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Wang J, Wen S, Chen M, Xie J, Lou X, Zhao H, Chen Y, Zhao M, Shi G. Regulation of endocrine cell alternative splicing revealed by single-cell RNA sequencing in type 2 diabetes pathogenesis. Commun Biol 2024; 7:778. [PMID: 38937540 PMCID: PMC11211498 DOI: 10.1038/s42003-024-06475-0] [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: 05/25/2023] [Accepted: 06/19/2024] [Indexed: 06/29/2024] Open
Abstract
The prevalent RNA alternative splicing (AS) contributes to molecular diversity, which has been demonstrated in cellular function regulation and disease pathogenesis. However, the contribution of AS in pancreatic islets during diabetes progression remains unclear. Here, we reanalyze the full-length single-cell RNA sequencing data from the deposited database to investigate AS regulation across human pancreatic endocrine cell types in non-diabetic (ND) and type 2 diabetic (T2D) individuals. Our analysis demonstrates the significant association between transcriptomic AS profiles and cell-type-specificity, which could be applied to distinguish the clustering of major endocrine cell types. Moreover, AS profiles are enabled to clearly define the mature subset of β-cells in healthy controls, which is completely lost in T2D. Further analysis reveals that RNA-binding proteins (RBPs), heterogeneous nuclear ribonucleoproteins (hnRNPs) and FXR1 family proteins are predicted to induce the functional impairment of β-cells through regulating AS profiles. Finally, trajectory analysis of endocrine cells suggests the β-cell identity shift through dedifferentiation and transdifferentiation of β-cells during the progression of T2D. Together, our study provides a mechanism for regulating β-cell functions and suggests the significant contribution of AS program during diabetes pathogenesis.
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Affiliation(s)
- Jin Wang
- Department of Endocrinology & Metabolism, Medical Center for Comprehensive Weight Control, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Shiyi Wen
- Department of Endocrinology & Metabolism, Medical Center for Comprehensive Weight Control, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Minqi Chen
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou, Guangdong, China
| | - Jiayi Xie
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou, Guangdong, China
| | - Xinhua Lou
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Haihan Zhao
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yanming Chen
- Department of Endocrinology & Metabolism, Medical Center for Comprehensive Weight Control, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Diabetology & Guangzhou Municipal Key Laboratory of Mechanistic and Translational Obesity Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Meng Zhao
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou, Guangdong, China.
| | - Guojun Shi
- Department of Endocrinology & Metabolism, Medical Center for Comprehensive Weight Control, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.
- Guangdong Provincial Key Laboratory of Diabetology & Guangzhou Municipal Key Laboratory of Mechanistic and Translational Obesity Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.
- State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.
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2
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Antón-Bolaños N, Faravelli I, Faits T, Andreadis S, Kastli R, Trattaro S, Adiconis X, Wei A, Sampath Kumar A, Di Bella DJ, Tegtmeyer M, Nehme R, Levin JZ, Regev A, Arlotta P. Brain Chimeroids reveal individual susceptibility to neurotoxic triggers. Nature 2024:10.1038/s41586-024-07578-8. [PMID: 38926573 DOI: 10.1038/s41586-024-07578-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 05/17/2024] [Indexed: 06/28/2024]
Abstract
Interindividual genetic variation affects the susceptibility to and progression of many diseases1,2. However, efforts to study how individual human brains differ in normal development and disease phenotypes are limited by the paucity of faithful cellular human models, and the difficulty of scaling current systems to represent multiple people. Here we present human brain Chimeroids, a highly reproducible, multidonor human brain cortical organoid model generated by the co-development of cells from a panel of individual donors in a single organoid. By reaggregating cells from multiple single-donor organoids at the neural stem cell or neural progenitor cell stage, we generate Chimeroids in which each donor produces all cell lineages of the cerebral cortex, even when using pluripotent stem cell lines with notable growth biases. We used Chimeroids to investigate interindividual variation in the susceptibility to neurotoxic triggers that exhibit high clinical phenotypic variability: ethanol and the antiepileptic drug valproic acid. Individual donors varied in both the penetrance of the effect on target cell types, and the molecular phenotype within each affected cell type. Our results suggest that human genetic background may be an important mediator of neurotoxin susceptibility and introduce Chimeroids as a scalable system for high-throughput investigation of interindividual variation in processes of brain development and disease.
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Affiliation(s)
- Noelia Antón-Bolaños
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Irene Faravelli
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tyler Faits
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sophia Andreadis
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Rahel Kastli
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sebastiano Trattaro
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xian Adiconis
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anqi Wei
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Abhishek Sampath Kumar
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniela J Di Bella
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew Tegtmeyer
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ralda Nehme
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joshua Z Levin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Boston, MA, USA
- Genentech, San Francisco, CA, USA
| | - Paola Arlotta
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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3
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Kilian C, Ulrich H, Zouboulis VA, Sprezyna P, Schreiber J, Landsberger T, Büttner M, Biton M, Villablanca EJ, Huber S, Adlung L. Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease. NPJ Syst Biol Appl 2024; 10:69. [PMID: 38914538 PMCID: PMC11196733 DOI: 10.1038/s41540-024-00395-9] [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: 12/21/2023] [Accepted: 06/14/2024] [Indexed: 06/26/2024] Open
Abstract
Single-cell-based methods such as flow cytometry or single-cell mRNA sequencing (scRNA-seq) allow deep molecular and cellular profiling of immunological processes. Despite their high throughput, however, these measurements represent only a snapshot in time. Here, we explore how longitudinal single-cell-based datasets can be used for deterministic ordinary differential equation (ODE)-based modelling to mechanistically describe immune dynamics. We derived longitudinal changes in cell numbers of colonic cell types during inflammatory bowel disease (IBD) from flow cytometry and scRNA-seq data of murine colitis using ODE-based models. Our mathematical model generalised well across different protocols and experimental techniques, and we hypothesised that the estimated model parameters reflect biological processes. We validated this prediction of cellular turnover rates with KI-67 staining and with gene expression information from the scRNA-seq data not used for model fitting. Finally, we tested the translational relevance of the mathematical model by deconvolution of longitudinal bulk mRNA-sequencing data from a cohort of human IBD patients treated with olamkicept. We found that neutrophil depletion may contribute to IBD patients entering remission. The predictive power of IBD deterministic modelling highlights its potential to advance our understanding of immune dynamics in health and disease.
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Affiliation(s)
- Christoph Kilian
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), D-20246, Hamburg, Germany
| | - Hanna Ulrich
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), D-20246, Hamburg, Germany
| | - Viktor A Zouboulis
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), D-20246, Hamburg, Germany
| | - Paulina Sprezyna
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), D-20246, Hamburg, Germany
| | - Jasmin Schreiber
- Leibniz Institute for the Analysis of Biodiversity Change, D-20146, Hamburg, Germany
| | - Tomer Landsberger
- Department of statistics and data science, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Maren Büttner
- Calico Life Sciences, LLC, South San Francisco, CA, USA
| | - Moshe Biton
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Eduardo J Villablanca
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Samuel Huber
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), D-20246, Hamburg, Germany
| | - Lorenz Adlung
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), D-20246, Hamburg, Germany.
- Hamburg Center for Translational Immunology (HCTI) and Center for Biomedical AI (bAIome), University Medical Center Hamburg-Eppendorf (UKE), D-20246, Hamburg, Germany.
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4
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Elias HK, Mitra S, da Silva MB, Rajagopalan A, Gipson B, Lee N, Kousa AI, Ali MAE, Grassman S, Zhang X, DeWolf S, Smith M, Andrlova H, Argyropoulos KV, Sharma R, Fei T, Sun JC, Dunbar CE, Park CY, Leslie CS, Bhandoola A, van den Brink MRM. An epigenetically distinct HSC subset supports thymic reconstitution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597775. [PMID: 38895335 PMCID: PMC11185715 DOI: 10.1101/2024.06.06.597775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Hematopoietic stem cells (HSCs) with multilineage potential are critical for effective T cell reconstitution and restoration of the adaptive immune system after allogeneic Hematopoietic Cell Transplantation (allo-HCT). The Kit lo subset of HSCs is enriched for multipotential precursors, 1, 2 but their T-cell lineage potential has not been well-characterized. We therefore studied the thymic reconstituting and T-cell potential of Kit lo HSCs. Using a preclinical allo-HCT model, we demonstrate that Kit lo HSCs support better thymic recovery, and T-cell reconstitution resulting in improved T cell responses to infection post-HCT. Furthermore, Kit lo HSCs with augmented BM lymphopoiesis mitigate age-associated thymic alterations, thus enhancing T-cell recovery in middle-aged hosts. We find the frequency of the Kit lo subset declines with age, providing one explanation for the reduced frequency of T-competent HSCs and reduced T-lymphopoietic potential in BM precursors of aged mice. 3, 4, 5 Chromatin profiling revealed that Kit lo HSCs exhibit higher activity of lymphoid-specifying transcription factors (TFs), including Zbtb1 . Deletion of Zbtb1 in Kit lo HSCs diminished their T-cell potential, while reinstating Zbtb1 in megakaryocytic-biased Kit hi HSCs rescued T-cell potential, in vitro and in vivo . Finally, we discover an analogous Kit lo HSC subset with enhanced lymphoid potential in human bone marrow. Our results demonstrate that Kit lo HSCs with enhanced lymphoid potential have a distinct underlying epigenetic program.
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5
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Verhagen MP, Joosten R, Schmitt M, Välimäki N, Sacchetti A, Rajamäki K, Choi J, Procopio P, Silva S, van der Steen B, van den Bosch TPP, Seinstra D, de Vries AC, Doukas M, Augenlicht LH, Aaltonen LA, Fodde R. Non-stem cell lineages as an alternative origin of intestinal tumorigenesis in the context of inflammation. Nat Genet 2024:10.1038/s41588-024-01801-y. [PMID: 38902475 DOI: 10.1038/s41588-024-01801-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 05/15/2024] [Indexed: 06/22/2024]
Abstract
According to conventional views, colon cancer originates from stem cells. However, inflammation, a key risk factor for colon cancer, has been shown to suppress intestinal stemness. Here, we used Paneth cells as a model to assess the capacity of differentiated lineages to trigger tumorigenesis in the context of inflammation in mice. Upon inflammation, Paneth cell-specific Apc mutations led to intestinal tumors reminiscent not only of those arising in patients with inflammatory bowel disease, but also of a larger fraction of human sporadic colon cancers. The latter is possibly because of the inflammatory consequences of western-style dietary habits, a major colon cancer risk factor. Machine learning methods designed to predict the cell-of-origin of cancer from patient-derived tumor samples confirmed that, in a substantial fraction of sporadic cases, the origins of colon cancer reside in secretory lineages and not in stem cells.
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Affiliation(s)
- Mathijs P Verhagen
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Rosalie Joosten
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mark Schmitt
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Institute of Pharmacology, University of Marburg, Marburg, Germany
| | - Niko Välimäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Andrea Sacchetti
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kristiina Rajamäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Jiahn Choi
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Paola Procopio
- Institute of Pharmacology, University of Marburg, Marburg, Germany
| | - Sara Silva
- Institute of Pharmacology, University of Marburg, Marburg, Germany
| | - Berdine van der Steen
- Department of Otorhinolaryngology and Head & Neck Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Danielle Seinstra
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Annemarie C de Vries
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Michail Doukas
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Leonard H Augenlicht
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Riccardo Fodde
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands.
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6
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Munro DAD, Bestard-Cuche N, McQuaid C, Chagnot A, Shabestari SK, Chadarevian JP, Maheshwari U, Szymkowiak S, Morris K, Mohammad M, Corsinotti A, Bradford B, Mabbott N, Lennen RJ, Jansen MA, Pridans C, McColl BW, Keller A, Blurton-Jones M, Montagne A, Williams A, Priller J. Microglia protect against age-associated brain pathologies. Neuron 2024:S0896-6273(24)00365-9. [PMID: 38897208 DOI: 10.1016/j.neuron.2024.05.018] [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: 11/16/2023] [Revised: 04/17/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024]
Abstract
Microglia are brain-resident macrophages that contribute to central nervous system (CNS) development, maturation, and preservation. Here, we examine the consequences of permanent microglial deficiencies on brain aging using the Csf1rΔFIRE/ΔFIRE mouse model. In juvenile Csf1rΔFIRE/ΔFIRE mice, we show that microglia are dispensable for the transcriptomic maturation of other brain cell types. By contrast, with advancing age, pathologies accumulate in Csf1rΔFIRE/ΔFIRE brains, macroglia become increasingly dysregulated, and white matter integrity declines, mimicking many pathological features of human CSF1R-related leukoencephalopathy. The thalamus is particularly vulnerable to neuropathological changes in the absence of microglia, with atrophy, neuron loss, vascular alterations, macroglial dysregulation, and severe tissue calcification. We show that populating Csf1rΔFIRE/ΔFIRE brains with wild-type microglia protects against many of these pathological changes. Together with the accompanying study by Chadarevian and colleagues1, our results indicate that the lifelong absence of microglia results in an age-related neurodegenerative condition that can be counteracted via transplantation of healthy microglia.
