (M.A.K.); (G.V.L.); (E.M.M.); (O.V.B.); (A.M.S.)
| | - Anna V. Sudarikova
- Federal State Autonomous Institution, N.N. Burdenko National Medical Research Center of Neurosurgery, the Ministry of Health of the Russian Federation, 125047 Moscow, Russia;
| | - Ekaterina M. Merzlyak
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (S.A.K.); (M.O.U.); (M.A.S.); (M.A.K.); (G.V.L.); (E.M.M.); (O.V.B.); (A.M.S.)
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Olga V. Britanova
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (S.A.K.); (M.O.U.); (M.A.S.); (M.A.K.); (G.V.L.); (E.M.M.); (O.V.B.); (A.M.S.)
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Alexandr M. Sapozhnikov
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (S.A.K.); (M.O.U.); (M.A.S.); (M.A.K.); (G.V.L.); (E.M.M.); (O.V.B.); (A.M.S.)
| | - Elena I. Kovalenko
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (S.A.K.); (M.O.U.); (M.A.S.); (M.A.K.); (G.V.L.); (E.M.M.); (O.V.B.); (A.M.S.)
| |
Collapse
|
20
|
Tian J, Bai X, Quek C. Single-Cell Informatics for Tumor Microenvironment and Immunotherapy. Int J Mol Sci 2024; 25:4485. [PMID: 38674070 PMCID: PMC11050520 DOI: 10.3390/ijms25084485] [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: 03/08/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Cancer comprises malignant cells surrounded by the tumor microenvironment (TME), a dynamic ecosystem composed of heterogeneous cell populations that exert unique influences on tumor development. The immune community within the TME plays a substantial role in tumorigenesis and tumor evolution. The innate and adaptive immune cells "talk" to the tumor through ligand-receptor interactions and signaling molecules, forming a complex communication network to influence the cellular and molecular basis of cancer. Such intricate intratumoral immune composition and interactions foster the application of immunotherapies, which empower the immune system against cancer to elicit durable long-term responses in cancer patients. Single-cell technologies have allowed for the dissection and characterization of the TME to an unprecedented level, while recent advancements in bioinformatics tools have expanded the horizon and depth of high-dimensional single-cell data analysis. This review will unravel the intertwined networks between malignancy and immunity, explore the utilization of computational tools for a deeper understanding of tumor-immune communications, and discuss the application of these approaches to aid in diagnosis or treatment decision making in the clinical setting, as well as the current challenges faced by the researchers with their potential future improvements.
Collapse
Affiliation(s)
| | | | - Camelia Quek
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (J.T.); (X.B.)
| |
Collapse
|
21
|
Cui Z, Li H, Liu C, Wang J, Chen C, Hu S, Zhao X, Li G. Single-cell data revealed exhaustion of characteristic NK cell subpopulations and T cell subpopulations in hepatocellular carcinoma. Aging (Albany NY) 2024; 16:6550-6565. [PMID: 38604154 PMCID: PMC11042964 DOI: 10.18632/aging.205723] [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: 10/30/2023] [Accepted: 03/13/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND The treatment and prognosis of patients with advanced hepatocellular carcinoma (HCC) have been a major medical challenge. Unraveling the landscape of tumor immune infiltrating cells (TIICs) in the immune microenvironment of HCC is of great significance to probe the molecular mechanisms. METHODS Based on single-cell data of HCC, the cell landscape was revealed from the perspective of TIICs. Special cell subpopulations were determined by the expression levels of marker genes. Differential expression analysis was conducted. The activity of each subpopulation was determined based on the highly expressed genes. CTLA4+ T-cell subpopulations affecting the prognosis of HCC were determined based on survival analysis. A single-cell regulatory network inference and clustering analysis was also performed to determine the transcription factor regulatory networks in the CTLA4+ T cell subpopulations. RESULTS 10 cell types were identified and NK cells and T cells showed high abundance in tumor tissues. Two NK cells subpopulations were present, FGFBP2+ NK cells, B3GNT7+ NK cells. Four T cells subpopulations were present, LAG3+ T cells, CTLA4+ T cells, RCAN3+ T cells, and HPGDS+ Th2 cells. FGFBP2+ NK cells, and CTLA4+ T cells were the exhaustive subpopulation. High CTLA4+ T cells contributed to poor prognostic outcomes and promoted tumor progression. Finally, a network of transcription factors regulated by NR3C1, STAT1, and STAT3, which were activated, was present in CTLA4+ T cells. CONCLUSION CTLA4+ T cell subsets in HCC exhibited functional exhaustion characteristics that probably inhibited T cell function through a transcription factor network dominated by NR3C1, STAT1, and STAT3.
Collapse
Affiliation(s)
- Zhongfeng Cui
- Department of Clinical Laboratory, Henan Provincial Infectious Disease Hospital, Zhengzhou 450000, China
| | - Hongzhi Li
- Department of Tuberculosis, Henan Provincial Infectious Disease Hospital, Zhengzhou 450000, China
| | - Chunli Liu
- Department of Infectious Diseases and Hepatology, Henan Provincial Infectious Disease Hospital, Zhengzhou 450000, China
| | - Juan Wang
- Department of Infectious Diseases and Hepatology, Henan Provincial Infectious Disease Hospital, Zhengzhou 450000, China
| | - Chunguang Chen
- Department of Clinical Laboratory, Henan Provincial Infectious Disease Hospital, Zhengzhou 450000, China
| | - Shanlei Hu
- Department of Infectious Diseases and Hepatology, Henan Provincial Infectious Disease Hospital, Zhengzhou 450000, China
| | - Xiaoli Zhao
- Department of Infectious Diseases and Hepatology, Henan Provincial Infectious Disease Hospital, Zhengzhou 450000, China
| | - Guangming Li
- Department of Infectious Diseases and Hepatology, Henan Provincial Infectious Disease Hospital, Zhengzhou 450000, China
| |
Collapse
|
22
|
Zhang Q, Lin J, Yang M, Li Z, Zhang M, Bu B. Therapeutic potential of natural killer cells in neuroimmunological diseases. Biomed Pharmacother 2024; 173:116371. [PMID: 38430631 DOI: 10.1016/j.biopha.2024.116371] [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: 12/17/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024] Open
Abstract
Natural killer (NK) cells, a major component of the innate immune system, have prominent immunoregulatory, antitumor proliferation, and antiviral activities. NK cells act as a double-edged sword with therapeutic potential in neurological autoimmunity. Emerging evidence has identified NK cells are involved in the development and progression of neuroimmunological diseases such as multiple sclerosis, neuromyelitis optica spectrum disorders, autoimmune encephalitis, Guillain-Barré Syndrome, chronic inflammatory demyelinating polyneuropathy, myasthenia gravis, and idiopathic inflammatory myopathy. However, the regulatory mechanisms and functional roles of NK cells are highly variable in different clinical states of neuroimmunological diseases and need to be further determined. In this review, we summarize the evidence for the heterogenic involvement of NK cells in the above conditions. Further, we describe cutting-edge NK-cell-based immunotherapy for neuroimmunological diseases in preclinical and clinical development and highlight challenges that must be overcome to fully realize the therapeutic potential of NK cells.
Collapse
Affiliation(s)
- Qing Zhang
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jing Lin
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mengge Yang
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhijun Li
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Min Zhang
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Bitao Bu
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China.
| |
Collapse
|
23
|
Wang Y, Xu M, Yao Y, Li Y, Zhang S, Fu Y, Wang X. Extracellular cancer‑associated fibroblasts: A novel subgroup in the cervical cancer microenvironment that exhibits tumor‑promoting roles and prognosis biomarker functions. Oncol Lett 2024; 27:167. [PMID: 38449793 PMCID: PMC10915806 DOI: 10.3892/ol.2024.14300] [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: 08/14/2023] [Accepted: 01/10/2024] [Indexed: 03/08/2024] Open
Abstract
Tumor invasion and metastasis are the processes that primarily cause adverse outcomes in patients with cervical cancer. Cancer-associated fibroblasts (CAFs), which participate in cancer progression and metastasis, are novel targets for the treatment of tumors. The present study aimed to assess the heterogeneity of CAFs in the cervical cancer microenvironment through single-cell RNA sequencing. After collecting five cervical cancer samples and obtaining the CAF-associated gene sets, the CAFs in the cervical cancer microenvironment were divided into myofibroblastic CAFs and extracellular (ec)CAFs. The ecCAFs appeared with more robust pro-tumorigenic effects than myCAFs according to enrichment analysis. Subsequently, through combining the ecCAF hub genes and bulk gene expression data for cervical cancer obtained from The Cancer Genome Atlas and Gene Ontology databases, univariate Cox regression and least absolute shrinkage and selection operator analyses were performed to establish a CAF-associated risk signature for patients with cancer. The established risk signature demonstrated a stable and strong prognostic capability in both the training and validation cohorts. Subsequently, the association between the risk signature and clinical data was evaluated, and a nomogram to facilitate clinical application was established. The risk score was demonstrated to be associated with both the tumor immune microenvironment and the therapeutic responses. Moreover, the signature also has predictive value for the prognosis of head and neck squamous cell carcinoma, and bladder urothelial carcinoma, which were also associated with human papillomavirus infection. In conclusion, the present study assessed the heterogeneity of CAFs in the cervical cancer microenvironment, and a subgroup of CAFs that may be closely associated with tumor progression was defined. Moreover, a signature based on the hub genes of ecCAFs was shown to have biomarker functionality in terms of predicting survival rates, and therefore this CAF subgroup may become a therapeutic target for cervical cancer in the future.
Collapse
Affiliation(s)
- Yuehan Wang
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Mingxia Xu
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Yeli Yao
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Ying Li
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Songfa Zhang
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Yunfeng Fu
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Xinyu Wang
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
- Department of Gynecology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, P.R. China
| |
Collapse
|
24
|
Tu C, Buckle I, Leal Rojas I, Rossi GR, Sester DP, Moore AS, Radford K, Guillerey C, Souza‐Fonseca‐Guimaraes F. Exploring NK cell receptor dynamics in paediatric leukaemias: implications for immunotherapy and prognosis. Clin Transl Immunology 2024; 13:e1501. [PMID: 38525380 PMCID: PMC10960520 DOI: 10.1002/cti2.1501] [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: 09/15/2023] [Revised: 02/11/2024] [Accepted: 03/13/2024] [Indexed: 03/26/2024] Open
Abstract
Objectives Immunotherapies targeting natural killer (NK) cell receptors have shown promise against leukaemia. Unfortunately, cancer immunosuppressive mechanisms that alter NK cell phenotype prevent such approaches from being successful. The study utilises advanced cytometry to examine how cancer immunosuppressive pathways affect NK cell phenotypic changes in clinical samples. Methods In this study, we conducted a high-dimensional examination of the cell surface expression of 16 NK cell receptors in paediatric patients with acute myeloid leukaemia and acute lymphoblastic leukaemia, as well as in samples of non-age matched adult peripheral blood (APB) and umbilical cord blood (UCB). An unsupervised analysis was carried out in order to identify NK cell populations present in paediatric leukaemias. Results We observed that leukaemia NK cells clustered together with UCB NK cells and expressed relatively higher levels of the NKG2A receptor compared to APB NK cells. In addition, CD56dimCD16+CD57- NK cells lacking NKG2A expression were mainly absent in paediatric leukaemia patients. However, CD56br NK cell populations expressing high levels of NKG2A were highly represented in paediatric leukaemia patients. NKG2A expression on leukaemia NK cells was found to be positively correlated with the expression of its ligand, suggesting that the NKG2A-HLA-E interaction may play a role in modifying NK cell responses to leukaemia cells. Conclusion We provide an in-depth analysis of NK cell populations in paediatric leukaemia patients. These results support the development of immunotherapies targeting immunosuppressive receptors, such as NKG2A, to enhance innate immunity against paediatric leukaemia.
Collapse
Affiliation(s)
- Cui Tu
- Cancer Immunotherapies Laboratory, Mater Research Institute, Translational Research InstituteUniversity of QueenslandBrisbaneQLDAustralia
- Frazer Institute, The University of QueenslandWoolloongabbaQLDAustralia
| | - Irina Buckle
- Cancer Immunotherapies Laboratory, Mater Research Institute, Translational Research InstituteUniversity of QueenslandBrisbaneQLDAustralia
| | - Ingrid Leal Rojas
- Cancer Immunotherapies Laboratory, Mater Research Institute, Translational Research InstituteUniversity of QueenslandBrisbaneQLDAustralia
| | | | - David P Sester
- TRI Flow Cytometry SuiteTranslational Research InstituteWoolloongabbaQLDAustralia
- Translational Research InstituteQueensland University of TechnologyBrisbaneQLDAustralia
| | - Andrew S Moore
- Oncology ServiceChildren's Health Queensland Hospital & Health ServiceSouth BrisbaneQLDAustralia
- Child Health Research CentreThe University of QueenslandSouth BrisbaneQLDAustralia
| | - Kristen Radford
- Cancer Immunotherapies Laboratory, Mater Research Institute, Translational Research InstituteUniversity of QueenslandBrisbaneQLDAustralia
| | - Camille Guillerey
- Cancer Immunotherapies Laboratory, Mater Research Institute, Translational Research InstituteUniversity of QueenslandBrisbaneQLDAustralia
| | | |
Collapse
|
25
|
Sheng B, Pan S, Ye M, Liu H, Zhang J, Zhao B, Ji H, Zhu X. Single-cell RNA sequencing of cervical exfoliated cells reveals potential biomarkers and cellular pathogenesis in cervical carcinogenesis. Cell Death Dis 2024; 15:130. [PMID: 38346944 PMCID: PMC10861450 DOI: 10.1038/s41419-024-06522-y] [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: 04/29/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/15/2024]
Abstract
Cervical cancer (CC) is a common gynecological malignancy. Despite the current screening methods have been proved effectively and significantly decreased CC morbidity and mortality, deficiencies still exist. Single-cell RNA sequencing (scRNA-seq) approach can identify the complex and rare cell populations at single-cell resolution. By scRNA-seq, the heterogeneity of tumor microenvironment across cervical carcinogenesis has been mapped and described. Whether these alterations could be detected and applied to CC screening is unclear. Herein, we performed scRNA-seq of 56,173 cervical exfoliated cells from 15 samples, including normal cervix, low-grade squamous intraepithelial lesion (LSIL), high-grade squamous intraepithelial lesion (HSIL), and malignancy. The present study delineated the alteration of immune and epithelial cells derived during the cervical lesion progression. A subset of lipid-associated macrophage was identified as a tumor-promoting element and could serve as a biomarker for predicting the progression of LSIL into HSIL, which was then verified by immunofluorescence. Furthermore, cell-cell communication analysis indicated the SPP1-CD44 axis might exhibit a protumor interaction between epithelial cell and macrophage. In this study, we investigated the cervical multicellular ecosystem in cervical carcinogenesis and identified potential biomarkers for early detection.
Collapse
Affiliation(s)
- Bo Sheng
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Shuya Pan
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Miaomiao Ye
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Hejing Liu
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Jiamin Zhang
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Bo Zhao
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Huihui Ji
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, China.
| | - Xueqiong Zhu
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, China.
| |
Collapse
|
26
|
Shekarkar Azgomi M, Badami GD, Lo Pizzo M, Tamburini B, Dieli C, La Manna MP, Dieli F, Caccamo N. Integrated Analysis of Single-Cell and Bulk RNA Sequencing Data Reveals Memory-like NK Cell Subset Associated with Mycobacterium tuberculosis Latency. Cells 2024; 13:293. [PMID: 38391906 PMCID: PMC10886487 DOI: 10.3390/cells13040293] [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: 12/22/2023] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/24/2024] Open
Abstract
Natural killer (NK) cells are innate-like lymphocytes that belong to the family of type-1 innate lymphoid cells and rapidly respond to virus-infected and tumor cells. In this study, we have combined scRNA-seq data and bulk RNA-seq data to define the phenotypic and molecular characteristics of peripheral blood NK cells. While the role of NK cells in immune surveillance against virus infections and tumors has been well established, their contribution to protective responses to other intracellular microorganisms, such as Mycobacterium tuberculosis (Mtb), is still poorly understood. In this study, we have combined scRNA-seq data and bulk RNA-seq data to illuminate the molecular characteristics of circulating NK cells in patients with active tuberculosis (TB) disease and subjects with latent Mtb infection (LTBI) and compared these characteristics with those of healthy donors (HDs) and patients with non-TB other pulmonary infectious diseases (ODs). We show here that the NK cell cluster was significantly increased in LTBI subjects, as compared to patients with active TB or other non-TB pulmonary diseases and HD, and this was mostly attributable to the expansion of an NK cell population expressing KLRC2, CD52, CCL5 and HLA-DRB1, which most likely corresponds to memory-like NK2.1 cells. These data were validated by flow cytometry analysis in a small cohort of samples, showing that LTBI subjects have a significant expansion of NK cells characterized by the prevalence of memory-like CD52+ NKG2C+ NK cells. Altogether, our results provide some new information on the role of NK cells in protective immune responses to Mtb.
Collapse
Affiliation(s)
- Mojtaba Shekarkar Azgomi
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR), Azienda Ospedaliera Universitaria Policlinico (AOUP) Paolo Giaccone, University of Palermo, 90127 Palermo, Italy; (M.S.A.); (G.D.B.); (M.L.P.); (B.T.); (C.D.); (M.P.L.M.); (N.C.)
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (BND), University of Palermo, 90127 Palermo, Italy
| | - Giusto Davide Badami
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR), Azienda Ospedaliera Universitaria Policlinico (AOUP) Paolo Giaccone, University of Palermo, 90127 Palermo, Italy; (M.S.A.); (G.D.B.); (M.L.P.); (B.T.); (C.D.); (M.P.L.M.); (N.C.)
| | - Marianna Lo Pizzo
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR), Azienda Ospedaliera Universitaria Policlinico (AOUP) Paolo Giaccone, University of Palermo, 90127 Palermo, Italy; (M.S.A.); (G.D.B.); (M.L.P.); (B.T.); (C.D.); (M.P.L.M.); (N.C.)
| | - Bartolo Tamburini
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR), Azienda Ospedaliera Universitaria Policlinico (AOUP) Paolo Giaccone, University of Palermo, 90127 Palermo, Italy; (M.S.A.); (G.D.B.); (M.L.P.); (B.T.); (C.D.); (M.P.L.M.); (N.C.)
- Department of Health Promotion, Mother and Childcare, Internal Medicine and Medical Specialties, University of Palermo, 90129 Palermo, Italy
| | - Costanza Dieli
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR), Azienda Ospedaliera Universitaria Policlinico (AOUP) Paolo Giaccone, University of Palermo, 90127 Palermo, Italy; (M.S.A.); (G.D.B.); (M.L.P.); (B.T.); (C.D.); (M.P.L.M.); (N.C.)
| | - Marco Pio La Manna
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR), Azienda Ospedaliera Universitaria Policlinico (AOUP) Paolo Giaccone, University of Palermo, 90127 Palermo, Italy; (M.S.A.); (G.D.B.); (M.L.P.); (B.T.); (C.D.); (M.P.L.M.); (N.C.)