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Affiliation(s)
- David A D Munro
- UK Dementia Research Institute at the University of Edinburgh, Edinburgh Medical School, Chancellor's Building, Edinburgh EH16 4SB, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK.
| | - Nadine Bestard-Cuche
- Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Conor McQuaid
- UK Dementia Research Institute at the University of Edinburgh, Edinburgh Medical School, Chancellor's Building, Edinburgh EH16 4SB, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Audrey Chagnot
- UK Dementia Research Institute at the University of Edinburgh, Edinburgh Medical School, Chancellor's Building, Edinburgh EH16 4SB, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Sepideh Kiani Shabestari
- Department of Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Jean Paul Chadarevian
- Department of Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA
| | - Upasana Maheshwari
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Stefan Szymkowiak
- UK Dementia Research Institute at the University of Edinburgh, Edinburgh Medical School, Chancellor's Building, Edinburgh EH16 4SB, UK; Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
| | - Kim Morris
- UK Dementia Research Institute at the University of Edinburgh, Edinburgh Medical School, Chancellor's Building, Edinburgh EH16 4SB, UK
| | - Mehreen Mohammad
- UK Dementia Research Institute at the University of Edinburgh, Edinburgh Medical School, Chancellor's Building, Edinburgh EH16 4SB, UK
| | - Andrea Corsinotti
- Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Barry Bradford
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush Campus, Midlothian, UK
| | - Neil Mabbott
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush Campus, Midlothian, UK
| | - Ross J Lennen
- Centre for Cardiovascular Science, University of Edinburgh, Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Maurits A Jansen
- Centre for Cardiovascular Science, University of Edinburgh, Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK; Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA
| | - Clare Pridans
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Barry W McColl
- UK Dementia Research Institute at the University of Edinburgh, Edinburgh Medical School, Chancellor's Building, Edinburgh EH16 4SB, UK; Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
| | - Annika Keller
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, Zurich, Switzerland; Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Mathew Blurton-Jones
- Department of Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA
| | - Axel Montagne
- UK Dementia Research Institute at the University of Edinburgh, Edinburgh Medical School, Chancellor's Building, Edinburgh EH16 4SB, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Anna Williams
- UK Dementia Research Institute at the University of Edinburgh, Edinburgh Medical School, Chancellor's Building, Edinburgh EH16 4SB, UK; Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Josef Priller
- UK Dementia Research Institute at the University of Edinburgh, Edinburgh Medical School, Chancellor's Building, Edinburgh EH16 4SB, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK; Department of Psychiatry and Psychotherapy, School of Medicine and Health, Klinikum rechts der Isar, Technical University Munich, and German Center for Mental Health (DZPG), 81675 Munich, Germany; Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité - Universitätsmedizin Berlin and DZNE, 10117 Berlin, Germany.
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7
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Manchester AC, Ammons DT, Lappin MR, Dow S. Single cell transcriptomic analysis of the canine duodenum in chronic inflammatory enteropathy and health. Front Immunol 2024; 15:1397590. [PMID: 38933260 PMCID: PMC11199541 DOI: 10.3389/fimmu.2024.1397590] [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: 03/07/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Chronic inflammatory enteropathy (CIE) is a common condition in dogs causing recurrent or persistent gastrointestinal clinical signs. Pathogenesis is thought to involve intestinal mucosal inflammatory infiltrates, but histopathological evaluation of intestinal biopsies from dogs with CIE fails to guide treatment, inform prognosis, or correlate with clinical remission. We employed single-cell RNA sequencing to catalog and compare the diversity of cells present in duodenal mucosal endoscopic biopsies from 3 healthy dogs and 4 dogs with CIE. Through characterization of 35,668 cells, we identified 31 transcriptomically distinct cell populations, including T cells, epithelial cells, and myeloid cells. Both healthy and CIE samples contributed to each cell population. T cells were broadly subdivided into GZMAhigh (putatively annotated as tissue resident) and IL7Rhigh (putatively annotated as non-resident) T cell categories, with evidence of a skewed proportion favoring an increase in the relative proportion of IL7Rhigh T cells in CIE dogs. Among the myeloid cells, neutrophils from CIE samples exhibited inflammatory (SOD2 and IL1A) gene expression signatures. Numerous differentially expressed genes were identified in epithelial cells, with gene set enrichment analysis suggesting enterocytes from CIE dogs may be undergoing stress responses and have altered metabolic properties. Overall, this work reveals the previously unappreciated cellular heterogeneity in canine duodenal mucosa and provides new insights into molecular mechanisms which may contribute to intestinal dysfunction in CIE. The cell type gene signatures developed through this study may also be used to better understand the subtleties of canine intestinal physiology in health and disease.
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Affiliation(s)
- Alison C. Manchester
- Colorado State University, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, CO, United States
| | - Dylan T. Ammons
- Colorado State University, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, CO, United States
| | - Michael R. Lappin
- Colorado State University, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, CO, United States
| | - Steven Dow
- Colorado State University, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, CO, United States
- Colorado State University, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, CO, United States
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8
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Liang Y, Bu Q, You W, Zhang R, Xu Z, Gan X, Zhou J, Qiao L, Huang T, Lu L. Single-cell analysis reveals hypoxia-induced immunosuppressive microenvironment in intrahepatic cholangiocarcinoma. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167276. [PMID: 38844114 DOI: 10.1016/j.bbadis.2024.167276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024]
Abstract
The role of hypoxia in the tumor microenvironment of intrahepatic cholangiocarcinoma (iCCA) remains unclear. Here, we generated a comprehensive atlas of the entire tumor microenvironment and delineated the multifaceted cell-cell interactions to decipher hypoxia-induced pro-tumor immune suppression. We discovered hypoxia is significantly associated with iCCA progression via the activation of HIF1A expression. Moreover, hypoxia-dependent PPARγ-mediated fatty acid oxidation in APOE+ TAMs promoted M2 macrophage polarization by activating the HIF1A-PPARG-CD36 axis. These polarized APOE+ TAMs recruited Treg cell infiltration via the CCL3-CCR5 pair to form an immunosuppressive microenvironment. APOE+ TAMs tended to co-localize spatially with Treg cells in the malignant tissue based on spatial transcriptome data and immunofluorescence analysis results. We identified tumor-reactive CXCL13+ CD8-PreTex with specific high expression of ENTPD1 and ITGAE, which acted as precursors of CD8-Tex and had higher cytotoxicity, lower exhaustion, and more vigorous proliferation. Consequently, CXCL13+ CD8-PreTex functioned as a positive regulator of antitumor immunity by expressing the pro-inflammatory cytokines IFNG and TNF, associated with a better survival outcome. Our study reveals the mechanisms involved in hypoxia-induced immunosuppression and suggests that targeting precursor-exhausted CXCL13+CD8+ T cells might provide a pratical immunotherapeutic approach.
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Affiliation(s)
- Yuan Liang
- School of Biological Science & Medical Engineering, Southeast University, Nanjing, China; Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Qingfa Bu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Wenhua You
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Rui Zhang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Zibo Xu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Xiaojie Gan
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Jinren Zhou
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Lei Qiao
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Tianning Huang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Ling Lu
- School of Biological Science & Medical Engineering, Southeast University, Nanjing, China; Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.
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9
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Wischnewski S, Thäwel T, Ikenaga C, Kocharyan A, Lerma-Martin C, Zulji A, Rausch HW, Brenner D, Thomas L, Kutza M, Wick B, Trobisch T, Preusse C, Haeussler M, Leipe J, Ludolph A, Rosenbohm A, Hoke A, Platten M, Weishaupt JH, Sommer CJ, Stenzel W, Lloyd TE, Schirmer L. Cell type mapping of inflammatory muscle diseases highlights selective myofiber vulnerability in inclusion body myositis. NATURE AGING 2024:10.1038/s43587-024-00645-9. [PMID: 38834884 DOI: 10.1038/s43587-024-00645-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 05/03/2024] [Indexed: 06/06/2024]
Abstract
Inclusion body myositis (IBM) is the most prevalent inflammatory muscle disease in older adults with no effective therapy available. In contrast to other inflammatory myopathies such as subacute, immune-mediated necrotizing myopathy (IMNM), IBM follows a chronic disease course with both inflammatory and degenerative features of pathology. Moreover, causal factors and molecular drivers of IBM progression are largely unknown. Therefore, we paired single-nucleus RNA sequencing with spatial transcriptomics from patient muscle biopsies to map cell-type-specific drivers underlying IBM pathogenesis compared with IMNM muscles and noninflammatory skeletal muscle samples. In IBM muscles, we observed a selective loss of type 2 myonuclei paralleled by increased levels of cytotoxic T and conventional type 1 dendritic cells. IBM myofibers were characterized by either upregulation of cell stress markers featuring GADD45A and NORAD or protein degradation markers including RNF7 associated with p62 aggregates. GADD45A upregulation was preferentially seen in type 2A myofibers associated with severe tissue inflammation. We also noted IBM-specific upregulation of ACHE encoding acetylcholinesterase, which can be regulated by NORAD activity and result in functional denervation of myofibers. Our results provide promising insights into possible mechanisms of myofiber degeneration in IBM and suggest a selective type 2 fiber vulnerability linked to genomic stress and denervation pathways.
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Affiliation(s)
- Sven Wischnewski
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Thomas Thäwel
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Chiseko Ikenaga
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anna Kocharyan
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Celia Lerma-Martin
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Amel Zulji
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Hans-Werner Rausch
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - David Brenner
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Department of Neurology, University of Ulm, Ulm, Germany
| | - Leonie Thomas
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Michael Kutza
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Brittney Wick
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Tim Trobisch
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Corinna Preusse
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | | | - Jan Leipe
- Division of Rheumatology, Department of Medicine V, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Albert Ludolph
- Department of Neurology, University of Ulm, Ulm, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen, Ulm, Germany
| | | | - Ahmet Hoke
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael Platten
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- DKTK Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Mannheim Institute for Innate Immunoscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Interdisciplinary Center for Neurosciences, Heidelberg University, Heidelberg, Germany
| | - Jochen H Weishaupt
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Mannheim Institute for Innate Immunoscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Interdisciplinary Center for Neurosciences, Heidelberg University, Heidelberg, Germany
| | - Clemens J Sommer
- Institute for Neuropathology, University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Werner Stenzel
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Thomas E Lloyd
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA.
| | - Lucas Schirmer
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- Mannheim Institute for Innate Immunoscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- Interdisciplinary Center for Neurosciences, Heidelberg University, Heidelberg, Germany.
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10
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Chen H, Ryu J, Vinyard ME, Lerer A, Pinello L. SIMBA: single-cell embedding along with features. Nat Methods 2024; 21:1003-1013. [PMID: 37248389 PMCID: PMC11166568 DOI: 10.1038/s41592-023-01899-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 04/26/2023] [Indexed: 05/31/2023]
Abstract
Most current single-cell analysis pipelines are limited to cell embeddings and rely heavily on clustering, while lacking the ability to explicitly model interactions between different feature types. Furthermore, these methods are tailored to specific tasks, as distinct single-cell problems are formulated differently. To address these shortcomings, here we present SIMBA, a graph embedding method that jointly embeds single cells and their defining features, such as genes, chromatin-accessible regions and DNA sequences, into a common latent space. By leveraging the co-embedding of cells and features, SIMBA allows for the study of cellular heterogeneity, clustering-free marker discovery, gene regulation inference, batch effect removal and omics data integration. We show that SIMBA provides a single framework that allows diverse single-cell problems to be formulated in a unified way and thus simplifies the development of new analyses and extension to new single-cell modalities. SIMBA is implemented as a comprehensive Python library ( https://simba-bio.readthedocs.io ).
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Affiliation(s)
- Huidong Chen
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jayoung Ryu
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Michael E Vinyard
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Adam Lerer
- Facebook AI Research, New York, NY, USA.
| | - Luca Pinello
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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11
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Bilous M, Hérault L, Gabriel AA, Teleman M, Gfeller D. Building and analyzing metacells in single-cell genomics data. Mol Syst Biol 2024:10.1038/s44320-024-00045-6. [PMID: 38811801 DOI: 10.1038/s44320-024-00045-6] [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: 02/04/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/31/2024] Open
Abstract
The advent of high-throughput single-cell genomics technologies has fundamentally transformed biological sciences. Currently, millions of cells from complex biological tissues can be phenotypically profiled across multiple modalities. The scaling of computational methods to analyze and visualize such data is a constant challenge, and tools need to be regularly updated, if not redesigned, to cope with ever-growing numbers of cells. Over the last few years, metacells have been introduced to reduce the size and complexity of single-cell genomics data while preserving biologically relevant information and improving interpretability. Here, we review recent studies that capitalize on the concept of metacells-and the many variants in nomenclature that have been used. We further outline how and when metacells should (or should not) be used to analyze single-cell genomics data and what should be considered when analyzing such data at the metacell level. To facilitate the exploration of metacells, we provide a comprehensive tutorial on the construction and analysis of metacells from single-cell RNA-seq data ( https://github.com/GfellerLab/MetacellAnalysisTutorial ) as well as a fully integrated pipeline to rapidly build, visualize and evaluate metacells with different methods ( https://github.com/GfellerLab/MetacellAnalysisToolkit ).
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Affiliation(s)
- Mariia Bilous
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, 1011, Lausanne, Switzerland
- Agora Cancer Research Centre, 1011, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Léonard Hérault
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, 1011, Lausanne, Switzerland
- Agora Cancer Research Centre, 1011, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Aurélie Ag Gabriel
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, 1011, Lausanne, Switzerland
- Agora Cancer Research Centre, 1011, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Matei Teleman
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, 1011, Lausanne, Switzerland
- Agora Cancer Research Centre, 1011, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - David Gfeller
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, 1011, Lausanne, Switzerland.
- Agora Cancer Research Centre, 1011, Lausanne, Switzerland.
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland.
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland.