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (BND), University of Palermo, 90127 Palermo, Italy
| | - Francesco Dieli
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR), Azienda Ospedaliera Universitaria Policlinico (AOUP) Paolo Giaccone, University of Palermo, 90127 Palermo, Italy; (M.S.A.); (G.D.B.); (M.L.P.); (B.T.); (C.D.); (M.P.L.M.); (N.C.)
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (BND), University of Palermo, 90127 Palermo, Italy
| | - Nadia Caccamo
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR), Azienda Ospedaliera Universitaria Policlinico (AOUP) Paolo Giaccone, University of Palermo, 90127 Palermo, Italy; (M.S.A.); (G.D.B.); (M.L.P.); (B.T.); (C.D.); (M.P.L.M.); (N.C.)
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (BND), University of Palermo, 90127 Palermo, Italy
| |
Collapse
|
27
|
Huuhtanen J, Adnan-Awad S, Theodoropoulos J, Forstén S, Warfvinge R, Dufva O, Bouhlal J, Dhapola P, Duàn H, Laajala E, Kasanen T, Klievink J, Ilander M, Jaatinen T, Olsson-Strömberg U, Hjorth-Hansen H, Burchert A, Karlsson G, Kreutzman A, Lähdesmäki H, Mustjoki S. Single-cell analysis of immune recognition in chronic myeloid leukemia patients following tyrosine kinase inhibitor discontinuation. Leukemia 2024; 38:109-125. [PMID: 37919606 PMCID: PMC10776410 DOI: 10.1038/s41375-023-02074-w] [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: 03/31/2023] [Revised: 09/19/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
Immunological control of residual leukemia cells is thought to occur in patients with chronic myeloid leukemia (CML) that maintain treatment-free remission (TFR) following tyrosine kinase inhibitor (TKI) discontinuation. To study this, we analyzed 55 single-cell RNA and T cell receptor (TCR) sequenced samples (scRNA+TCRαβ-seq) from patients with CML (n = 13, N = 25), other cancers (n = 28), and healthy (n = 7). The high number and active phenotype of natural killer (NK) cells in CML separated them from healthy and other cancers. Most NK cells in CML belonged to the active CD56dim cluster with high expression of GZMA/B, PRF1, CCL3/4, and IFNG, with interactions with leukemic cells via inhibitory LGALS9-TIM3 and PVR-TIGIT interactions. Accordingly, upregulation of LGALS9 was observed in CML target cells and TIM3 in NK cells when co-cultured together. Additionally, we created a classifier to identify TCRs targeting leukemia-associated antigen PR1 and quantified anti-PR1 T cells in 90 CML and 786 healthy TCRβ-sequenced samples. Anti-PR1 T cells were more prevalent in CML, enriched in bone marrow samples, and enriched in the mature, cytotoxic CD8 + TEMRA cluster, especially in a patient maintaining TFR. Our results highlight the role of NK cells and anti-PR1 T cells in anti-leukemic immune responses in CML.
Collapse
Affiliation(s)
- Jani Huuhtanen
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.
- Department of Computer Science, Aalto University, Espoo, Finland.
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
| | - Shady Adnan-Awad
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
| | - Jason Theodoropoulos
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Sofia Forstén
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Rebecca Warfvinge
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Olli Dufva
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Jonas Bouhlal
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Parashar Dhapola
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Hanna Duàn
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Essi Laajala
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Tiina Kasanen
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Jay Klievink
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Mette Ilander
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Taina Jaatinen
- Histocompatibility Testing Laboratory, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Ulla Olsson-Strömberg
- Department of Medical Sciences, Uppsala University and Hematology Section, Uppsala University Hospital, Uppsala, Sweden
| | - Henrik Hjorth-Hansen
- Department of Hematology, St. Olavs Hospital, Trondheim, Norway
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Andreas Burchert
- Department of Hematology, Oncology and Immunology, Philipps University Marburg, and University Medical Center Giessen and Marburg, Marburg, Germany
| | - Göran Karlsson
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Anna Kreutzman
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Satu Mustjoki
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
| |
Collapse
|
28
|
Dufva O, Gandolfi S, Huuhtanen J, Dashevsky O, Duàn H, Saeed K, Klievink J, Nygren P, Bouhlal J, Lahtela J, Näätänen A, Ghimire BR, Hannunen T, Ellonen P, Lähteenmäki H, Rumm P, Theodoropoulos J, Laajala E, Härkönen J, Pölönen P, Heinäniemi M, Hollmén M, Yamano S, Shirasaki R, Barbie DA, Roth JA, Romee R, Sheffer M, Lähdesmäki H, Lee DA, De Matos Simoes R, Kankainen M, Mitsiades CS, Mustjoki S. Single-cell functional genomics reveals determinants of sensitivity and resistance to natural killer cells in blood cancers. Immunity 2023; 56:2816-2835.e13. [PMID: 38091953 DOI: 10.1016/j.immuni.2023.11.008] [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: 10/31/2022] [Revised: 06/19/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023]
Abstract
Cancer cells can evade natural killer (NK) cell activity, thereby limiting anti-tumor immunity. To reveal genetic determinants of susceptibility to NK cell activity, we examined interacting NK cells and blood cancer cells using single-cell and genome-scale functional genomics screens. Interaction of NK and cancer cells induced distinct activation and type I interferon (IFN) states in both cell types depending on the cancer cell lineage and molecular phenotype, ranging from more sensitive myeloid to less sensitive B-lymphoid cancers. CRISPR screens in cancer cells uncovered genes regulating sensitivity and resistance to NK cell-mediated killing, including adhesion-related glycoproteins, protein fucosylation genes, and transcriptional regulators, in addition to confirming the importance of antigen presentation and death receptor signaling pathways. CRISPR screens with a single-cell transcriptomic readout provided insight into underlying mechanisms, including regulation of IFN-γ signaling in cancer cells and NK cell activation states. Our findings highlight the diversity of mechanisms influencing NK cell susceptibility across different cancers and provide a resource for NK cell-based therapies.
Collapse
Affiliation(s)
- Olli Dufva
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Sara Gandolfi
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jani Huuhtanen
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland; Department of Computer Science, Aalto University, 02150 Espoo, Finland
| | - Olga Dashevsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Hanna Duàn
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Khalid Saeed
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Jay Klievink
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Petra Nygren
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Jonas Bouhlal
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Jenni Lahtela
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Anna Näätänen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Bishwa R Ghimire
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Tiina Hannunen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Pekka Ellonen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Hanna Lähteenmäki
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Pauliina Rumm
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Jason Theodoropoulos
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Essi Laajala
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Jouni Härkönen
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Petri Pölönen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Merja Heinäniemi
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Maija Hollmén
- Medicity Research Laboratory, University of Turku, 20014 Turku, Finland
| | - Shizuka Yamano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Ryosuke Shirasaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - David A Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jennifer A Roth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rizwan Romee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Michal Sheffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, 02150 Espoo, Finland
| | - Dean A Lee
- Hematology/Oncology/BMT, Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Ricardo De Matos Simoes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Matti Kankainen
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland; Laboratory of Genetics, HUS Diagnostic Center, Hospital District of Helsinki and Uusima (HUS), 00290 Helsinki, Finland
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA.
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland.
| |
Collapse
|
29
|
Li H, Rahman MA, Ruesch M, Eisele CD, Anderson EM, Wright PW, Cao J, Ratnayake S, Chen Q, Yan C, Meerzaman D, Abraham RS, Freud AG, Anderson SK. Abundant binary promoter switches in lineage-determining transcription factors indicate a digital component of cell fate determination. Cell Rep 2023; 42:113454. [PMID: 37976160 PMCID: PMC10842785 DOI: 10.1016/j.celrep.2023.113454] [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: 10/28/2022] [Revised: 10/02/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Previous studies of the murine Ly49 and human KIR gene clusters implicated competing sense and antisense promoters in the control of variegated gene expression. In the current study, an examination of transcription factor genes defines an abundance of convergent and divergent sense/antisense promoter pairs, suggesting that competing promoters may control cell fate determination. Differentiation of CD34+ hematopoietic progenitors in vitro shows that cells with GATA1 antisense transcription have enhanced GATA2 transcription and a mast cell phenotype, whereas cells with GATA2 antisense transcription have increased GATA1 transcripts and an erythroblast phenotype. Detailed analyses of the AHR and RORC genes demonstrate the ability of competing promoters to act as binary switches and the association of antisense transcription with an immature/progenitor cell phenotype. These data indicate that alternative cell fates generated by promoter competition in lineage-determining transcription factors contribute to the programming of cell differentiation.