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12
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Zhang Z, Kean IRL, Dratva LM, Clark JA, Syrimi E, Khan N, Daubney E, White D, O'Neill L, Chisholm C, Payne C, Benkenstein S, Kupiec K, Galassini R, Wright V, Winmill H, Robbins C, Brown K, Ramnarayan P, Scholefield B, Peters M, Klein N, Montgomery H, Meyer KB, Teichmann SA, Bryant C, Taylor G, Pathan N. Enhanced CD95 and interleukin 18 signalling accompany T cell receptor Vβ21.3+ activation in multi-inflammatory syndrome in children. Nat Commun 2024; 15:4227. [PMID: 38762592 PMCID: PMC11102542 DOI: 10.1038/s41467-024-48699-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: 10/31/2022] [Accepted: 05/10/2024] [Indexed: 05/20/2024] Open
Abstract
Multisystem inflammatory syndrome in children is a post-infectious presentation SARS-CoV-2 associated with expansion of the T cell receptor Vβ21.3+ T-cell subgroup. Here we apply muti-single cell omics to compare the inflammatory process in children with acute respiratory COVID-19 and those presenting with non SARS-CoV-2 infections in children. Here we show that in Multi-Inflammatory Syndrome in Children (MIS-C), the natural killer cell and monocyte population demonstrate heightened CD95 (Fas) and Interleuking 18 receptor expression. Additionally, TCR Vβ21.3+ CD4+ T-cells exhibit skewed differentiation towards T helper 1, 17 and regulatory T cells, with increased expression of the co-stimulation receptors ICOS, CD28 and interleukin 18 receptor. We observe no functional evidence for NLRP3 inflammasome pathway overactivation, though MIS-C monocytes show elevated active caspase 8. This, coupled with raised IL18 mRNA expression in CD16- NK cells on single cell RNA sequencing analysis, suggests interleukin 18 and CD95 signalling may trigger activation of TCR Vβ21.3+ T-cells in MIS-C, driven by increased IL-18 production from activated monocytes and CD16- Natural Killer cells.
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MESH Headings
- Humans
- Interleukin-18/metabolism
- Child
- Signal Transduction
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- fas Receptor/metabolism
- fas Receptor/genetics
- Monocytes/immunology
- Monocytes/metabolism
- Systemic Inflammatory Response Syndrome/immunology
- Systemic Inflammatory Response Syndrome/metabolism
- COVID-19/immunology
- COVID-19/virology
- COVID-19/metabolism
- COVID-19/complications
- Inflammasomes/metabolism
- Inflammasomes/immunology
- SARS-CoV-2/immunology
- Adolescent
- Male
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Female
- Child, Preschool
- Single-Cell Analysis
- NLR Family, Pyrin Domain-Containing 3 Protein/metabolism
- NLR Family, Pyrin Domain-Containing 3 Protein/genetics
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- CD28 Antigens/metabolism
- Lymphocyte Activation/immunology
- Receptors, Interleukin-18/metabolism
- Receptors, Interleukin-18/genetics
- Receptors, Interleukin-18/immunology
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Affiliation(s)
- Zhenguang Zhang
- Departments of Paediatrics, University of Cambridge, Cambridge, UK
| | - Iain R L Kean
- Departments of Paediatrics, University of Cambridge, Cambridge, UK
| | - Lisa M Dratva
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - John A Clark
- Departments of Paediatrics, University of Cambridge, Cambridge, UK
| | - Eleni Syrimi
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Naeem Khan
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Esther Daubney
- Paediatric Intensive Care Unit, Addenbrookes Hospital, Cambridge, UK
| | - Deborah White
- Paediatric Intensive Care Unit, Addenbrookes Hospital, Cambridge, UK
| | - Lauran O'Neill
- Paediatric Intensive Care Unit, Great Ormond Street Hospital, London, UK
| | - Catherine Chisholm
- Paediatric Intensive Care Unit, Great Ormond Street Hospital, London, UK
| | - Caroline Payne
- Paediatric Intensive Care Unit, Great Ormond Street Hospital, London, UK
| | - Sarah Benkenstein
- Paediatric Intensive Care Unit, Great Ormond Street Hospital, London, UK
| | - Klaudia Kupiec
- Paediatric Intensive Care Unit, Great Ormond Street Hospital, London, UK
| | | | - Victoria Wright
- Department of Paediatrics, Imperial College London, London, UK
| | - Helen Winmill
- Paediatric Intensive Care Unit, Birmingham Children's Hospital, Birmingham, UK
| | - Ceri Robbins
- Paediatric Intensive Care Unit, Birmingham Children's Hospital, Birmingham, UK
| | - Katherine Brown
- Paediatric Intensive Care Unit, Great Ormond Street Hospital, London, UK
| | | | - Barnaby Scholefield
- Paediatric Intensive Care Unit, Birmingham Children's Hospital, Birmingham, UK
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Mark Peters
- Paediatric Intensive Care Unit, Great Ormond Street Hospital, London, UK
- Departments of Paediatrics, University College London, London, UK
| | - Nigel Klein
- Paediatric Intensive Care Unit, Great Ormond Street Hospital, London, UK
- Departments of Paediatrics, University College London, London, UK
| | | | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Theory of Condensed Matter, Cavendish Laboratory, Department of Physics University of Cambridge, Cambridge, UK
| | - Clare Bryant
- Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Graham Taylor
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK.
| | - Nazima Pathan
- Departments of Paediatrics, University of Cambridge, Cambridge, UK.
- Paediatric Intensive Care Unit, Addenbrookes Hospital, Cambridge, UK.
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13
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Gupta T, Antanaviciute A, Hyun-Jung Lee C, Ottakandathil Babu R, Aulicino A, Christoforidou Z, Siejka-Zielinska P, O'Brien-Ball C, Chen H, Fawkner-Corbett D, Geros AS, Bridges E, McGregor C, Cianci N, Fryer E, Alham NK, Jagielowicz M, Santos AM, Fellermeyer M, Davis SJ, Parikh K, Cheung V, Al-Hillawi L, Sasson S, Slevin S, Brain O, Fernandes RA, Koohy H, Simmons A. Tracking in situ checkpoint inhibitor-bound target T cells in patients with checkpoint-induced colitis. Cancer Cell 2024; 42:797-814.e15. [PMID: 38744246 DOI: 10.1016/j.ccell.2024.04.010] [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: 05/23/2023] [Revised: 02/09/2024] [Accepted: 04/17/2024] [Indexed: 05/16/2024]
Abstract
The success of checkpoint inhibitors (CPIs) for cancer has been tempered by immune-related adverse effects including colitis. CPI-induced colitis is hallmarked by expansion of resident mucosal IFNγ cytotoxic CD8+ T cells, but how these arise is unclear. Here, we track CPI-bound T cells in intestinal tissue using multimodal single-cell and subcellular spatial transcriptomics (ST). Target occupancy was increased in inflamed tissue, with drug-bound T cells located in distinct microdomains distinguished by specific intercellular signaling and transcriptional gradients. CPI-bound cells were largely CD4+ T cells, including enrichment in CPI-bound peripheral helper, follicular helper, and regulatory T cells. IFNγ CD8+ T cells emerged from both tissue-resident memory (TRM) and peripheral populations, displayed more restricted target occupancy profiles, and co-localized with damaged epithelial microdomains lacking effective regulatory cues. Our multimodal analysis identifies causal pathways and constitutes a resource to inform novel preventive strategies.
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Affiliation(s)
- Tarun Gupta
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Agne Antanaviciute
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.
| | - Chloe Hyun-Jung Lee
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Rosana Ottakandathil Babu
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Anna Aulicino
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Zoe Christoforidou
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Paulina Siejka-Zielinska
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Caitlin O'Brien-Ball
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7BN, UK
| | - Hannah Chen
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - David Fawkner-Corbett
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Academic Paediatric Surgery Unit (APSU), Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK
| | - Ana Sousa Geros
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Esther Bridges
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Colleen McGregor
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Nicole Cianci
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Eve Fryer
- Pathology, Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Nasullah Khalid Alham
- Nuffield Department of Surgical Sciences and Oxford NIHR Biomedical Research Centre (BRC), University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Marta Jagielowicz
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Ana Mafalda Santos
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Martin Fellermeyer
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Simon J Davis
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Kaushal Parikh
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Vincent Cheung
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Lulia Al-Hillawi
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Sarah Sasson
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Stephanie Slevin
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Oliver Brain
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Ricardo A Fernandes
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7BN, UK
| | - Hashem Koohy
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.
| | - Alison Simmons
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK.
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14
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Lotfollahi M, Yuhan Hao, Theis FJ, Satija R. The future of rapid and automated single-cell data analysis using reference mapping. Cell 2024; 187:2343-2358. [PMID: 38729109 PMCID: PMC11184658 DOI: 10.1016/j.cell.2024.03.009] [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: 01/05/2023] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 05/12/2024]
Abstract
As the number of single-cell datasets continues to grow rapidly, workflows that map new data to well-curated reference atlases offer enormous promise for the biological community. In this perspective, we discuss key computational challenges and opportunities for single-cell reference-mapping algorithms. We discuss how mapping algorithms will enable the integration of diverse datasets across disease states, molecular modalities, genetic perturbations, and diverse species and will eventually replace manual and laborious unsupervised clustering pipelines.
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Affiliation(s)
- Mohammad Lotfollahi
- Institute of Computational Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Yuhan Hao
- Center for Genomics and Systems Biology, New York University, New York, NY, USA; New York Genome Center, New York, NY, USA
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Department of Mathematics, Technical University of Munich, Garching, Germany.
| | - Rahul Satija
- Center for Genomics and Systems Biology, New York University, New York, NY, USA; New York Genome Center, New York, NY, USA.
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15
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Ozier-Lafontaine A, Fourneaux C, Durif G, Arsenteva P, Vallot C, Gandrillon O, Gonin-Giraud S, Michel B, Picard F. Kernel-based testing for single-cell differential analysis. Genome Biol 2024; 25:114. [PMID: 38702740 PMCID: PMC11069218 DOI: 10.1186/s13059-024-03255-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 04/22/2024] [Indexed: 05/06/2024] Open
Abstract
Single-cell technologies offer insights into molecular feature distributions, but comparing them poses challenges. We propose a kernel-testing framework for non-linear cell-wise distribution comparison, analyzing gene expression and epigenomic modifications. Our method allows feature-wise and global transcriptome/epigenome comparisons, revealing cell population heterogeneities. Using a classifier based on embedding variability, we identify transitions in cell states, overcoming limitations of traditional single-cell analysis. Applied to single-cell ChIP-Seq data, our approach identifies untreated breast cancer cells with an epigenomic profile resembling persister cells. This demonstrates the effectiveness of kernel testing in uncovering subtle population variations that might be missed by other methods.
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Affiliation(s)
- A Ozier-Lafontaine
- Nantes Université, Centrale Nantes, Laboratoire de Mathématiques Jean Leray, CNRS UMR 6629, F-44000, Nantes, France.
| | - C Fourneaux
- Laboratory of Biology and Modelling of the Cell, Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - G Durif
- Laboratory of Biology and Modelling of the Cell, Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - P Arsenteva
- Nantes Université, Centrale Nantes, Laboratoire de Mathématiques Jean Leray, CNRS UMR 6629, F-44000, Nantes, France
| | - C Vallot
- CNRS UMR3244, Institut Curie, PSL University, Paris, France
- Translational Research Department, Institut Curie, PSL University, Paris, France
| | - O Gandrillon
- Laboratory of Biology and Modelling of the Cell, Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - S Gonin-Giraud
- Laboratory of Biology and Modelling of the Cell, Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - B Michel
- Nantes Université, Centrale Nantes, Laboratoire de Mathématiques Jean Leray, CNRS UMR 6629, F-44000, Nantes, France.
| | - F Picard
- Laboratory of Biology and Modelling of the Cell, Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France.
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16
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Mannens CCA, Hu L, Lönnerberg P, Schipper M, Reagor CC, Li X, He X, Barker RA, Sundström E, Posthuma D, Linnarsson S. Chromatin accessibility during human first-trimester neurodevelopment. Nature 2024:10.1038/s41586-024-07234-1. [PMID: 38693260 DOI: 10.1038/s41586-024-07234-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/02/2024] [Indexed: 05/03/2024]
Abstract
The human brain develops through a tightly organized cascade of patterning events, induced by transcription factor expression and changes in chromatin accessibility. Although gene expression across the developing brain has been described at single-cell resolution1, similar atlases of chromatin accessibility have been primarily focused on the forebrain2-4. Here we describe chromatin accessibility and paired gene expression across the entire developing human brain during the first trimester (6-13 weeks after conception). We defined 135 clusters and used multiomic measurements to link candidate cis-regulatory elements to gene expression. The number of accessible regions increased both with age and along neuronal differentiation. Using a convolutional neural network, we identified putative functional transcription factor-binding sites in enhancers characterizing neuronal subtypes. We applied this model to cis-regulatory elements linked to ESRRB to elucidate its activation mechanism in the Purkinje cell lineage. Finally, by linking disease-associated single nucleotide polymorphisms to cis-regulatory elements, we validated putative pathogenic mechanisms in several diseases and identified midbrain-derived GABAergic neurons as being the most vulnerable to major depressive disorder-related mutations. Our findings provide a more detailed view of key gene regulatory mechanisms underlying the emergence of brain cell types during the first trimester and a comprehensive reference for future studies related to human neurodevelopment.
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Affiliation(s)
- Camiel C A Mannens
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Lijuan Hu
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Peter Lönnerberg
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Marijn Schipper
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Caleb C Reagor
- Howard Hughes Medical Institute and Laboratory of Sensory Neuroscience, The Rockefeller University, New York, NY, USA
| | - Xiaofei Li
- Division of Neurodegeneration, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden
| | - Xiaoling He
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Roger A Barker
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Erik Sundström
- Division of Neurodegeneration, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sten Linnarsson
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden.
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17
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Kedlian VR, Wang Y, Liu T, Chen X, Bolt L, Tudor C, Shen Z, Fasouli ES, Prigmore E, Kleshchevnikov V, Pett JP, Li T, Lawrence JEG, Perera S, Prete M, Huang N, Guo Q, Zeng X, Yang L, Polański K, Chipampe NJ, Dabrowska M, Li X, Bayraktar OA, Patel M, Kumasaka N, Mahbubani KT, Xiang AP, Meyer KB, Saeb-Parsy K, Teichmann SA, Zhang H. Human skeletal muscle aging atlas. NATURE AGING 2024; 4:727-744. [PMID: 38622407 PMCID: PMC11108788 DOI: 10.1038/s43587-024-00613-3] [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: 11/20/2023] [Accepted: 03/19/2024] [Indexed: 04/17/2024]
Abstract
Skeletal muscle aging is a key contributor to age-related frailty and sarcopenia with substantial implications for global health. Here we profiled 90,902 single cells and 92,259 single nuclei from 17 donors to map the aging process in the adult human intercostal muscle, identifying cellular changes in each muscle compartment. We found that distinct subsets of muscle stem cells exhibit decreased ribosome biogenesis genes and increased CCL2 expression, causing different aging phenotypes. Our atlas also highlights an expansion of nuclei associated with the neuromuscular junction, which may reflect re-innervation, and outlines how the loss of fast-twitch myofibers is mitigated through regeneration and upregulation of fast-type markers in slow-twitch myofibers with age. Furthermore, we document the function of aging muscle microenvironment in immune cell attraction. Overall, we present a comprehensive human skeletal muscle aging resource ( https://www.muscleageingcellatlas.org/ ) together with an in-house mouse muscle atlas to study common features of muscle aging across species.
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Affiliation(s)
- Veronika R Kedlian
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yaning Wang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Tianliang Liu
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaoping Chen
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Catherine Tudor
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Zhuojian Shen
- Department of Thoracic Surgery, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Eirini S Fasouli
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Jan Patrick Pett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tong Li
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - John E G Lawrence
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Shani Perera
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Qin Guo
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xinrui Zeng
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Lu Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krzysztof Polański
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nana-Jane Chipampe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Monika Dabrowska
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Xiaobo Li
- Core Facilities for Medical Science, Sun Yat-sen University, Guangzhou, China
| | - Omer Ali Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Minal Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Natsuhiko Kumasaka
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, Cambridge, UK
- Collaborative Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Andy Peng Xiang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK.
- Collaborative Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
| | - Hongbo Zhang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
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18
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Barboy O, Bercovich A, Li H, Eyal-Lubling Y, Yalin A, Shapir Itai Y, Abadie K, Zada M, David E, Shlomi-Loubaton S, Katzenelenbogen Y, Jaitin DA, Gur C, Yofe I, Feferman T, Cohen M, Dahan R, Newell EW, Lifshitz A, Tanay A, Amit I. Modeling T cell temporal response to cancer immunotherapy rationalizes development of combinatorial treatment protocols. NATURE CANCER 2024; 5:742-759. [PMID: 38429414 DOI: 10.1038/s43018-024-00734-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 01/19/2024] [Indexed: 03/03/2024]
Abstract
Successful immunotherapy relies on triggering complex responses involving T cell dynamics in tumors and the periphery. Characterizing these responses remains challenging using static human single-cell atlases or mouse models. To address this, we developed a framework for in vivo tracking of tumor-specific CD8+ T cells over time and at single-cell resolution. Our tools facilitate the modeling of gene program dynamics in the tumor microenvironment (TME) and the tumor-draining lymph node (tdLN). Using this approach, we characterize two modes of anti-programmed cell death protein 1 (PD-1) activity, decoupling induced differentiation of tumor-specific activated precursor cells from conventional type 1 dendritic cell (cDC1)-dependent proliferation and recruitment to the TME. We demonstrate that combining anti-PD-1 therapy with anti-4-1BB agonist enhances the recruitment and proliferation of activated precursors, resulting in tumor control. These data suggest that effective response to anti-PD-1 therapy is dependent on sufficient influx of activated precursor CD8+ cells to the TME and highlight the importance of understanding system-level dynamics in optimizing immunotherapies.
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Affiliation(s)
- Oren Barboy
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Akhiad Bercovich
- Department of Computer Science and Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hanjie Li
- Department of Synthetic Immunology, Shenzhen Institutes of Advanced Technology, Shenzhen, China
| | - Yaniv Eyal-Lubling
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Adam Yalin
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Yuval Shapir Itai
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Kathleen Abadie
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Mor Zada
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Eyal David
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Shir Shlomi-Loubaton
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Diego Adhemar Jaitin
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Chamutal Gur
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
- The Hebrew University, Jerusalem, Israel
| | - Ido Yofe
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Tali Feferman
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Merav Cohen
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rony Dahan
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Evan W Newell
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA, USA
| | - Aviezer Lifshitz
- Department of Computer Science and Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Ido Amit
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
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19
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Alhamdan F, Koutsogiannaki S, Yuki K. The landscape of immune dysregulation in pediatric sepsis at a single-cell resolution. Clin Immunol 2024; 262:110175. [PMID: 38460893 PMCID: PMC11009045 DOI: 10.1016/j.clim.2024.110175] [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: 01/17/2024] [Revised: 02/09/2024] [Accepted: 02/15/2024] [Indexed: 03/11/2024]
Abstract
Recognizing immune dysregulation as a hallmark of sepsis pathophysiology, leukocytes have attracted major attention of investigation. While adult and pediatric sepsis are clinically distinct, their immunological delineation remains limited. Single cell technologies facilitated the characterization of immune signatures. We tackled to delineate immunological profiles of pediatric sepsis at a single-cell level by analyzing blood samples from six septic children, at both acute and recovery phases, and four healthy children. 16 single-cell transcriptomic datasets were analyzed and compared to adult sepsis dataset. We showed a unique shift in neutrophil subpopulations and functions between acute and recovery phases, along with the regulatory role of resistin. Neutrophil signatures were comparable between adult and pediatric sepsis. Innate-like CD4 T cells were predominantly and uniquely observed in acute phase of pediatric sepsis. Our study serves as a rich source of information about the phenotypic diversity and trajectory of circulating immune cells during pediatric sepsis.
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Affiliation(s)
- Fahd Alhamdan
- Department of Anesthesiology, Critical Care, and Pain Medicine, Cardiac Anesthesia Division, Boston Children's Hospital, USA; Department of Immunology and Anaesthesia, Harvard Medical School, USA; Broad Institute of MIT and Harvard, USA
| | - Sophia Koutsogiannaki
- Department of Anesthesiology, Critical Care, and Pain Medicine, Cardiac Anesthesia Division, Boston Children's Hospital, USA; Department of Immunology and Anaesthesia, Harvard Medical School, USA; Broad Institute of MIT and Harvard, USA.
| | - Koichi Yuki
- Department of Anesthesiology, Critical Care, and Pain Medicine, Cardiac Anesthesia Division, Boston Children's Hospital, USA; Department of Immunology and Anaesthesia, Harvard Medical School, USA; Broad Institute of MIT and Harvard, USA.
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20
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Woodall MNJ, Cujba AM, Worlock KB, Case KM, Masonou T, Yoshida M, Polanski K, Huang N, Lindeboom RGH, Mamanova L, Bolt L, Richardson L, Cakir B, Ellis S, Palor M, Burgoyne T, Pinto A, Moulding D, McHugh TD, Saleh A, Kilich E, Mehta P, O'Callaghan C, Zhou J, Barclay W, De Coppi P, Butler CR, Cortina-Borja M, Vinette H, Roy S, Breuer J, Chambers RC, Heywood WE, Mills K, Hynds RE, Teichmann SA, Meyer KB, Nikolić MZ, Smith CM. Age-specific nasal epithelial responses to SARS-CoV-2 infection. Nat Microbiol 2024; 9:1293-1311. [PMID: 38622380 PMCID: PMC11087271 DOI: 10.1038/s41564-024-01658-1] [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: 03/24/2023] [Accepted: 03/04/2024] [Indexed: 04/17/2024]
Abstract
Children infected with SARS-CoV-2 rarely progress to respiratory failure. However, the risk of mortality in infected people over 85 years of age remains high. Here we investigate differences in the cellular landscape and function of paediatric (<12 years), adult (30-50 years) and older adult (>70 years) ex vivo cultured nasal epithelial cells in response to infection with SARS-CoV-2. We show that cell tropism of SARS-CoV-2, and expression of ACE2 and TMPRSS2 in nasal epithelial cell subtypes, differ between age groups. While ciliated cells are viral replication centres across all age groups, a distinct goblet inflammatory subtype emerges in infected paediatric cultures and shows high expression of interferon-stimulated genes and incomplete viral replication. In contrast, older adult cultures infected with SARS-CoV-2 show a proportional increase in basaloid-like cells, which facilitate viral spread and are associated with altered epithelial repair pathways. We confirm age-specific induction of these cell types by integrating data from in vivo COVID-19 studies and validate that our in vitro model recapitulates early epithelial responses to SARS-CoV-2 infection.
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Affiliation(s)
| | | | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Tereza Masonou
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Ni Huang
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Liam Bolt
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Samuel Ellis
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Machaela Palor
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Thomas Burgoyne
- UCL Institute of Ophthalmology, University College London, London, UK
- Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Andreia Pinto
- Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Dale Moulding
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Timothy D McHugh
- UCL Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, UK
| | - Aarash Saleh
- Royal Free Hospital NHS Foundation Trust, London, UK
| | - Eliz Kilich
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Puja Mehta
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | | | - Jie Zhou
- Department of Infectious Disease, Imperial College London, London, UK
| | - Wendy Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | - Paolo De Coppi
- Great Ormond Street UCL Institute of Child Health, London, UK
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Colin R Butler
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, Great Ormond Street UCL Institute of Child Health, University College London, London, UK
| | | | - Heloise Vinette
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Sunando Roy
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Judith Breuer
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Rachel C Chambers
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Wendy E Heywood
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Kevin Mills
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Robert E Hynds
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, Great Ormond Street UCL Institute of Child Health, University College London, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory/Dept Physics, University of Cambridge, Cambridge, UK.
| | | | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, UK.
- University College London Hospitals NHS Foundation Trust, London, UK.
| | - Claire M Smith
- Great Ormond Street UCL Institute of Child Health, London, UK.
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21
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Provine NM, Al-Diwani A, Agarwal D, Dooley K, Heslington A, Murchison AG, Garner LC, Sheerin F, Klenerman P, Irani SR. Fine needle aspiration of human lymph nodes reveals cell populations and soluble interactors pivotal to immunological priming. Eur J Immunol 2024; 54:e2350872. [PMID: 38388988 DOI: 10.1002/eji.202350872] [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: 11/01/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Lymph node (LN) fine needle aspiration (LN FNA) represents a powerful technique for minimally invasive sampling of human LNs in vivo and has been used effectively to directly study aspects of the human germinal center response. However, systematic deep phenotyping of the cellular populations and cell-free proteins recovered by LN FNA has not been performed. Thus, we studied human cervical LN FNAs as a proof-of-concept and used single-cell RNA-sequencing and proteomic analysis to benchmark this compartment, define the purity of LN FNA material, and facilitate future studies in this immunologically pivotal environment. Our data provide evidence that LN FNAs contain bone-fide LN-resident innate immune populations, with minimal contamination of blood material. Examination of these populations reveals unique biology not predictable from equivalent blood-derived populations. LN FNA supernatants represent a specific source of lymph- and lymph node-derived proteins, and can, aided by transcriptomics, identify likely receptor-ligand interactions. This represents the first description of the types and abundance of immune cell populations and cell-free proteins that can be efficiently studied by LN FNA. These findings are of broad utility for understanding LN physiology in health and disease, including infectious or autoimmune perturbations, and in the case of cervical nodes, neuroscience.
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Affiliation(s)
- Nicholas M Provine
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Adam Al-Diwani
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- University Department of Psychiatry, University of Oxford, Oxford, UK
| | - Devika Agarwal
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kyla Dooley
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Amelia Heslington
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew G Murchison
- Department of Radiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Fintan Sheerin
- Department of Radiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Paul Klenerman
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Sarosh R Irani
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Department of Neurology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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22
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Irac SE, Soon MSF, Borcherding N, Tuong ZK. Single-cell immune repertoire analysis. Nat Methods 2024; 21:777-792. [PMID: 38637691 DOI: 10.1038/s41592-024-02243-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/12/2024] [Indexed: 04/20/2024]
Abstract
Single-cell T cell and B cell antigen receptor-sequencing data analysis can potentially perform in-depth assessments of adaptive immune cells that inform on understanding immune cell development to tracking clonal expansion in disease and therapy. However, it has been extremely challenging to analyze and interpret T cells and B cells and their adaptive immune receptor repertoires at the single-cell level due to not only the complexity of the data but also the underlying biology. In this Review, we delve into the computational breakthroughs that have transformed the analysis of single-cell T cell and B cell antigen receptor-sequencing data.
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Affiliation(s)
- Sergio E Irac
- Cancer Immunoregulation and Immunotherapy, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Megan Sioe Fei Soon
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicholas Borcherding
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Omniscope, Palo Alto, CA, USA
| | - Zewen Kelvin Tuong
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.