Collapse
Affiliation(s)
- Hongchuan Li
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Md Ahasanur Rahman
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Michael Ruesch
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH 43210, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Medical Scientist Training Program, The Ohio State University, Columbus, OH 43210, USA
| | - Caprice D Eisele
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH 43210, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Erik M Anderson
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Paul W Wright
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jennie Cao
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Shashikala Ratnayake
- Cancer Genomics and Bioinformatics Branch, Center for Biomedical Informatics & Information Technology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Qingrong Chen
- Cancer Genomics and Bioinformatics Branch, Center for Biomedical Informatics & Information Technology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Chunhua Yan
- Cancer Genomics and Bioinformatics Branch, Center for Biomedical Informatics & Information Technology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Daoud Meerzaman
- Cancer Genomics and Bioinformatics Branch, Center for Biomedical Informatics & Information Technology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Roshini S Abraham
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH 43210, USA; Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
| | - Aharon G Freud
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
| | - Stephen K Anderson
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
| |
Collapse
|
30
|
Dooley NL, Chabikwa TG, Pava Z, Loughland JR, Hamelink J, Berry K, Andrew D, Soon MSF, SheelaNair A, Piera KA, William T, Barber BE, Grigg MJ, Engwerda CR, Lopez JA, Anstey NM, Boyle MJ. Single cell transcriptomics shows that malaria promotes unique regulatory responses across multiple immune cell subsets. Nat Commun 2023; 14:7387. [PMID: 37968278 PMCID: PMC10651914 DOI: 10.1038/s41467-023-43181-7] [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: 11/23/2022] [Accepted: 11/02/2023] [Indexed: 11/17/2023] Open
Abstract
Plasmodium falciparum malaria drives immunoregulatory responses across multiple cell subsets, which protects from immunopathogenesis, but also hampers the development of effective anti-parasitic immunity. Understanding malaria induced tolerogenic responses in specific cell subsets may inform development of strategies to boost protective immunity during drug treatment and vaccination. Here, we analyse the immune landscape with single cell RNA sequencing during P. falciparum malaria. We identify cell type specific responses in sub-clustered major immune cell types. Malaria is associated with an increase in immunosuppressive monocytes, alongside NK and γδ T cells which up-regulate tolerogenic markers. IL-10-producing Tr1 CD4 T cells and IL-10-producing regulatory B cells are also induced. Type I interferon responses are identified across all cell types, suggesting Type I interferon signalling may be linked to induction of immunoregulatory networks during malaria. These findings provide insights into cell-specific and shared immunoregulatory changes during malaria and provide a data resource for further analysis.
Collapse
Affiliation(s)
- Nicholas L Dooley
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Environment and Sciences, Griffith University, Brisbane, QLD, Australia
| | | | - Zuleima Pava
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Julianne Hamelink
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- University of Queensland, Brisbane, QLD, Australia
| | - Kiana Berry
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Queensland University of Technology, Brisbane, QLD, Australia
| | - Dean Andrew
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Megan S F Soon
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Arya SheelaNair
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Kim A Piera
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Timothy William
- Infectious Diseases Society Kota Kinabalu Sabah-Menzies School of Health Research Program, Kota Kinabalu, Sabah, Malaysia
- Subang Jaya Medical Centre, Selangor, Malaysia
| | - Bridget E Barber
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Infectious Diseases Society Kota Kinabalu Sabah-Menzies School of Health Research Program, Kota Kinabalu, Sabah, Malaysia
| | - Matthew J Grigg
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Infectious Diseases Society Kota Kinabalu Sabah-Menzies School of Health Research Program, Kota Kinabalu, Sabah, Malaysia
| | | | - J Alejandro Lopez
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Environment and Sciences, Griffith University, Brisbane, QLD, Australia
| | - Nicholas M Anstey
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Infectious Diseases Society Kota Kinabalu Sabah-Menzies School of Health Research Program, Kota Kinabalu, Sabah, Malaysia
| | - Michelle J Boyle
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
- School of Environment and Sciences, Griffith University, Brisbane, QLD, Australia.
- University of Queensland, Brisbane, QLD, Australia.
- Queensland University of Technology, Brisbane, QLD, Australia.
- Burnet Institute, Melbourne, VIC, Australia.
| |
Collapse
|
31
|
Yue S, Wang Q, Zhang J, Hu Q, Liu C. Understanding cervical cancer at single-cell resolution. Cancer Lett 2023; 576:216408. [PMID: 37769795 DOI: 10.1016/j.canlet.2023.216408] [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: 05/24/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 10/03/2023]
Abstract
Cervical cancer is now the fourth most prevalent malignancy in women worldwide, representing a tremendous burden of cancer. The heterogeneity of complex tumor ecosystem impacts tumorigenesis, malignant progression, and response to treatment; thus, a thorough understanding of the tumor ecosystem is vital for enhancing the prognosis of patients with cervical cancer. The rapid development and widespread use of single-cell sequencing have generated a new paradigm of cancer research, providing a comprehensive and in-depth understanding of cancers. In this review, we give an overview of the recent advances made by leveraging single-cell sequencing studies in the dissection of cervical cancer ecosystem heterogeneity. We highlight the evolution of the cervical cancer ecosystem during tumor initiation, progression, and treatment. High-resolution dissection of cervical cancer at the single-cell level has the potential to drive the development of targeted therapies and enable the realization of personalized medicine.
Collapse
Affiliation(s)
- Shengqin Yue
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Qian Wang
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Jiajun Zhang
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Qinyong Hu
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
| | - Chao Liu
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
| |
Collapse
|
32
|
Tangherloni A, Riva SG, Myers B, Buffa FM, Cazzaniga P. MAGNETO: Cell type marker panel generator from single-cell transcriptomic data. J Biomed Inform 2023; 147:104510. [PMID: 37797704 DOI: 10.1016/j.jbi.2023.104510] [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: 02/28/2023] [Revised: 09/12/2023] [Accepted: 09/29/2023] [Indexed: 10/07/2023]
Abstract
Single-cell RNA sequencing experiments produce data useful to identify different cell types, including uncharacterized and rare ones. This enables us to study the specific functional roles of these cells in different microenvironments and contexts. After identifying a (novel) cell type of interest, it is essential to build succinct marker panels, composed of a few genes referring to cell surface proteins and clusters of differentiation molecules, able to discriminate the desired cells from the other cell populations. In this work, we propose a fully-automatic framework called MAGNETO, which can help construct optimal marker panels starting from a single-cell gene expression matrix and a cell type identity for each cell. MAGNETO builds effective marker panels solving a tailored bi-objective optimization problem, where the first objective regards the identification of the genes able to isolate a specific cell type, while the second conflicting objective concerns the minimization of the total number of genes included in the panel. Our results on three public datasets show that MAGNETO can identify marker panels that identify the cell populations of interest better than state-of-the-art approaches. Finally, by fine-tuning MAGNETO, our results demonstrate that it is possible to obtain marker panels with different specificity levels.
Collapse
Affiliation(s)
- Andrea Tangherloni
- Department of Computing Sciences, Bocconi University, Via Guglielmo Röntgen 1, Milan, 20136, Italy; Bocconi Institute for Data Science and Analytics, Bocconi University, Via Guglielmo Röntgen 1, Milan, 20136, Italy; Department of Human and Social Sciences, University of Bergamo, Piazzale S. Agostino 2, Bergamo, 24129, Italy.
| | - Simone G Riva
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
| | - Brynelle Myers
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
| | - Francesca M Buffa
- Department of Computing Sciences, Bocconi University, Via Guglielmo Röntgen 1, Milan, 20136, Italy; Bocconi Institute for Data Science and Analytics, Bocconi University, Via Guglielmo Röntgen 1, Milan, 20136, Italy; Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, United Kingdom
| | - Paolo Cazzaniga
- Department of Human and Social Sciences, University of Bergamo, Piazzale S. Agostino 2, Bergamo, 24129, Italy; Bicocca Bioinformatics, Biostatistics, and Bioimaging Centre - B4, Via Follereau 3, Vedano al Lambro, 20854, Italy
| |
Collapse
|
33
|
Hegewisch-Solloa E, Nalin AP, Freud AG, Mace EM. Deciphering the localization and trajectory of human natural killer cell development. J Leukoc Biol 2023; 114:487-506. [PMID: 36869821 DOI: 10.1093/jleuko/qiad027] [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: 11/21/2022] [Revised: 02/07/2023] [Accepted: 02/12/2023] [Indexed: 03/05/2023] Open
Abstract
Innate immune cells represent the first line of cellular immunity, comprised of both circulating and tissue-resident natural killer cells and innate lymphoid cells. These innate lymphocytes arise from a common CD34+ progenitor that differentiates into mature natural killer cells and innate lymphoid cells. The successive stages in natural killer cell maturation are characterized by increased lineage restriction and changes to phenotype and function. Mechanisms of human natural killer cell development have not been fully elucidated, especially the role of signals that drive the spatial localization and maturation of natural killer cells. Cytokines, extracellular matrix components, and chemokines provide maturation signals and influence the trafficking of natural killer cell progenitors to peripheral sites of differentiation. Here we present the latest advances in our understanding of natural killer and innate lymphoid cell development in peripheral sites, including secondary lymphoid tissues (i.e. tonsil). Recent work in the field has provided a model for the spatial distribution of natural killer cell and innate lymphoid cell developmental intermediates in tissue and generated further insights into the developmental niche. In support of this model, future studies using multifaceted approaches seek to fully map the developmental trajectory of human natural killer cells and innate lymphoid cells in secondary lymphoid tissues.