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23
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Quan P, Li X, Si Y, Sun L, Ding FF, Fan Y, Liu H, Wei C, Li R, Zhao X, Yang F, Yao L. Single cell analysis reveals the roles and regulatory mechanisms of type-I interferons in Parkinson's disease. Cell Commun Signal 2024; 22:212. [PMID: 38566100 PMCID: PMC10985960 DOI: 10.1186/s12964-024-01590-1] [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: 01/25/2024] [Accepted: 03/23/2024] [Indexed: 04/04/2024] Open
Abstract
The pathogenesis of Parkinson's disease (PD) is strongly associated with neuroinflammation, and type I interferons (IFN-I) play a crucial role in regulating immune and inflammatory responses. However, the specific features of IFN in different cell types and the underlying mechanisms of PD have yet to be fully described. In this study, we analyzed the GSE157783 dataset, which includes 39,024 single-cell RNA sequencing results for five PD patients and six healthy controls from the Gene Expression Omnibus database. After cell type annotation, we intersected differentially expressed genes in each cell subcluster with genes collected in The Interferome database to generate an IFN-I-stimulated gene set (ISGs). Based on this gene set, we used the R package AUCell to score each cell, representing the IFN-I activity. Additionally, we performed monocle trajectory analysis, and single-cell regulatory network inference and clustering (SCENIC) to uncover the underlying mechanisms. In silico gene perturbation and subsequent experiments confirm NFATc2 regulation of type I interferon response and neuroinflammation. Our analysis revealed that microglia, endothelial cells, and pericytes exhibited the highest activity of IFN-I. Furthermore, single-cell trajectory detection demonstrated that microglia in the midbrain of PD patients were in a pro-inflammatory activation state, which was validated in the 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced PD mouse model as well. We identified transcription factors NFATc2, which was significantly up-regulated and involved in the expression of ISGs and activation of microglia in PD. In the 1-Methyl-4-phenylpyridinium (MPP+)-induced BV2 cell model, the suppression of NFATc2 resulted in a reduction in IFN-β levels, impeding the phosphorylation of STAT1, and attenuating the activation of the NF-κB pathway. Furthermore, the downregulation of NFATc2 mitigated the detrimental effects on SH-SY5Y cells co-cultured in conditioned medium. Our study highlights the critical role of microglia in type I interferon responses in PD. Additionally, we identified transcription factors NFATc2 as key regulators of aberrant type I interferon responses and microglial pro-inflammatory activation in PD. These findings provide new insights into the pathogenesis of PD and may have implications for the development of novel therapeutic strategies.
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Affiliation(s)
- Pusheng Quan
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, China
- Department of Neurology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Xueying Li
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yao Si
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Linlin Sun
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Fei Fan Ding
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yuwei Fan
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Han Liu
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Chengqun Wei
- Department of General Practice, Heilongjiang Provincial Hospital, Harbin, China
| | - Ruihua Li
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Xue Zhao
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Fan Yang
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, China.
| | - Lifen Yao
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, China.
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24
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Rauber S, Mohammadian H, Schmidkonz C, Atzinger A, Soare A, Treutlein C, Kemble S, Mahony CB, Geisthoff M, Angeli MR, Raimondo MG, Xu C, Yang KT, Lu L, Labinsky H, Saad MSA, Gwellem CA, Chang J, Huang K, Kampylafka E, Knitza J, Bilyy R, Distler JHW, Hanlon MM, Fearon U, Veale DJ, Roemer FW, Bäuerle T, Maric HM, Maschauer S, Ekici AB, Buckley CD, Croft AP, Kuwert T, Prante O, Cañete JD, Schett G, Ramming A. CD200 + fibroblasts form a pro-resolving mesenchymal network in arthritis. Nat Immunol 2024; 25:682-692. [PMID: 38396288 DOI: 10.1038/s41590-024-01774-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 01/30/2024] [Indexed: 02/25/2024]
Abstract
Fibroblasts are important regulators of inflammation, but whether fibroblasts change phenotype during resolution of inflammation is not clear. Here we use positron emission tomography to detect fibroblast activation protein (FAP) as a means to visualize fibroblast activation in vivo during inflammation in humans. While tracer accumulation is high in active arthritis, it decreases after tumor necrosis factor and interleukin-17A inhibition. Biopsy-based single-cell RNA-sequencing analyses in experimental arthritis show that FAP signal reduction reflects a phenotypic switch from pro-inflammatory MMP3+/IL6+ fibroblasts (high FAP internalization) to pro-resolving CD200+DKK3+ fibroblasts (low FAP internalization). Spatial transcriptomics of human joints indicates that pro-resolving niches of CD200+DKK3+ fibroblasts cluster with type 2 innate lymphoid cells, whereas MMP3+/IL6+ fibroblasts colocalize with inflammatory immune cells. CD200+DKK3+ fibroblasts stabilized the type 2 innate lymphoid cell phenotype and induced resolution of arthritis via CD200-CD200R1 signaling. Taken together, these data suggest a dynamic molecular regulation of the mesenchymal compartment during resolution of inflammation.
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Affiliation(s)
- Simon Rauber
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Hashem Mohammadian
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Christian Schmidkonz
- Department of Nuclear Medicine, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Department of Industrial Engineering and Health, Technical University Amberg-Weiden, Institute of Medical Engineering, Weiden, Germany
| | - Armin Atzinger
- Department of Nuclear Medicine, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Alina Soare
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Christoph Treutlein
- Institute of Radiology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Samuel Kemble
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
- NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Christopher B Mahony
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
- NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Manuel Geisthoff
- Department of Nuclear Medicine, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Mario R Angeli
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Maria G Raimondo
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Cong Xu
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Kai-Ting Yang
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Le Lu
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Hannah Labinsky
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Mina S A Saad
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Charles A Gwellem
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Jiyang Chang
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Kaiyue Huang
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Eleni Kampylafka
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Johannes Knitza
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Rostyslav Bilyy
- Department of Histology, Cytology, Embryology, Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
- Institute of Cellular Biology and Pathology 'Nicolae Simionescu', Bucharest, Romania
| | - Jörg H W Distler
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Clinic for Rheumatology, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Hiller Research Center, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Megan M Hanlon
- Molecular Rheumatology, School of Medicine, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Ursula Fearon
- Molecular Rheumatology, School of Medicine, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Douglas J Veale
- EULAR Centre for Arthritis & Rheumatic Diseases, St. Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Frank W Roemer
- Institute of Radiology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Tobias Bäuerle
- Institute of Radiology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Hans M Maric
- Rudolf-Virchow-Center for Integrative and Translational Imaging, University of Würzburg, Würzburg, Germany
| | - Simone Maschauer
- Department of Nuclear Medicine, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | | | - Adam P Croft
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
- NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Torsten Kuwert
- Department of Nuclear Medicine, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Olaf Prante
- Department of Nuclear Medicine, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | | | - Georg Schett
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Andreas Ramming
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany.
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany.
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25
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Reed AD, Pensa S, Steif A, Stenning J, Kunz DJ, Porter LJ, Hua K, He P, Twigger AJ, Siu AJQ, Kania K, Barrow-McGee R, Goulding I, Gomm JJ, Speirs V, Jones JL, Marioni JC, Khaled WT. A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast. Nat Genet 2024; 56:652-662. [PMID: 38548988 PMCID: PMC11018528 DOI: 10.1038/s41588-024-01688-9] [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: 03/28/2023] [Accepted: 02/09/2024] [Indexed: 04/17/2024]
Abstract
Here we use single-cell RNA sequencing to compile a human breast cell atlas assembled from 55 donors that had undergone reduction mammoplasties or risk reduction mastectomies. From more than 800,000 cells we identified 41 cell subclusters across the epithelial, immune and stromal compartments. The contribution of these different clusters varied according to the natural history of the tissue. Age, parity and germline mutations, known to modulate the risk of developing breast cancer, affected the homeostatic cellular state of the breast in different ways. We found that immune cells from BRCA1 or BRCA2 carriers had a distinct gene expression signature indicative of potential immune exhaustion, which was validated by immunohistochemistry. This suggests that immune-escape mechanisms could manifest in non-cancerous tissues very early during tumor initiation. This atlas is a rich resource that can be used to inform novel approaches for early detection and prevention of breast cancer.
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Affiliation(s)
- Austin D Reed
- Department of Pharmacology, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Sara Pensa
- Department of Pharmacology, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Adi Steif
- CRUK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Jack Stenning
- Department of Pharmacology, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | | | - Linsey J Porter
- Department of Pharmacology, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Kui Hua
- CRUK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Peng He
- EMBL European Bioinformatics Institute, Hinxton, UK
- Sanger Institute, Hinxton, UK
| | - Alecia-Jane Twigger
- Department of Pharmacology, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Abigail J Q Siu
- Department of Pharmacology, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Katarzyna Kania
- CRUK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Rachel Barrow-McGee
- Breast Cancer Now Tissue Bank, Centre for Tumour Biology, Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, London, UK
| | - Iain Goulding
- Breast Cancer Now Tissue Bank, Centre for Tumour Biology, Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, London, UK
| | - Jennifer J Gomm
- Breast Cancer Now Tissue Bank, Centre for Tumour Biology, Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, London, UK
| | - Valerie Speirs
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
- Aberdeen Cancer Centre, Aberdeen, UK
| | - J Louise Jones
- Breast Cancer Now Tissue Bank, Centre for Tumour Biology, Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, London, UK
| | - John C Marioni
- CRUK, Cambridge Institute, University of Cambridge, Cambridge, UK.
- EMBL European Bioinformatics Institute, Hinxton, UK.
- Sanger Institute, Hinxton, UK.
- Genentech, San Francisco, CA, USA.
| | - Walid T Khaled
- Department of Pharmacology, University of Cambridge, Cambridge, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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26
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Gu W, Eke C, Gonzalez Santiago E, Olaloye O, Konnikova L. Single-cell atlas of the small intestine throughout the human lifespan demonstrates unique features of fetal immune cells. Mucosal Immunol 2024:S1933-0219(24)00031-X. [PMID: 38555026 DOI: 10.1016/j.mucimm.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/15/2024] [Accepted: 03/23/2024] [Indexed: 04/02/2024]
Abstract
Proper development of mucosal immunity is critical for human health. Over the past decade, it has become evident that in humans, this process begins in utero. However, there are limited data on the unique features and functions of fetal mucosal immune cells. To address this gap, we integrated several single-cell ribonucleic acid sequencing datasets of the human small intestine (SI) to create an SI transcriptional atlas throughout the human life span, ranging from the first trimester to adulthood, with a focus on immune cells. Fetal SI displayed a complex immune landscape comprising innate and adaptive immune cells that exhibited distinct transcriptional programs from postnatal samples, especially compared with pediatric and adult samples. We identified shifts in myeloid populations across gestation and progression of memory T-cell states throughout the human lifespan. In particular, there was a marked shift of memory T cells from those with stem-like properties in the fetal samples to fully differentiated cells with a high expression of activation and effector function genes in adult samples, with neonatal samples containing both features. Finally, we demonstrate that the SI developmental atlas can be used to elucidate improper trajectories linked to mucosal diseases by implicating developmental abnormalities underlying necrotizing enterocolitis, a severe intestinal complication of prematurity. Collectively, our data provide valuable resources and important insights into intestinal immunity that will facilitate regenerative medicine and disease understanding.
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Affiliation(s)
- Weihong Gu
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Chino Eke
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | | | - Oluwabunmi Olaloye
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Liza Konnikova
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA; Department of Obstetrics, Gynecology and Reproductive Science, Yale University School of Medicine, New Haven, CT, USA; Program in Translational Biomedicine, Yale University School of Medicine, New Haven, CT, USA; Program in Human Translational Immunology, Yale University School of Medicine, New Haven, CT, USA.
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27
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Singh V, Kirtipal N, Song B, Lee S. Normalization of RNA-Seq data using adaptive trimmed mean with multi-reference. Brief Bioinform 2024; 25:bbae241. [PMID: 38770720 PMCID: PMC11107385 DOI: 10.1093/bib/bbae241] [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: 01/09/2024] [Revised: 04/04/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024] Open
Abstract
The normalization of RNA sequencing data is a primary step for downstream analysis. The most popular method used for the normalization is the trimmed mean of M values (TMM) and DESeq. The TMM tries to trim away extreme log fold changes of the data to normalize the raw read counts based on the remaining non-deferentially expressed genes. However, the major problem with the TMM is that the values of trimming factor M are heuristic. This paper tries to estimate the adaptive value of M in TMM based on Jaeckel's Estimator, and each sample acts as a reference to find the scale factor of each sample. The presented approach is validated on SEQC, MAQC2, MAQC3, PICKRELL and two simulated datasets with two-group and three-group conditions by varying the percentage of differential expression and the number of replicates. The performance of the present approach is compared with various state-of-the-art methods, and it is better in terms of area under the receiver operating characteristic curve and differential expression.
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Affiliation(s)
- Vikas Singh
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, 61005, Gwangju, South Korea
| | - Nikhil Kirtipal
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, 61005, Gwangju, South Korea
| | - Byeongsop Song
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, 61005, Gwangju, South Korea
| | - Sunjae Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, 61005, Gwangju, South Korea
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28
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Launonen IM, Erkan EP, Niemiec I, Junquera A, Hincapié-Otero M, Afenteva D, Liang Z, Salko M, Szabo A, Perez-Villatoro F, Falco MM, Li Y, Micoli G, Nagaraj A, Haltia UM, Kahelin E, Oikkonen J, Hynninen J, Virtanen A, Nirmal AJ, Vallius T, Hautaniemi S, Sorger P, Vähärautio A, Färkkilä A. Chemotherapy induces myeloid-driven spatial T-cell exhaustion in ovarian cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585657. [PMID: 38562799 PMCID: PMC10983974 DOI: 10.1101/2024.03.19.585657] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
To uncover the intricate, chemotherapy-induced spatiotemporal remodeling of the tumor microenvironment, we conducted integrative spatial and molecular characterization of 97 high-grade serous ovarian cancer (HGSC) samples collected before and after chemotherapy. Using single-cell and spatial analyses, we identify increasingly versatile immune cell states, which form spatiotemporally dynamic microcommunities at the tumor-stroma interface. We demonstrate that chemotherapy triggers spatial redistribution and exhaustion of CD8+ T cells due to prolonged antigen presentation by macrophages, both within interconnected myeloid networks termed "Myelonets" and at the tumor stroma interface. Single-cell and spatial transcriptomics identifies prominent TIGIT-NECTIN2 ligand-receptor interactions induced by chemotherapy. Using a functional patient-derived immuno-oncology platform, we show that CD8+T-cell activity can be boosted by combining immune checkpoint blockade with chemotherapy. Our discovery of chemotherapy-induced myeloid-driven spatial T-cell exhaustion paves the way for novel immunotherapeutic strategies to unleash CD8+ T-cell-mediated anti-tumor immunity in HGSC.
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Affiliation(s)
- Inga-Maria Launonen
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | | | - Iga Niemiec
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Ada Junquera
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | | | - Daria Afenteva
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Zhihan Liang
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Matilda Salko
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Angela Szabo
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | | | - Matias M Falco
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Yilin Li
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Giulia Micoli
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Ashwini Nagaraj
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Ulla-Maija Haltia
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
- Department of Obstetrics and Gynecology, Department of Oncology, Clinical trials unit, Comprehensive Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | - Essi Kahelin
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
- Department of Pathology, University of Helsinki and HUS Diagnostic Center, Helsinki University Hospital
| | - Jaana Oikkonen
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Johanna Hynninen
- Department of Obstetrics and Gynecology, University of Turku and Turku University Hospital, Turku, Finland
| | - Anni Virtanen
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
- Department of Pathology, University of Helsinki and HUS Diagnostic Center, Helsinki University Hospital
| | - Ajit J Nirmal
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, USA
| | - Tuulia Vallius
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, USA
- Ludwig Center at Harvard
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Peter Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, USA
| | - Anna Vähärautio
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
- Foundation for the Finnish Cancer Institute, Finland
| | - Anniina Färkkilä
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
- Department of Obstetrics and Gynecology, Department of Oncology, Clinical trials unit, Comprehensive Cancer Center, Helsinki University Hospital, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Institute for Molecular Medicine Finland, Helsinki Institute for Life Sciences, University of Helsinki, Finland
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29
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Li Y, Qin S, Dong L, Qiao S, Wang X, Yu D, Gao P, Hou Y, Quan S, Li Y, Fan F, Zhao X, Ma Y, Gao GF. Long-term effects of Omicron BA.2 breakthrough infection on immunity-metabolism balance: a 6-month prospective study. Nat Commun 2024; 15:2444. [PMID: 38503738 PMCID: PMC10951309 DOI: 10.1038/s41467-024-46692-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: 07/28/2023] [Accepted: 03/06/2024] [Indexed: 03/21/2024] Open
Abstract
There have been reports of long coronavirus disease (long COVID) and breakthrough infections (BTIs); however, the mechanisms and pathological features of long COVID after Omicron BTIs remain unclear. Assessing long-term effects of COVID-19 and immune recovery after Omicron BTIs is crucial for understanding the disease and managing new-generation vaccines. Here, we followed up mild BA.2 BTI convalescents for six-month with routine blood tests, proteomic analysis and single-cell RNA sequencing (scRNA-seq). We found that major organs exhibited ephemeral dysfunction and recovered to normal in approximately six-month after BA.2 BTI. We also observed durable and potent levels of neutralizing antibodies against major circulating sub-variants, indicating that hybrid humoral immunity stays active. However, platelets may take longer to recover based on proteomic analyses, which also shows coagulation disorder and an imbalance between anti-pathogen immunity and metabolism six-month after BA.2 BTI. The immunity-metabolism imbalance was then confirmed with retrospective analysis of abnormal levels of hormones, low blood glucose level and coagulation profile. The long-term malfunctional coagulation and imbalance in the material metabolism and immunity may contribute to the development of long COVID and act as useful indicator for assessing recovery and the long-term impacts after Omicron sub-variant BTIs.
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Affiliation(s)
- Yanhua Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Shijie Qin
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, 518026, China
| | - Lei Dong
- Department of Clinical Laboratory, Air Force Medical Center, 100142, Beijing, China
| | - Shitong Qiao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 101408, Beijing, China
| | - Xiao Wang
- School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Dongshan Yu
- Department of Infectious Diseases, The Second Affiliated Hospital of Nanchang University, Nanchang, 330008, China
| | - Pengyue Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yali Hou
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, 030032, China
| | - Shouzhen Quan
- Department of Clinical Laboratory, Air Force Medical Center, 100142, Beijing, China
| | - Ying Li
- Department of Clinical Laboratory, Air Force Medical Center, 100142, Beijing, China
| | - Fengyan Fan
- Department of Clinical Laboratory, Air Force Medical Center, 100142, Beijing, China
| | - Xin Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 101408, Beijing, China.
- Beijing Life Science Academy, 102209, Beijing, China.
| | - Yueyun Ma
- Department of Clinical Laboratory, Air Force Medical Center, 100142, Beijing, China.
| | - George Fu Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 101408, Beijing, China.
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, 030032, China.
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30
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Kazer SW, Match CM, Langan EM, Messou MA, LaSalle TJ, O’Leary E, Marbourg J, Naughton K, von Andrian UH, Ordovas-Montanes J. Primary nasal viral infection rewires the tissue-scale memory response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.11.539887. [PMID: 38562902 PMCID: PMC10983857 DOI: 10.1101/2023.05.11.539887] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The nasal mucosa is frequently the initial site of respiratory viral infection, replication, and transmission. Recent work has started to clarify the independent responses of epithelial, myeloid, and lymphoid cells to viral infection in the nasal mucosa, but their spatiotemporal coordination and relative contributions remain unclear. Furthermore, understanding whether and how primary infection shapes tissue-scale memory responses to secondary challenge is critical for the rational design of nasal-targeting therapeutics and vaccines. Here, we generated a single-cell RNA-sequencing (scRNA-seq) atlas of the murine nasal mucosa sampling three distinct regions before and during primary and secondary influenza infection. Primary infection was largely restricted to respiratory mucosa and induced stepwise changes in cell type, subset, and state composition over time. Type I Interferon (IFN)-responsive neutrophils appeared 2 days post infection (dpi) and preceded transient IFN-responsive/cycling epithelial cell responses 5 dpi, which coincided with broader antiviral monocyte and NK cell accumulation. By 8 dpi, monocyte-derived macrophages (MDMs) expressing Cxcl9 and Cxcl16 arose alongside effector cytotoxic CD8 and Ifng-expressing CD4 T cells. Following viral clearance (14 dpi), rare, previously undescribed Krt13+ nasal immune-interacting floor epithelial (KNIIFE) cells expressing multiple genes with immune communication potential increased concurrently with tissue-resident memory T (TRM)-like cells and early IgG+/IgA+ plasmablasts. Proportionality analysis coupled with cell-cell communication inference, alongside validation by in situ microscopy, underscored the CXCL16-CXCR6 signaling axis between MDMs and effector CD8 T cells 8dpi and KNIIFE cells and TRM cells 14 dpi. Secondary influenza challenge with a homologous or heterologous strain administered 60 dpi induced an accelerated and coordinated myeloid and lymphoid response without epithelial proliferation, illustrating how tissue-scale memory to natural infection engages both myeloid and lymphoid cells to reduce epithelial regenerative burden. Together, this atlas serves as a reference for viral infection in the upper respiratory tract and highlights the efficacy of local coordinated memory responses upon rechallenge.
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Affiliation(s)
- Samuel W. Kazer
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Colette Matysiak Match
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Erica M. Langan
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Marie-Angèle Messou
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Thomas J. LaSalle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Health Sciences and Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA
| | - Elise O’Leary
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | | | | | - Ulrich H. von Andrian
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
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31
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Franken A, Bila M, Mechels A, Kint S, Van Dessel J, Pomella V, Vanuytven S, Philips G, Bricard O, Xiong J, Boeckx B, Hatse S, Van Brussel T, Schepers R, Van Aerde C, Geurs S, Vandecaveye V, Hauben E, Vander Poorten V, Verbandt S, Vandereyken K, Qian J, Tejpar S, Voet T, Clement PM, Lambrechts D. CD4 + T cell activation distinguishes response to anti-PD-L1+anti-CTLA4 therapy from anti-PD-L1 monotherapy. Immunity 2024; 57:541-558.e7. [PMID: 38442708 DOI: 10.1016/j.immuni.2024.02.007] [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: 12/26/2022] [Revised: 11/30/2023] [Accepted: 02/08/2024] [Indexed: 03/07/2024]
Abstract
Cancer patients often receive a combination of antibodies targeting programmed death-ligand 1 (PD-L1) and cytotoxic T lymphocyte antigen-4 (CTLA4). We conducted a window-of-opportunity study in head and neck squamous cell carcinoma (HNSCC) to examine the contribution of anti-CTLA4 to anti-PD-L1 therapy. Single-cell profiling of on- versus pre-treatment biopsies identified T cell expansion as an early response marker. In tumors, anti-PD-L1 triggered the expansion of mostly CD8+ T cells, whereas combination therapy expanded both CD4+ and CD8+ T cells. Such CD4+ T cells exhibited an activated T helper 1 (Th1) phenotype. CD4+ and CD8+ T cells co-localized with and were surrounded by dendritic cells expressing T cell homing factors or antibody-producing plasma cells. T cell receptor tracing suggests that anti-CTLA4, but not anti-PD-L1, triggers the trafficking of CD4+ naive/central-memory T cells from tumor-draining lymph nodes (tdLNs), via blood, to the tumor wherein T cells acquire a Th1 phenotype. Thus, CD4+ T cell activation and recruitment from tdLNs are hallmarks of early response to anti-PD-L1 plus anti-CTLA4 in HNSCC.
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Affiliation(s)
- Amelie Franken
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Michel Bila
- Laboratory of Experimental Oncology (LEO), Department of Oncology, KU Leuven, 3000 Leuven, Belgium; Department of General Medical Oncology, UZ Leuven, 3000 Leuven, Belgium; Department of Oral and Maxillofacial Surgery, UZ Leuven, Leuven 3000, Belgium
| | - Aurelie Mechels
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Sam Kint
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), Leuven 3000, Belgium
| | - Jeroen Van Dessel
- Department of Oral and Maxillofacial Surgery, UZ Leuven, Leuven 3000, Belgium
| | | | - Sebastiaan Vanuytven
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), Leuven 3000, Belgium
| | - Gino Philips
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Orian Bricard
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Jieyi Xiong
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Bram Boeckx
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Sigrid Hatse
- Laboratory of Experimental Oncology (LEO), Department of Oncology, KU Leuven, 3000 Leuven, Belgium; Department of General Medical Oncology, UZ Leuven, 3000 Leuven, Belgium
| | - Thomas Van Brussel
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Rogier Schepers
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Cedric Van Aerde
- Department of Imaging and Pathology, KU Leuven, UZ Leuven, Leuven 3000, Belgium
| | - Sarah Geurs
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), Leuven 3000, Belgium; Department of Biomolecular Medicine, UZ Ghent, Ghent 9052, Belgium
| | | | - Esther Hauben
- Otorhinolaryngology, Head and Neck Surgery, Leuven 3000, Belgium
| | - Vincent Vander Poorten
- Otorhinolaryngology, Head and Neck Surgery, Leuven 3000, Belgium; Department of Oncology, Section Head and Neck Oncology, Leuven 3000, Belgium
| | - Sara Verbandt
- Digestive Oncology, KU Leuven, UZ Leuven, Leuven 3000, Belgium
| | - Katy Vandereyken
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), Leuven 3000, Belgium
| | - Junbin Qian
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Sabine Tejpar
- Digestive Oncology, KU Leuven, UZ Leuven, Leuven 3000, Belgium
| | - Thierry Voet
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), Leuven 3000, Belgium
| | - Paul M Clement
- Laboratory of Experimental Oncology (LEO), Department of Oncology, KU Leuven, 3000 Leuven, Belgium; Department of General Medical Oncology, UZ Leuven, 3000 Leuven, Belgium.
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; VIB Center for Cancer Biology, Leuven 3000, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), Leuven 3000, Belgium.
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32
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Root JL, Desai PN, Ly C, Wang B, Jelloul FZ, Zhou J, Mackay S, Alfayez M, Matthews J, Pierce S, Reville PK, Daver N, Abbas HA. Single-Cell CD4 and CD8 T-Cell Secretome Profiling Reveals Temporal and Niche Differences in Acute Myeloid Leukemia Following Immune Checkpoint Blockade Therapy. CANCER RESEARCH COMMUNICATIONS 2024; 4:671-681. [PMID: 38391202 PMCID: PMC10916538 DOI: 10.1158/2767-9764.crc-23-0402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/06/2023] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous malignancy of the blood primarily treated with intensive chemotherapy. The allogeneic T-cell antileukemic activity via donor lymphocyte infusions and stem cell transplantation suggests a potential role for checkpoint blockade therapy in AML. While clinical trials employing these treatments have fallen short of expected results, a deeper exploration into the functional states of T cells in AML could bridge this knowledge gap. In this study, we analyzed the polyfunctional activity of T cells in a cohort of patients with relapsed/refractory (RelRef) AML treated on the clinical trial (ClinicalTrials.gov identifier: NCT02397720) of combination therapy using azacitidine and nivolumab (Aza/Nivo). We utilized the single-cell polyfunctional multiplexed immune assay IsoPlexis to evaluate the CD4 and CD8 T cells in peripheral blood and bone marrow samples collected before and after immunotherapy. This revealed at a pseudobulk level that the CD4 T cells exhibited higher functional activity post-immunotherapy (post-IO), suggesting that CD4-directed therapies may play a role in RelRef AML. Additional single-cell analysis revealed significant differences in baseline polyfunctionality in bone marrows of responders as compared with nonresponders for both CD4 and CD8 T cells. Overall, this study highlights the impact of polyfunctional assessment in understanding CD4 and CD8 dynamics in contexts of therapy in AML. SIGNIFICANCE We found T-cell polyfunctionality differs between local and systemic microenvironments. Enhanced variability in proteomic profiles of bone marrow CD4 T cells post-IO suggests their pivotal role in AML treatment response. Single-cell analysis identified novel CD4 and CD8 T-cell functional groups linked to immunotherapy response within the bone marrow.