Collapse
Affiliation(s)
- Everardo Hegewisch-Solloa
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 630 W 168th St. New York, NY 10032, USA
| | - Ansel P Nalin
- Biomedical Sciences Graduate Program, Medical Scientist Training Program, Comprehensive Cancer Center and The James Cancer Hospital and Solove Research Institute, The Ohio State University, 460 W 10th Ave. Columbus, OH 43210, USA
| | - Aharon G Freud
- Department of Pathology, Comprehensive Cancer Center and The James Cancer Hospital and Solove Research Institute, The Ohio State University, 460 W 12th Ave. Columbus, OH 43210, USA
| | - Emily M Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 630 W 168th St. New York, NY 10032, USA
| |
Collapse
|
34
|
van der Ploeg K, Sottile R, Kontopoulos T, Shaffer BC, Papanicolaou GA, Maloy MA, Cho C, Robinson KS, Perales MA, Le Luduec JB, Hsu KC. Emergence of human CMV-induced NKG2C+ NK cells is associated with CD8+ T-cell recovery after allogeneic HCT. Blood Adv 2023; 7:5784-5798. [PMID: 37196646 PMCID: PMC10561005 DOI: 10.1182/bloodadvances.2022008952] [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: 09/14/2022] [Revised: 04/19/2023] [Accepted: 04/23/2023] [Indexed: 05/19/2023] Open
Abstract
Cytomegalovirus (CMV) infection is associated with the expansion of a mature NKG2C+FcεR1γ- natural killer (NK) cell population. The exact mechanism underlying the emergence of NKG2C+ NK cells, however, remains unknown. Allogeneic hematopoietic cell transplantation (HCT) provides an opportunity to longitudinally study lymphocyte recovery in the setting of CMV reactivation, particularly in patients receiving T-cell-depleted (TCD) allografts. We analyzed peripheral blood lymphocytes from 119 patients at serial time points after infusion of their TCD allograft and compared immune recovery with that in samples obtained from recipients of T-cell-replete (T-replete) (n = 96) or double umbilical cord blood (DUCB) (n = 52) allografts. NKG2C+ NK cells were detected in 92% (45 of 49) of recipients of TCD HCT who experienced CMV reactivation. Although NKG2A+ cells were routinely identifiable early after HCT, NKG2C+ NK cells were identified only after T cells could be detected. T-cell reconstitution occurred at variable times after HCT among patients and predominantly comprised CD8+ T cells. In patients with CMV reactivation, recipients of TCD HCT expressed significantly higher frequencies of NKG2C+ and CD56neg NK cells compared with patients who received T-replete HCT or DUCB transplantation. NKG2C+ NK cells after TCD HCT were CD57+FcεR1γ+ and degranulated significantly more in response to target cells compared with the adaptive the NKG2C+CD57+FcεR1γ- NK cell population. We conclude that the presence of circulating T cells is associated with the expansion of a CMV-induced NKG2C+ NK cell population, a potentially novel example of developmental cooperation between lymphocyte populations in response to viral infection.
Collapse
Affiliation(s)
- Kattria van der Ploeg
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rosa Sottile
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Theodota Kontopoulos
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Brian C. Shaffer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Genovefa A. Papanicolaou
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Molly A. Maloy
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Christina Cho
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Kevin S. Robinson
- Department of Medicine, Weill Cornell Medical College, New York, NY
- Adult BMT Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Miguel-Angel Perales
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Jean-Benoît Le Luduec
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Katharine C. Hsu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
35
|
van der Leun AM, Traets JJ, Vos JL, Elbers JB, Patiwael S, Qiao X, Machuca-Ostos M, Thommen DS, Haanen JB, Schumacher TN, Zuur CL. Dual Immune Checkpoint Blockade Induces Analogous Alterations in the Dysfunctional CD8+ T-cell and Activated Treg Compartment. Cancer Discov 2023; 13:2212-2227. [PMID: 37548431 PMCID: PMC10551666 DOI: 10.1158/2159-8290.cd-22-0851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 05/02/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
To dissect the effect of neoadjuvant PD-1 and CTLA4 blockade on intratumoral T cells in treatment-naive head and neck squamous cell carcinoma, we analyzed primary tumor immune infiltrates from responding and nonresponding patients. At baseline, a higher ratio between active (4-1BB/OX40+) and inactive regulatory CD4+ T cells was associated with immunotherapy response. Furthermore, upon therapy, this active regulatory T-cell (Treg) population showed a profound decrease in responding patients. In an analogous process, intratumoral dysfunctional CD8+ T cells displayed decreased expression of activity and dysfunction-related genes in responding patients, whereas in clinical nonresponders, natural killer cells showed an increased cytotoxic profile early upon treatment. These data reveal immunologic changes in response to dual PD-1/CTLA4 blockade, including a parallel remodeling of presumed tumor-reactive Treg and CD8+ T-cell compartments in responding patients, and indicate that the presence of activated Tregs at baseline may be associated with response. SIGNIFICANCE In head and neck squamous cell carcinoma, neoadjuvant PD-1/CTLA4 blockade has shown substantial response rates (20%-35%). As recognition of tumor antigens by T cells appears to be a critical driver of therapy response, a better understanding of alterations in T-cell state that are associated with response and resistance is of importance. This article is featured in Selected Articles from This Issue, p. 2109.
Collapse
Affiliation(s)
- Anne M. van der Leun
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Joleen J.H. Traets
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Joris L. Vos
- Department of Head and Neck Surgery and Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Joris B.W. Elbers
- Department of Head and Neck Surgery and Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Sanne Patiwael
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Xiaohang Qiao
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mercedes Machuca-Ostos
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Daniela S. Thommen
- Division of Molecular Oncology and Immunology, 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
| | - Ton N.M. Schumacher
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Charlotte L. Zuur
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Head and Neck Surgery and Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Otorhinolaryngology Head and Neck Surgery, Leiden University Medical Center, Leiden, the Netherlands
| |
Collapse
|
36
|
Shin HS, Park J, Lee SY, Yun HG, Kim B, Kim J, Han S, Cho D, Doh J, Choi S. Integrative Magneto-Microfluidic Separation of Immune Cells Facilitates Clinical Functional Assays. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2302809. [PMID: 37365959 DOI: 10.1002/smll.202302809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/05/2023] [Indexed: 06/28/2023]
Abstract
Accurately analyzing the functional activities of natural killer (NK) cells in clinical diagnosis remains challenging due to their coupling with other immune effectors. To address this, an integrated immune cell separator is required, which necessitates a streamlined sample preparation workflow including immunological cell isolation, removal of excess red blood cells (RBCs), and buffer exchange for downstream analysis. Here, a self-powered integrated magneto-microfluidic cell separation (SMS) chip is presented, which outputs high-purity target immune cells by simply inputting whole blood. The SMS chip intensifies the magnetic field gradient using an iron sphere-filled inlet reservoir for high-performance immuno-magnetic cell selection and separates target cells size-selectively using a microfluidic lattice for RBC removal and buffer exchange. In addition, the chip incorporates self-powered microfluidic pumping through a degassed polydimethylsiloxane chip, enabling the rapid isolation of NK cells at the place of blood collection within 40 min. This chip is used to isolate NK cells from whole blood samples of hepatocellular cancer patients and healthy volunteers and examined their functional activities to identify potential abnormalities in NK cell function. The SMS chip is simple to use, rapid to sort, and requires small blood volumes, thus facilitating the use of immune cell subtypes for cell-based diagnosis.
Collapse
Affiliation(s)
- Hee Sik Shin
- Department of Electrical Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jeehun Park
- Soft Foundry Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Seung Yeop Lee
- Department of Biomedical Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Hyo Geun Yun
- Department of Electrical Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Byeongyeon Kim
- Department of Electrical Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jinho Kim
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, 25-2, Seonggyungwan-ro, Jongno-gu, Seoul, 03063, Republic of Korea
| | - Sangbin Han
- Department of Anesthesiology and Pain Medicine Samsung Medical Center, Sungkyunkwan University School of Medicine, 81, Irwon-Ro, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Duck Cho
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, 25-2, Seonggyungwan-ro, Jongno-gu, Seoul, 03063, Republic of Korea
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81, Irwon-Ro, Gangnam-gu, Seoul, 06351, Republic of Korea
- Cell and Gene Therapy Institute (CGTI), Samsung Medical Center, 81, Irwon-Ro, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Junsang Doh
- Soft Foundry Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
- Department of Materials Science and Engineering, Institute of Engineering Research, BioMAX, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Sungyoung Choi
- Department of Electrical Engineering, Hanyang University, Seoul, 04763, Republic of Korea
- Department of Biomedical Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| |
Collapse
|
37
|
Lachota M, Zielniok K, Palacios D, Kanaya M, Penna L, Hoel HJ, Wiiger MT, Kveberg L, Hautz W, Zagożdżon R, Malmberg KJ. Mapping the chemotactic landscape in NK cells reveals subset-specific synergistic migratory responses to dual chemokine receptor ligation. EBioMedicine 2023; 96:104811. [PMID: 37741009 PMCID: PMC10520535 DOI: 10.1016/j.ebiom.2023.104811] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/25/2023] Open
Abstract
BACKGROUND Natural killer (NK) cells have a unique capability of spontaneous cytotoxicity against malignant cells and hold promise for off-the-shelf cell therapy against cancer. One of the key challenges in the field is to improve NK cell homing to solid tumors. METHODS To gain a deeper understanding of the cellular mechanisms regulating trafficking of NK cells into the tumor, we used high-dimensional flow cytometry, mass cytometry, and single-cell RNA-sequencing combined with functional assays, creating a comprehensive map of human NK cell migration phenotypes. FINDINGS We found that the chemokine receptor repertoire of peripheral blood NK cells changes in a coordinated manner becoming progressively more diversified during NK cell differentiation and correlating tightly with the migratory response of the distinct NK cell subsets. Simultaneous ligation of CXCR1/2 and CX3CR1, synergistically potentiated the migratory response of NK cells. Analysis of 9471 solid cancers from publicly available TCGA/TARGET repositories revealed dominant chemokine patterns that varied across tumor types but with no tumor group expressing ligands for more than one chemokine receptor present on mature NK cells. INTERPRETATION The finding that chemokine stimulation can elicit a synergistic migratory response in NK cells combined with the identified lack of naturally occurring pairs of chemokines-chemokine receptors in human cancers may explain the systematic exclusion of NK cells from the tumor microenvironment and provides a basis for engineering next-generation NK cell therapies against malignancies. FUNDING The Polish Ministry of Science and Higher Education, the National Science Centre, Poland, The Norwegian Cancer Society, the Norwegian Research Council, the South-Eastern Norway Regional Health Authority, The Swedish Cancer Society, the Swedish Children's Cancer Foundation, The Swedish Research Council, The Center of Excellence: Precision Immunotherapy Alliance, Knut and Alice Wallenberg Foundation and National Cancer Institute.
Collapse
Affiliation(s)
- Mieszko Lachota
- Department of Clinical Immunology, Medical University of Warsaw, Warsaw, Poland; Department of Ophthalmology, Children's Memorial Health Institute, Warsaw, Poland
| | - Katarzyna Zielniok
- Department of Clinical Immunology, Medical University of Warsaw, Warsaw, Poland
| | - Daniel Palacios
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, University of Oslo, Norway
| | - Minoru Kanaya
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, University of Oslo, Norway
| | - Leena Penna
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland
| | - Hanna Julie Hoel
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, University of Oslo, Norway
| | - Merete Thune Wiiger
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, University of Oslo, Norway
| | - Lise Kveberg
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, University of Oslo, Norway
| | - Wojciech Hautz
- Department of Ophthalmology, Children's Memorial Health Institute, Warsaw, Poland
| | - Radosław Zagożdżon
- Department of Clinical Immunology, Medical University of Warsaw, Warsaw, Poland
| | - Karl-Johan Malmberg
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, University of Oslo, Norway; Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
38
|
Zanwar S, Jacob EK, Greiner C, Pavelko K, Strausbauch M, Anderson E, Arsana A, Weivoda M, Shah MV, Kourelis T. The immunome of mobilized peripheral blood stem cells is predictive of long-term outcomes and therapy-related myeloid neoplasms in patients with multiple myeloma undergoing autologous stem cell transplant. Blood Cancer J 2023; 13:151. [PMID: 37752130 PMCID: PMC10522581 DOI: 10.1038/s41408-023-00920-9] [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: 06/12/2023] [Revised: 08/22/2023] [Accepted: 09/01/2023] [Indexed: 09/28/2023] Open
Abstract
Upfront autologous stem cell transplant (ASCT) is the standard of care for newly diagnosed multiple myeloma (MM) patients. However, relapse is ubiquitous and therapy-related myeloid neoplasms (t-MN) post-ASCT are commonly associated with poor outcomes. We hypothesized that the enrichment of abnormal myeloid progenitors and immune effector cells (IEC) in the peripheral blood stem cells (PBSCs) is associated with a higher risk of relapse and/or development of t-MN. We performed a comprehensive myeloid and lymphoid immunophenotyping on PBSCs from 54 patients with MM who underwent ASCT. Median progression-free (PFS), myeloid neoplasm-free (MNFS), and overall survival (OS) from ASCT were 49.6 months (95% CI: 39.5-Not Reached), 59.7 months (95% CI: 55-74), and 75.6 months (95% CI: 62-105), respectively. Abnormal expression of CD7 and HLA-DR on the myeloid progenitor cells was associated with an inferior PFS, MNFS, and OS. Similarly, enrichment of terminally differentiated (CD27/CD28-, CD57/KLRG1+) and exhausted (TIGIT/PD-1+) T-cells, and inhibitory NK-T like (CD159a+/CD56+) T-cells was associated with inferior PFS, MNFS, and OS post-transplant. Our observation of abnormal myeloid and IEC phenotype being present even before ASCT and maintenance therapy suggests an early predisposition to t-MN and inferior outcomes for MM, and has the potential to guide sequencing of future treatment modalities.
Collapse
Affiliation(s)
| | - Eapen K Jacob
- Division of Transfusion Medicine, Human Cellular Therapy Laboratory, Rochester, MN, USA
| | - Carl Greiner
- Division of Transfusion Medicine, Human Cellular Therapy Laboratory, Rochester, MN, USA
| | - Kevin Pavelko
- Immune Monitoring Core, Mayo Clinic, Rochester, MN, USA
| | | | - Emilie Anderson
- Division of Hematology Research, Mayo Clinic, Rochester, MN, USA
| | - Arini Arsana
- Division of Hematology Research, Mayo Clinic, Rochester, MN, USA
| | - Megan Weivoda
- Division of Hematology Research, Mayo Clinic, Rochester, MN, USA
| | | | | |
Collapse
|
39
|
Tang F, Li J, Qi L, Liu D, Bo Y, Qin S, Miao Y, Yu K, Hou W, Li J, Peng J, Tian Z, Zhu L, Peng H, Wang D, Zhang Z. A pan-cancer single-cell panorama of human natural killer cells. Cell 2023; 186:4235-4251.e20. [PMID: 37607536 DOI: 10.1016/j.cell.2023.07.034] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/28/2023] [Accepted: 07/28/2023] [Indexed: 08/24/2023]
Abstract
Natural killer (NK) cells play indispensable roles in innate immune responses against tumor progression. To depict their phenotypic and functional diversities in the tumor microenvironment, we perform integrative single-cell RNA sequencing analyses on NK cells from 716 patients with cancer, covering 24 cancer types. We observed heterogeneity in NK cell composition in a tumor-type-specific manner. Notably, we have identified a group of tumor-associated NK cells that are enriched in tumors, show impaired anti-tumor functions, and are associated with unfavorable prognosis and resistance to immunotherapy. Specific myeloid cell subpopulations, in particular LAMP3+ dendritic cells, appear to mediate the regulation of NK cell anti-tumor immunity. Our study provides insights into NK-cell-based cancer immunity and highlights potential clinical utilities of NK cell subsets as therapeutic targets.
Collapse
Affiliation(s)
- Fei Tang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jinhu Li
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China
| | - Lu Qi
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China
| | - Dongfang Liu
- Department of Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Yufei Bo
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China
| | - Shishang Qin
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yuhui Miao
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Kezhuo Yu
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wenhong Hou
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Jianan Li
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jirun Peng
- Department of Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China; Ninth School of Clinical Medicine, Peking University, Beijing 100038, China
| | - Zhigang Tian
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Linnan Zhu
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China.
| | - Hui Peng
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Dongfang Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China.
| | - Zemin Zhang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| |
Collapse
|
40
|
Lee M, Bell CJM, Rubio Garcia A, Godfrey L, Pekalski M, Wicker LS, Todd JA, Ferreira RC. CD56 bright natural killer cells preferentially kill proliferating CD4 + T cells. DISCOVERY IMMUNOLOGY 2023; 2:kyad012. [PMID: 37649552 PMCID: PMC10465185 DOI: 10.1093/discim/kyad012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/14/2023] [Accepted: 08/10/2023] [Indexed: 09/01/2023]
Abstract
Human CD56br natural killer (NK) cells represent a small subset of CD56+ NK cells in circulation and are largely tissue-resident. The frequency and number of CD56br NK cells in blood has been shown to increase following administration of low-dose IL-2 (LD-IL2), a therapy aimed to specifically expand CD4+ regulatory T cells (Tregs). Given the potential clinical application of LD-IL-2 immunotherapy across several immune diseases, including the autoimmune disease type 1 diabetes, a better understanding of the functional consequences of this expansion is urgently needed. In this study, we developed an in vitro co-culture assay with activated CD4+ T cells to measure NK cell killing efficiency. We show that CD56br and CD56dim NK cells show similar efficiency at killing activated CD4+ conventional T (Tconv) and Treg cell subsets. However, in contrast to CD56dim cells, CD56br NK cells preferentially target highly proliferative cells. We hypothesize that CD56br NK cells have an immunoregulatory role through the elimination of proliferating autoreactive CD4+ Tconv cells that have escaped Treg suppression. These results have implications for the interpretation of current and future trials of LD-IL-2 by providing evidence for a new, possibly beneficial immunomodulatory mechanism of LD-IL-2-expanded CD56br NK cells.
Collapse
Affiliation(s)
- Mercede Lee
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Charles J M Bell
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Arcadio Rubio Garcia
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Leila Godfrey
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Marcin Pekalski
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Linda S Wicker
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - John A Todd
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Ricardo C Ferreira
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| |
Collapse
|
41
|
Park SY, Ter-Saakyan S, Faraci G, Lee HY. Immune cell identifier and classifier (ImmunIC) for single cell transcriptomic readouts. Sci Rep 2023; 13:12093. [PMID: 37495649 PMCID: PMC10372073 DOI: 10.1038/s41598-023-39282-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 07/22/2023] [Indexed: 07/28/2023] Open
Abstract
Single cell RNA sequencing has a central role in immune profiling, identifying specific immune cells as disease markers and suggesting therapeutic target genes of immune cells. Immune cell-type annotation from single cell transcriptomics is in high demand for dissecting complex immune signatures from multicellular blood and organ samples. However, accurate cell type assignment from single-cell RNA sequencing data alone is complicated by a high level of gene expression heterogeneity. Many computational methods have been developed to respond to this challenge, but immune cell annotation accuracy is not highly desirable. We present ImmunIC, a simple and robust tool for immune cell identification and classification by combining marker genes with a machine learning method. With over two million immune cells and half-million non-immune cells from 66 single cell RNA sequencing studies, ImmunIC shows 98% accuracy in the identification of immune cells. ImmunIC outperforms existing immune cell classifiers, categorizing into ten immune cell types with 92% accuracy. We determine peripheral blood mononuclear cell compositions of severe COVID-19 cases and healthy controls using previously published single cell transcriptomic data, permitting the identification of immune cell-type specific differential pathways. Our publicly available tool can maximize the utility of single cell RNA profiling by functioning as a stand-alone bioinformatic cell sorter, advancing cell-type specific immune profiling for the discovery of disease-specific immune signatures and therapeutic targets.