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Affiliation(s)
- Jessica L. Root
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- School of Biomedical Informatics, The University of Texas Health Science Center, Houston, Texas
| | - Poonam N. Desai
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- School of Biomedical Informatics, The University of Texas Health Science Center, Houston, Texas
| | - Christopher Ly
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- School of Biomedical Informatics, The University of Texas Health Science Center, Houston, Texas
| | - Bofei Wang
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Fatima Zahra Jelloul
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jing Zhou
- IsoPlexis Corporation, Branford, Connecticut
| | - Sean Mackay
- IsoPlexis Corporation, Branford, Connecticut
| | - Mansour Alfayez
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jairo Matthews
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sherry Pierce
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patrick K. Reville
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Naval Daver
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hussein A. Abbas
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- School of Biomedical Informatics, The University of Texas Health Science Center, Houston, Texas
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33
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Peidli S, Green TD, Shen C, Gross T, Min J, Garda S, Yuan B, Schumacher LJ, Taylor-King JP, Marks DS, Luna A, Blüthgen N, Sander C. scPerturb: harmonized single-cell perturbation data. Nat Methods 2024; 21:531-540. [PMID: 38279009 DOI: 10.1038/s41592-023-02144-y] [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: 01/28/2023] [Accepted: 12/04/2023] [Indexed: 01/28/2024]
Abstract
Analysis across a growing number of single-cell perturbation datasets is hampered by poor data interoperability. To facilitate development and benchmarking of computational methods, we collect a set of 44 publicly available single-cell perturbation-response datasets with molecular readouts, including transcriptomics, proteomics and epigenomics. We apply uniform quality control pipelines and harmonize feature annotations. The resulting information resource, scPerturb, enables development and testing of computational methods, and facilitates comparison and integration across datasets. We describe energy statistics (E-statistics) for quantification of perturbation effects and significance testing, and demonstrate E-distance as a general distance measure between sets of single-cell expression profiles. We illustrate the application of E-statistics for quantifying similarity and efficacy of perturbations. The perturbation-response datasets and E-statistics computation software are publicly available at scperturb.org. This work provides an information resource for researchers working with single-cell perturbation data and recommendations for experimental design, including optimal cell counts and read depth.
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Affiliation(s)
- Stefan Peidli
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität, Berlin, Germany.
- Institute of Biology, Humboldt-Universität, Berlin, Germany.
| | - Tessa D Green
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Ciyue Shen
- Departments of Cell Biology and Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | | | - Joseph Min
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Samuele Garda
- Institute of Biology, Humboldt-Universität, Berlin, Germany
- Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Bo Yuan
- Departments of Cell Biology and Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Linus J Schumacher
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | | | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Augustin Luna
- Departments of Cell Biology and Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute, Cambridge, MA, USA.
- Computational Biology Branch, National Library of Medicine and Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD, USA.
| | - Nils Blüthgen
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität, Berlin, Germany.
- Institute of Biology, Humboldt-Universität, Berlin, Germany.
| | - Chris Sander
- Departments of Cell Biology and Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute, Cambridge, MA, USA.
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34
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Bouman BJ, Demerdash Y, Sood S, Grünschläger F, Pilz F, Itani AR, Kuck A, Marot-Lassauzaie V, Haas S, Haghverdi L, Essers MA. Single-cell time series analysis reveals the dynamics of HSPC response to inflammation. Life Sci Alliance 2024; 7:e202302309. [PMID: 38110222 PMCID: PMC10728485 DOI: 10.26508/lsa.202302309] [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: 08/08/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) are known to respond to acute inflammation; however, little is understood about the dynamics and heterogeneity of these stress responses in HSPCs. Here, we performed single-cell sequencing during the sensing, response, and recovery phases of the inflammatory response of HSPCs to treatment (a total of 10,046 cells from four time points spanning the first 72 h of response) with the pro-inflammatory cytokine IFNα to investigate the HSPCs' dynamic changes during acute inflammation. We developed the essential novel computational approaches to process and analyze the resulting single-cell time series dataset. This includes an unbiased cell type annotation and abundance analysis post inflammation, tools for identification of global and cell type-specific responding genes, and a semi-supervised linear regression approach for response pseudotime reconstruction. We discovered a variety of different gene responses of the HSPCs to the treatment. Interestingly, we were able to associate a global reduced myeloid differentiation program and a locally enhanced pyroptosis activity with reduced myeloid progenitor and differentiated cells after IFNα treatment. Altogether, the single-cell time series analyses have allowed us to unbiasedly study the heterogeneous and dynamic impact of IFNα on the HSPCs.
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Affiliation(s)
- Brigitte J Bouman
- Berlin Institute for Medical Systems Biology, Max Delbrück Center in the Helmholtz Association, Berlin, Germany
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Yasmin Demerdash
- Division Inflammatory Stress in Stem Cells, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGMBH), Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Shubhankar Sood
- Division Inflammatory Stress in Stem Cells, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGMBH), Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Florian Grünschläger
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGMBH), Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Franziska Pilz
- Division Inflammatory Stress in Stem Cells, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGMBH), Heidelberg, Germany
| | - Abdul R Itani
- Division Inflammatory Stress in Stem Cells, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGMBH), Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Andrea Kuck
- Division Inflammatory Stress in Stem Cells, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGMBH), Heidelberg, Germany
| | - Valérie Marot-Lassauzaie
- Berlin Institute for Medical Systems Biology, Max Delbrück Center in the Helmholtz Association, Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
| | - Simon Haas
- Berlin Institute for Medical Systems Biology, Max Delbrück Center in the Helmholtz Association, Berlin, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGMBH), Heidelberg, Germany
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
| | - Laleh Haghverdi
- Berlin Institute for Medical Systems Biology, Max Delbrück Center in the Helmholtz Association, Berlin, Germany
| | - Marieke Ag Essers
- Division Inflammatory Stress in Stem Cells, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGMBH), Heidelberg, Germany
- DKFZ-ZMBH Alliance, Heidelberg, Germany
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Wertheimer T, Zwicky P, Rindlisbacher L, Sparano C, Vermeer M, de Melo BMS, Haftmann C, Rückert T, Sethi A, Schärli S, Huber A, Ingelfinger F, Xu C, Kim D, Häne P, Fonseca da Silva A, Muschaweckh A, Nunez N, Krishnarajah S, Köhler N, Zeiser R, Oukka M, Korn T, Tugues S, Becher B. IL-23 stabilizes an effector T reg cell program in the tumor microenvironment. Nat Immunol 2024; 25:512-524. [PMID: 38356059 PMCID: PMC10907296 DOI: 10.1038/s41590-024-01755-7] [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: 01/20/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
Interleukin-23 (IL-23) is a proinflammatory cytokine mainly produced by myeloid cells that promotes tumor growth in various preclinical cancer models and correlates with adverse outcomes. However, as to how IL-23 fuels tumor growth is unclear. Here, we found tumor-associated macrophages to be the main source of IL-23 in mouse and human tumor microenvironments. Among IL-23-sensing cells, we identified a subset of tumor-infiltrating regulatory T (Treg) cells that display a highly suppressive phenotype across mouse and human tumors. The use of three preclinical models of solid cancer in combination with genetic ablation of Il23r in Treg cells revealed that they are responsible for the tumor-promoting effect of IL-23. Mechanistically, we found that IL-23 sensing represents a crucial signal driving the maintenance and stabilization of effector Treg cells involving the transcription factor Foxp3. Our data support that targeting the IL-23/IL-23R axis in cancer may represent a means of eliciting antitumor immunity.
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Affiliation(s)
- Tobias Wertheimer
- Department of Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Pascale Zwicky
- Department of Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Lukas Rindlisbacher
- Department of Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Colin Sparano
- Department of Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Marijne Vermeer
- Department of Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Bruno Marcel Silva de Melo
- Department of Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
- Department of Pharmacology, Center for Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil
| | - Claudia Haftmann
- Department of Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Tamina Rückert
- Department of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Aakriti Sethi
- Department of Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Stefanie Schärli
- Department of Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Anna Huber
- Department of Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Florian Ingelfinger
- Department of Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Caroline Xu
- Department of Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Daehong Kim
- Department of Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Philipp Häne
- Department of Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - André Fonseca da Silva
- Department of Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Andreas Muschaweckh
- Institute for Experimental Neuroimmunology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Nicolas Nunez
- Department of Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Sinduya Krishnarajah
- Department of Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Natalie Köhler
- Department of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Robert Zeiser
- Department of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Mohamed Oukka
- Department of Immunology, University of Washington, Seattle, WA, USA
| | - Thomas Korn
- Institute for Experimental Neuroimmunology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Sonia Tugues
- Department of Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland.
| | - Burkhard Becher
- Department of Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland.
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Bendixen SM, Jakobsgaard PR, Hansen D, Hejn KH, Terkelsen MK, Bjerre FA, Thulesen AP, Eriksen NG, Hallenborg P, Geng Y, Dam TV, Larsen FT, Wernberg CW, Vijayathurai J, Scott EAH, Marcher AB, Detlefsen S, Grøntved L, Dimke H, Berdeaux R, de Aguiar Vallim TQ, Olinga P, Lauridsen MM, Krag A, Blagoev B, Ravnskjaer K. Single cell-resolved study of advanced murine MASH reveals a homeostatic pericyte signaling module. J Hepatol 2024; 80:467-481. [PMID: 37972658 DOI: 10.1016/j.jhep.2023.11.001] [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: 12/10/2022] [Revised: 10/06/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND & AIMS Metabolic dysfunction-associated steatohepatitis (MASH) is linked to insulin resistance and type 2 diabetes and marked by hepatic inflammation, microvascular dysfunction, and fibrosis, impairing liver function and aggravating metabolic derangements. The liver homeostatic interactions disrupted in MASH are still poorly understood. We aimed to elucidate the plasticity and changing interactions of non-parenchymal cells associated with advanced MASH. METHODS We characterized a diet-induced mouse model of advanced MASH at single-cell resolution and validated findings by assaying chromatin accessibility, bioimaging murine and human livers, and via functional experiments in vivo and in vitro. RESULTS The fibrogenic activation of hepatic stellate cells (HSCs) led to deterioration of a signaling module consisting of the bile acid receptor NR1H4/FXR and HSC-specific GS-protein-coupled receptors (GSPCRs) capable of preserving stellate cell quiescence. Accompanying HSC activation, we further observed the attenuation of HSC Gdf2 expression, and a MASH-associated expansion of a CD207-positive macrophage population likely derived from both incoming monocytes and Kupffer cells. CONCLUSION We conclude that HSC-expressed NR1H4 and GSPCRs of the healthy liver integrate postprandial cues, which sustain HSC quiescence and, through paracrine signals, overall sinusoidal health. Hence HSC activation in MASH not only drives fibrogenesis but may desensitize the hepatic sinusoid to liver homeostatic signals. IMPACT AND IMPLICATIONS Homeostatic interactions between hepatic cell types and their deterioration in metabolic dysfunction-associated steatohepatitis are poorly characterized. In our current single cell-resolved study of advanced murine metabolic dysfunction-associated steatohepatitis, we identified a quiescence-associated hepatic stellate cell-signaling module with potential to preserve normal sinusoid function. As expression levels of its constituents are conserved in the human liver, stimulation of the identified signaling module is a promising therapeutic strategy to restore sinusoid function in chronic liver disease.
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Affiliation(s)
- Sofie M Bendixen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Peter R Jakobsgaard
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Daniel Hansen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Kamilla H Hejn
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Mike K Terkelsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Frederik A Bjerre
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Annemette P Thulesen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Niels G Eriksen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Philip Hallenborg
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Yana Geng
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, the Netherlands
| | - Trine V Dam
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Frederik T Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Charlotte W Wernberg
- Department of Gastroenterology and Hepatology, Odense University Hospital, Denmark; Department of Gastroenterology and Hepatology, University Hospital of South Denmark Esbjerg, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Janusa Vijayathurai
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Emma A H Scott
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Ann-Britt Marcher
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Sönke Detlefsen
- Department of Pathology, Odense University Hospital, Denmark; Department of Clinical Research, University of Southern Denmark, Denmark
| | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Henrik Dimke
- Department of Molecular Medicine, University of Southern Denmark, Denmark; Department of Nephrology, Odense University Hospital, Denmark
| | - Rebecca Berdeaux
- Department of Integrative Biology and Pharmacology, McGovern Medical School, UT Health Houston, USA
| | - Thomas Q de Aguiar Vallim
- Department of Medicine, Division of Cardiology, University of California, Los Angeles, USA; Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Peter Olinga
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, the Netherlands
| | - Mette M Lauridsen
- Department of Gastroenterology and Hepatology, University Hospital of South Denmark Esbjerg, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Aleksander Krag
- Department of Gastroenterology and Hepatology, Odense University Hospital, Denmark; Department of Clinical Research, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Kim Ravnskjaer
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark.