Collapse
Affiliation(s)
- Sung Yong Park
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Sonia Ter-Saakyan
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Gina Faraci
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Ha Youn Lee
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, USA.
| |
Collapse
|
42
|
Chasman DA, Welch Schwartz R, Vazquez J, Chavarria M, Jenkins ET, Lopez GE, Tyler CT, Stanic AK, Ong IM. Proteogenomic and V(D)J Analysis of Human Decidual T Cells Highlights Unique Transcriptional Programming and Clonal Distribution. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:154-162. [PMID: 37195197 PMCID: PMC10330249 DOI: 10.4049/jimmunol.2200061] [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: 01/18/2022] [Accepted: 04/25/2023] [Indexed: 05/18/2023]
Abstract
Immunological tolerance toward the semiallogeneic fetus is one of many maternal adaptations required for a successful pregnancy. T cells are major players of the adaptive immune system and balance tolerance and protection at the maternal-fetal interface; however, their repertoire and subset programming are still poorly understood. Using emerging single-cell RNA sequencing technologies, we simultaneously obtained transcript, limited protein, and receptor repertoire at the single-cell level, from decidual and matched maternal peripheral human T cells. The decidua maintains a tissue-specific distribution of T cell subsets compared with the periphery. We find that decidual T cells maintain a unique transcriptome programming, characterized by restraint of inflammatory pathways by overexpression of negative regulators (DUSP, TNFAIP3, ZFP36) and expression of PD-1, CTLA-4, TIGIT, and LAG3 in some CD8 clusters. Finally, analyzing TCR clonotypes demonstrated decreased diversity in specific decidual T cell populations. Overall, our data demonstrate the power of multiomics analysis in revealing regulation of fetal-maternal immune coexistence.
Collapse
Affiliation(s)
- Deborah A. Chasman
- Departments of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI
- Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI
| | - Rene Welch Schwartz
- Departments of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI
- Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI
- University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, WI
| | - Jessica Vazquez
- Departments of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI
| | - Melina Chavarria
- Departments of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI
| | - Eryne T. Jenkins
- Departments of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI
| | - Gladys E. Lopez
- Departments of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI
| | - Chanel T. Tyler
- Departments of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI
| | - Aleksandar K. Stanic
- Departments of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI
| | - Irene M. Ong
- Departments of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI
- Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI
- University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, WI
- Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, WI
| |
Collapse
|
43
|
Guilz NC, Ahn YO, Seo S, Mace EM. Unwinding the Role of the CMG Helicase in Inborn Errors of Immunity. J Clin Immunol 2023; 43:847-861. [PMID: 36809597 PMCID: PMC10789183 DOI: 10.1007/s10875-023-01437-3] [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: 10/31/2022] [Accepted: 01/20/2023] [Indexed: 02/23/2023]
Abstract
Inborn errors of immunity (IEI) are a collection of diseases resulting from genetic causes that impact the immune system through multiple mechanisms. Natural killer cell deficiency (NKD) is one such IEI where natural killer (NK) cells are the main immune lineage affected. Though rare, the deficiency of several genes has been described as underlying causes of NKD, including MCM4, GINS1, MCM10 , and GINS4 , all of which are involved in the eukaryotic CMG helicase. The CMG helicase is made up of C DC45 – M CM – G INS and accessory proteins including MCM10. The CMG helicase plays a critical role in DNA replication by unwinding the double helix and enabling access of polymerases to single-stranded DNA, and thus helicase proteins are active in any proliferating cell. Replication stress, DNA damage, and cell cycle arrest are among the cellular phenotypes attributed to loss of function variants in CMG helicase proteins. Despite the ubiquitous function of the CMG helicase, NK cells have an apparent susceptibility to the deficiency of helicase proteins. This review will examine the role of the CMG helicase in inborn errors of immunity through the lens of NKD and further discuss why natural killer cells can be so strongly affected by helicase deficiency.
Collapse
Affiliation(s)
- Nicole C Guilz
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA
| | - Yong-Oon Ahn
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA
| | - Seungmae Seo
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA
| | - Emily M Mace
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA.
| |
Collapse
|
44
|
Lee MH, Theodoropoulos J, Huuhtanen J, Bhattacharya D, Järvinen P, Tornberg S, Nísen H, Mirtti T, Uski I, Kumari A, Peltonen K, Draghi A, Donia M, Kreutzman A, Mustjoki S. Immunologic Characterization and T cell Receptor Repertoires of Expanded Tumor-infiltrating Lymphocytes in Patients with Renal Cell Carcinoma. CANCER RESEARCH COMMUNICATIONS 2023; 3:1260-1276. [PMID: 37484198 PMCID: PMC10361538 DOI: 10.1158/2767-9764.crc-22-0514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/27/2023] [Accepted: 06/21/2023] [Indexed: 07/25/2023]
Abstract
The successful use of expanded tumor-infiltrating lymphocytes (TIL) in adoptive TIL therapies has been reported, but the effects of the TIL expansion, immunophenotype, function, and T cell receptor (TCR) repertoire of the infused products relative to the tumor microenvironment (TME) are not well understood. In this study, we analyzed the tumor samples (n = 58) from treatment-naïve patients with renal cell carcinoma (RCC), "pre-rapidly expanded" TILs (pre-REP TIL, n = 15) and "rapidly expanded" TILs (REP TIL, n = 25) according to a clinical-grade TIL production protocol, with single-cell RNA (scRNA)+TCRαβ-seq (TCRαβ sequencing), TCRβ-sequencing (TCRβ-seq), and flow cytometry. REP TILs encompassed a greater abundance of CD4+ than CD8+ T cells, with increased LAG-3 and low PD-1 expressions in both CD4+ and CD8+ T cell compartments compared with the pre-REP TIL and tumor T cells. The REP protocol preferentially expanded small clones of the CD4+ phenotype (CD4, IL7R, KLRB1) in the TME, indicating that the largest exhausted T cell clones in the tumor do not expand during the expansion protocol. In addition, by generating a catalog of RCC-associated TCR motifs from >1,000 scRNA+TCRαβ-seq and TCRβ-seq RCC, healthy and other cancer sample cohorts, we quantified the RCC-associated TCRs from the expansion protocol. Unlike the low-remaining amount of anti-viral TCRs throughout the expansion, the quantity of the RCC-associated TCRs was high in the tumors and pre-REP TILs but decreased in the REP TILs. Our results provide an in-depth understanding of the origin, phenotype, and TCR specificity of RCC TIL products, paving the way for a more rationalized production of TILs. Significance TILs are a heterogenous group of immune cells that recognize and attack the tumor, thus are utilized in various clinical trials. In our study, we explored the TILs in patients with kidney cancer by expanding the TILs using a clinical-grade protocol, as well as observed their characteristics and ability to recognize the tumor using in-depth experimental and computational tools.
Collapse
Affiliation(s)
- Moon Hee Lee
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Jason Theodoropoulos
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Jani Huuhtanen
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Dipabarna Bhattacharya
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Petrus Järvinen
- Abdominal Center, Urology, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Sara Tornberg
- Abdominal Center, Urology, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Harry Nísen
- Abdominal Center, Urology, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Tuomas Mirtti
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- Department of Pathology, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Biomedical Engineering, School of Medicine, Emory University, Atlanta, Georgia
| | - Ilona Uski
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Anita Kumari
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Karita Peltonen
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Arianna Draghi
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Marco Donia
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Anna Kreutzman
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| |
Collapse
|
45
|
Kaulfuss M, Mietz J, Fabri A, Vom Berg J, Münz C, Chijioke O. The NK cell checkpoint NKG2A maintains expansion capacity of human NK cells. Sci Rep 2023; 13:10555. [PMID: 37386090 PMCID: PMC10310841 DOI: 10.1038/s41598-023-37779-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/27/2023] [Indexed: 07/01/2023] Open
Abstract
Human natural killer (NK) cells are cytotoxic effector cells that are increasingly harnessed in cancer immunotherapy. NKG2A/CD94 is an inhibitory receptor on NK cells that has established regulatory functions in the direct interaction with target cells when engaged with its ligand, the non-classical HLA class I molecule HLA-E. Here, we confirmed NKG2A as a checkpoint molecule in primary human NK cells and identified a novel role for NKG2A in maintaining NK cell expansion capacity by dampening both proliferative activity and excessive activation-induced cell death. Maintenance of NK cell expansion capacity might contribute to the preferential accumulation of human NKG2A+ NK cells after hematopoietic cell transplantation and enrichment of functionally impaired NK cells in human cancers. Functional silencing of NKG2A for cancer immunotherapy is highly attractive but will need to consider that this might also lead to a reduced survival by driving activation-induced cell death in targeted NK cells.
Collapse
Affiliation(s)
- Meike Kaulfuss
- Cellular Immunotherapy, Institute of Experimental Immunology, University of Zürich, Zurich, Switzerland
| | - Juliane Mietz
- Cellular Immunotherapy, Institute of Experimental Immunology, University of Zürich, Zurich, Switzerland
| | - Astrid Fabri
- Cellular Immunotherapy, Institute of Experimental Immunology, University of Zürich, Zurich, Switzerland
- Institute of Immunity & Transplantation, University College London Division of Infection & Immunity, London, UK
| | - Johannes Vom Berg
- Institute of Laboratory Animal Science, University of Zürich, Schlieren, Switzerland
| | - Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, Zurich, Switzerland
| | - Obinna Chijioke
- Cellular Immunotherapy, Institute of Experimental Immunology, University of Zürich, Zurich, Switzerland.
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.
| |
Collapse
|
46
|
Alisjahbana A, Mohammad I, Gao Y, Evren E, Willinger T. Single-cell RNA sequencing of human lung innate lymphoid cells in the vascular and tissue niche reveals molecular features of tissue adaptation. DISCOVERY IMMUNOLOGY 2023; 2:kyad007. [PMID: 38650756 PMCID: PMC11034571 DOI: 10.1093/discim/kyad007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/06/2023] [Accepted: 06/23/2023] [Indexed: 04/25/2024]
Abstract
Innate lymphoid cells (ILCs) are sentinels of healthy organ function, yet it is unknown how ILCs adapt to distinct anatomical niches within tissues. Here, we used a unique humanized mouse model, MISTRG mice transplanted with human hematopoietic stem and progenitor cells (HSPCs), to define the gene signatures of human ILCs in the vascular versus the tissue (extravascular) compartment of the lung. Single-cell RNA sequencing in combination with intravascular cell labeling demonstrated that heterogeneous populations of human ILCs and natural killer (NK) cells occupied the vascular and tissue niches in the lung of HSPC-engrafted MISTRG mice. Moreover, we discovered that niche-specific cues shape the molecular programs of human ILCs in the distinct sub-anatomical compartments of the lung. Specifically, extravasation of ILCs into the lung tissue was associated with the upregulation of genes involved in the acquisition of tissue residency, cell positioning within the lung, sensing of tissue-derived signals, cellular stress responses, nutrient uptake, and interaction with other tissue-resident immune cells. We also defined a core tissue signature shared between human ILCs and NK cells in the extravascular space of the lung, consistent with imprinting by signals from the local microenvironment. The molecular characterization of human ILCs and NK cells in the vascular and tissue niches of the lung provides new knowledge on the mechanisms of ILC tissue adaptation and represents a resource for further studies.
Collapse
Affiliation(s)
- Arlisa Alisjahbana
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Imran Mohammad
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Department of Otolaryngology-Head and Neck Surgery, Stanford Cancer Institute, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Yu Gao
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Elza Evren
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Zentrum München; Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Tim Willinger
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
47
|
Werner G, Sanyal A, Mirizio E, Hutchins T, Tabib T, Lafyatis R, Jacobe H, Torok KS. Single-Cell Transcriptome Analysis Identifies Subclusters with Inflammatory Fibroblast Responses in Localized Scleroderma. Int J Mol Sci 2023; 24:9796. [PMID: 37372943 DOI: 10.3390/ijms24129796] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/19/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
Localized scleroderma (LS) is an autoimmune disease with both inflammatory and fibrotic components causing an abnormal deposition of collagen in the skin and underlying tissue, often leading to disfigurement and disability. Much of its pathophysiology is extrapolated from systemic sclerosis (SSc) since the histopathology findings in the skin are nearly identical. However, LS is critically understudied. Single-cell RNA sequencing (scRNA seq) technology provides a novel way to obtain detailed information at the individual cellular level, overcoming this barrier. Here, we analyzed the affected skin of 14 patients with LS (pediatric and adult) and 14 healthy controls. Fibroblast populations were the focus, since they are the main drivers of fibrosis in SSc. We identified 12 fibroblast subclusters in LS, which overall had an inflammatory gene expression (IFN and HLA-associated genes). A myofibroblast-like cluster (SFRP4/PRSS23) was more prevalent in LS subjects and shared many upregulated genes expressed in SSc-associated myofibroblasts, though it also had strong expression of CXCL9/10/11, known CXCR3 ligands. A CXCL2/IRF1 cluster identified was unique to LS, with a robust inflammatory gene signature, including IL-6, and according to cell communication analysis are influenced by macrophages. In summary, potential disease-propagating fibroblasts and associated gene signatures were identified in LS skin via scRNA seq.
Collapse
Affiliation(s)
- Giffin Werner
- Department of Pediatrics (Rheumatology), University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Anwesha Sanyal
- Department of Pediatrics (Rheumatology), University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Emily Mirizio
- Department of Pediatrics (Rheumatology), University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Theresa Hutchins
- Department of Pediatrics (Rheumatology), University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Heidi Jacobe
- Department of Dermatology, University of Texas Southwestern, Dallas, TX 75390, USA
| | - Kathryn S Torok
- Department of Pediatrics (Rheumatology), University of Pittsburgh, Pittsburgh, PA 15224, USA
| |
Collapse
|
48
|
Kim Y, Greenleaf WJ, Bendall SC. Systems biology approaches to unravel lymphocyte subsets and function. Curr Opin Immunol 2023; 82:102323. [PMID: 37028221 PMCID: PMC10330158 DOI: 10.1016/j.coi.2023.102323] [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: 02/02/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 04/09/2023]
Abstract
Single-cell technologies have revealed the extensive heterogeneity and complexity of the immune system. Systems biology approaches in immunology have taken advantage of the high-parameter, high-throughput data and analyzed immune cell types in a 'bottom-up' data-driven method. This approach has discovered previously unrecognized cell types and functions. Especially for human immunology, in which experimental manipulations are challenging, systems approach has become a successful means to investigate physiologically relevant contexts. This review focuses on the recent findings in lymphocyte biology, from their development, differentiation into subsets, and heterogeneity in their functions, enabled by these systems approaches. Furthermore, we review examples of the application of findings from systems approach studies and discuss how now to leave the rich dataset in the curse of high dimensionality.
Collapse
Affiliation(s)
- YeEun Kim
- Immunology Graduate Program, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA.
| |
Collapse
|
49
|
Qi C, Liu Q. Natural killer cells in aging and age-related diseases. Neurobiol Dis 2023; 183:106156. [PMID: 37209924 DOI: 10.1016/j.nbd.2023.106156] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/10/2023] [Accepted: 05/17/2023] [Indexed: 05/22/2023] Open
Abstract
Aging leads to escalated systemic inflammation. As the sentinel of immune system, natural killer (NK) cells are early responders that sense cues and signals from target organs and swiftly orchestrate local inflammation upon their arrival. Emerging evidence indicates a profound role of NK cells in the initiation and evolution of neuroinflammation in aging and age-related diseases. Here we discuss recent advances in NK cell biology and the organ-specific features of NK cells in normal brain aging, Alzheimer's disease, Parkinson's disease and stroke. Our increasing understanding of NK cells and their unique features in aging and age-related diseases may facilitate the future design of immune therapies targeting NK cells to benefit the old population.
Collapse
Affiliation(s)
- Caiyun Qi
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Qiang Liu
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China; Tianjin Institute of Immunology, Tianjin Medical University, Tianjin 300070, China.
| |
Collapse
|
50
|
Hasan MF, Croom-Perez TJ, Oyer JL, Dieffenthaller TA, Robles-Carrillo LD, Eloriaga JE, Kumar S, Andersen BW, Copik AJ. TIGIT Expression on Activated NK Cells Correlates with Greater Anti-Tumor Activity but Promotes Functional Decline upon Lung Cancer Exposure: Implications for Adoptive Cell Therapy and TIGIT-Targeted Therapies. Cancers (Basel) 2023; 15:2712. [PMID: 37345049 DOI: 10.3390/cancers15102712] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/02/2023] [Accepted: 05/07/2023] [Indexed: 06/23/2023] Open
Abstract
Treatments targeting TIGIT have gained a lot of attention due to strong preclinical and early clinical results, particularly with anti-PD-(L)1 therapeutics. However, this combination has failed to meet progression-free survival endpoints in phase III trials. Most of our understanding of TIGIT comes from studies of T cell function. Yet, this inhibitory receptor is often upregulated to the same, or higher, extent on NK cells in cancers. Studies in murine models have demonstrated that TIGIT inhibits NK cells and promotes exhaustion, with its effects on tumor control also being dependent on NK cells. However, there are limited studies assessing the role of TIGIT on the function of human NK cells (hNK), particularly in lung cancer. Most studies used NK cell lines or tested TIGIT blockade to reactivate exhausted cells obtained from cancer patients. For therapeutic advancement, a better understanding of TIGIT in the context of activated hNK cells is crucial, which is different than exhausted NK cells, and critical in the context of adoptive NK cell therapeutics that may be combined with TIGIT blockade. In this study, the effect of TIGIT blockade on the anti-tumor activities of human ex vivo-expanded NK cells was evaluated in vitro in the context of lung cancer. TIGIT expression was higher on activated and/or expanded NK cells compared to resting NK cells. More TIGIT+ NK cells expressed major activating receptors and exerted anti-tumor response as compared to TIGIT- cells, indicating that NK cells with greater anti-tumor function express more TIGIT. However, long-term TIGIT engagement upon exposure to PVR+ tumors downregulated the cytotoxic function of expanded NK cells while the inclusion of TIGIT blockade increased cytotoxicity, restored the effector functions against PVR-positive targets, and upregulated immune inflammation-related gene sets. These combined results indicate that TIGIT blockade can preserve the activation state of NK cells during exposure to PVR+ tumors. These results support the notion that a functional NK cell compartment is critical for anti-tumor response and anti-TIGIT/adoptive NK cell combinations have the potential to improve outcomes.
Collapse
Affiliation(s)
- Md Faqrul Hasan
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Tayler J Croom-Perez
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Jeremiah L Oyer
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Thomas A Dieffenthaller
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Liza D Robles-Carrillo
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Jonathan E Eloriaga
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Sanjana Kumar
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Brendan W Andersen
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Alicja J Copik
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| |
Collapse
|