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Kaur H, Jha P, Ochatt SJ, Kumar V. Single-cell transcriptomics is revolutionizing the improvement of plant biotechnology research: recent advances and future opportunities. Crit Rev Biotechnol 2024; 44:202-217. [PMID: 36775666 DOI: 10.1080/07388551.2023.2165900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 11/04/2022] [Accepted: 12/08/2022] [Indexed: 02/14/2023]
Abstract
Single-cell approaches are a promising way to obtain high-resolution transcriptomics data and have the potential to revolutionize the study of plant growth and development. Recent years have seen the advent of unprecedented technological advances in the field of plant biology to study the transcriptional information of individual cells by single-cell RNA sequencing (scRNA-seq). This review focuses on the modern advancements of single-cell transcriptomics in plants over the past few years. In addition, it also offers a new insight of how these emerging methods will expedite advance research in plant biotechnology in the near future. Lastly, the various technological hurdles and inherent limitations of single-cell technology that need to be conquered to develop such outstanding possible knowledge gain is critically analyzed and discussed.
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Affiliation(s)
- Harmeet Kaur
- Division of Research and Development, Plant Biotechnology Lab, Lovely Professional University, Phagwara, Punjab, India
- Department of Biotechnology, Lovely Faculty of Technology and Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Priyanka Jha
- Department of Biotechnology, Lovely Faculty of Technology and Sciences, Lovely Professional University, Phagwara, Punjab, India
- Department of Research Facilitation, Division of Research and Development, Lovely Professional University, Phagwara, Punjab, India
| | - Sergio J Ochatt
- Agroécologie, InstitutAgro Dijon, INRAE, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Vijay Kumar
- Division of Research and Development, Plant Biotechnology Lab, Lovely Professional University, Phagwara, Punjab, India
- Department of Biotechnology, Lovely Faculty of Technology and Sciences, Lovely Professional University, Phagwara, Punjab, India
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Guo S, Mohan GS, Wang B, Li T, Daver N, Zhao Y, Reville PK, Hao D, Abbas HA. Paired single-B-cell transcriptomics and receptor sequencing reveal activation states and clonal signatures that characterize B cells in acute myeloid leukemia. J Immunother Cancer 2024; 12:e008318. [PMID: 38418394 PMCID: PMC10910691 DOI: 10.1136/jitc-2023-008318] [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] [Accepted: 01/23/2024] [Indexed: 03/01/2024] Open
Abstract
BACKGROUND Acute myeloid leukemia (AML) is associated with a dismal prognosis. Immune checkpoint blockade (ICB) to induce antitumor activity in AML patients has yielded mixed results. Despite the pivotal role of B cells in antitumor immunity, a comprehensive assessment of B lymphocytes within AML's immunological microenvironment along with their interaction with ICB remains rather constrained. METHODS We performed an extensive analysis that involved paired single-cell RNA and B-cell receptor (BCR) sequencing on 52 bone marrow aspirate samples. These samples included 6 from healthy bone marrow donors (normal), 24 from newly diagnosed AML patients (NewlyDx), and 22 from 8 relapsed or refractory AML patients (RelRef), who underwent assessment both before and after azacitidine/nivolumab treatment. RESULTS We delineated nine distinct subtypes of B cell lineage in the bone marrow. AML patients exhibited reduced nascent B cell subgroups but increased differentiated B cells compared with healthy controls. The limited diversity of BCR profiles and extensive somatic hypermutation indicated antigen-driven affinity maturation within the tumor microenvironment of RelRef patients. We established a strong connection between the activation or stress status of naïve and memory B cells, as indicated by AP-1 activity, and their differentiation state. Remarkably, atypical memory B cells functioned as specialized antigen-presenting cells closely interacting with AML malignant cells, correlating with AML stemness and worse clinical outcomes. In the AML microenvironment, plasma cells demonstrated advanced differentiation and heightened activity. Notably, the clinical response to ICB was associated with B cell clonal expansion and plasma cell function. CONCLUSIONS Our findings establish a comprehensive framework for profiling the phenotypic diversity of the B cell lineage in AML patients, while also assessing the implications of immunotherapy. This will serve as a valuable guide for future inquiries into AML treatment strategies.
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Affiliation(s)
- Shengnan Guo
- School of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang, China
| | - Gopi S Mohan
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Bofei Wang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tianhao Li
- School of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang, China
| | - Naval Daver
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yuting Zhao
- School of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang, China
| | - Patrick K Reville
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dapeng Hao
- School of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang, China
| | - Hussein A Abbas
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Lodge M, Scheidemantle G, Adams VR, Cottam MA, Richard D, Breuer D, Thompson P, Shrestha K, Liu X, Kennedy A. Fructose regulates the pentose phosphate pathway and induces an inflammatory and resolution phenotype in Kupffer cells. Sci Rep 2024; 14:4020. [PMID: 38369593 PMCID: PMC10874942 DOI: 10.1038/s41598-024-54272-w] [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: 06/02/2023] [Accepted: 02/10/2024] [Indexed: 02/20/2024] Open
Abstract
Over-consumption of fructose in adults and children has been linked to increased risk of non-alcoholic fatty liver disease (NAFLD). Recent studies have highlighted the effect of fructose on liver inflammation, fibrosis, and immune cell activation. However, little work summarizes the direct impact of fructose on macrophage infiltration, phenotype, and function within the liver. We demonstrate that chronic fructose diet decreased Kupffer cell populations while increasing transitioning monocytes. In addition, fructose increased fibrotic gene expression of collagen 1 alpha 1 (Col1a1) and tissue metallopeptidase inhibitor 1 (Timp1) as well as inflammatory gene expression of tumor necrosis factor alpha (Tnfa) and expression of transmembrane glycoprotein NMB (Gpnmb) in liver tissue compared to glucose and control diets. Single cell RNA sequencing (scRNAseq) revealed fructose elevated expression of matrix metallopeptidase 12 (Mmp12), interleukin 1 receptor antagonist (Il1rn), and radical S-adenosyl methionine domain (Rsad2) in liver and hepatic macrophages. In vitro studies using IMKC and J774.1 cells demonstrated decreased viability when exposed to fructose. Additionally, fructose increased Gpnmb, Tnfa, Mmp12, Il1rn, and Rsad2 in unpolarized IMKC. By mass spectrometry, C13 fructose tracing detected fructose metabolites in glycolysis and the pentose phosphate pathway (PPP). Inhibition of the PPP further increased fructose induced Il6, Gpnmb, Mmp12, Il1rn, and Rsad2 in nonpolarized IMKC. Taken together, fructose decreases cell viability while upregulating resolution and anti-inflammatory associated genes in Kupffer cells.
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Affiliation(s)
- Mareca Lodge
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, NC, USA
| | - Grace Scheidemantle
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, NC, USA
| | - Victoria R Adams
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, NC, USA
| | - Matthew A Cottam
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Daniel Richard
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, NC, USA
| | - Denitra Breuer
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, NC, USA
| | - Peter Thompson
- Molecular Education, Technology and Research Innovation Center (METRIC), NC State University, Raleigh, NC, USA
| | - Kritika Shrestha
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, NC, USA
| | - Xiaojing Liu
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, NC, USA
| | - Arion Kennedy
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, NC, USA.
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40
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Van Melkebeke L, Verbeek J, Bihary D, Boesch M, Boeckx B, Feio-Azevedo R, Smets L, Wallays M, Claus E, Bonne L, Maleux G, Govaere O, Korf H, Lambrechts D, van der Merwe S. Comparison of the single-cell and single-nucleus hepatic myeloid landscape within decompensated cirrhosis patients. Front Immunol 2024; 15:1346520. [PMID: 38380322 PMCID: PMC10878168 DOI: 10.3389/fimmu.2024.1346520] [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: 11/29/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
Background and aims A complete understanding of disease pathophysiology in advanced liver disease is hampered by the challenges posed by clinical specimen collection. Notably, in these patients, a transjugular liver biopsy (TJB) is the only safe way to obtain liver tissue. However, it remains unclear whether successful sequencing of this extremely small and fragile tissue can be achieved for downstream characterization of the hepatic landscape. Methods Here we leveraged in-house available single-cell RNA-sequencing (scRNA-seq) and single-nucleus (snRNA-seq) technologies and accompanying tissue processing protocols and performed an in-patient comparison on TJB's from decompensated cirrhosis patients (n = 3). Results We confirmed a high concordance between nuclear and whole cell transcriptomes and captured 31,410 single nuclei and 6,152 single cells, respectively. The two platforms revealed similar diversity since all 8 major cell types could be identified, albeit with different cellular proportions thereof. Most importantly, hepatocytes were most abundant in snRNA-seq, while lymphocyte frequencies were elevated in scRNA-seq. We next focused our attention on hepatic myeloid cells due to their key role in injury and repair during chronic liver disease. Comparison of their transcriptional signatures indicated that these were largely overlapping between the two platforms. However, the scRNA-seq platform failed to recover sufficient Kupffer cell numbers, and other monocytes/macrophages featured elevated expression of stress-related parameters. Conclusion Our results indicate that single-nucleus transcriptome sequencing provides an effective means to overcome complications associated with clinical specimen collection and could sufficiently profile all major hepatic cell types including all myeloid cell subsets.
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Affiliation(s)
- Lukas Van Melkebeke
- Laboratory of Hepatology, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Jef Verbeek
- Laboratory of Hepatology, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Dora Bihary
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, Leuven, Belgium
| | - Markus Boesch
- Laboratory of Hepatology, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Bram Boeckx
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, Leuven, Belgium
| | - Rita Feio-Azevedo
- Laboratory of Hepatology, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Lena Smets
- Laboratory of Hepatology, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Marie Wallays
- Laboratory of Hepatology, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Eveline Claus
- Department of Interventional Radiology, University Hospitals Leuven, Leuven, Belgium
| | - Lawrence Bonne
- Department of Interventional Radiology, University Hospitals Leuven, Leuven, Belgium
| | - Geert Maleux
- Department of Interventional Radiology, University Hospitals Leuven, Leuven, Belgium
| | - Olivier Govaere
- Department of Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven and University Hospitals Leuven, Leuven, Belgium
| | - Hannelie Korf
- Laboratory of Hepatology, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, Leuven, Belgium
| | - Schalk van der Merwe
- Laboratory of Hepatology, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
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du Halgouet A, Bruder K, Peltokangas N, Darbois A, Obwegs D, Salou M, Thimme R, Hofmann M, Lantz O, Sagar. Multimodal profiling reveals site-specific adaptation and tissue residency hallmarks of γδ T cells across organs in mice. Nat Immunol 2024; 25:343-356. [PMID: 38177282 PMCID: PMC10834366 DOI: 10.1038/s41590-023-01710-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: 04/02/2023] [Accepted: 11/13/2023] [Indexed: 01/06/2024]
Abstract
γδ T cells perform heterogeneous functions in homeostasis and disease across tissues. However, it is unclear whether these roles correspond to distinct γδ subsets or to a homogeneous population of cells exerting context-dependent functions. Here, by cross-organ multimodal single-cell profiling, we reveal that various mouse tissues harbor unique site-adapted γδ subsets. Epidermal and intestinal intraepithelial γδ T cells are transcriptionally homogeneous and exhibit epigenetic hallmarks of functional diversity. Through parabiosis experiments, we uncovered cellular states associated with cytotoxicity, innate-like rapid interferon-γ production and tissue repair functions displaying tissue residency hallmarks. Notably, our observations add nuance to the link between interleukin-17-producing γδ T cells and tissue residency. Moreover, transcriptional programs associated with tissue-resident γδ T cells are analogous to those of CD8+ tissue-resident memory T cells. Altogether, this study provides a multimodal landscape of tissue-adapted γδ T cells, revealing heterogeneity, lineage relationships and their tissue residency program.
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Affiliation(s)
- Anastasia du Halgouet
- Institut National de la Santé et de la Recherche Médicale U932, PSL University, Institut Curie, Paris, France
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Kerstin Bruder
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Nina Peltokangas
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Aurélie Darbois
- Institut National de la Santé et de la Recherche Médicale U932, PSL University, Institut Curie, Paris, France
| | - David Obwegs
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marion Salou
- Institut National de la Santé et de la Recherche Médicale U932, PSL University, Institut Curie, Paris, France
| | - Robert Thimme
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Maike Hofmann
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Olivier Lantz
- Institut National de la Santé et de la Recherche Médicale U932, PSL University, Institut Curie, Paris, France
- Laboratoire d'Immunologie Clinique, Institut Curie, Paris, France
- Centre d'Investigation Clinique en Biothérapie Gustave-Roussy Institut Curie (CIC-BT1428) Institut Curie, Paris, France
| | - Sagar
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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42
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Li Q, Sharkey A, Sheridan M, Magistrati E, Arutyunyan A, Huhn O, Sancho-Serra C, Anderson H, McGovern N, Esposito L, Fernando R, Gardner L, Vento-Tormo R, Turco MY, Moffett A. Human uterine natural killer cells regulate differentiation of extravillous trophoblast early in pregnancy. Cell Stem Cell 2024; 31:181-195.e9. [PMID: 38237587 DOI: 10.1016/j.stem.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 10/19/2023] [Accepted: 12/20/2023] [Indexed: 02/04/2024]
Abstract
In humans, balanced invasion of trophoblast cells into the uterine mucosa, the decidua, is critical for successful pregnancy. Evidence suggests that this process is regulated by uterine natural killer (uNK) cells, but how they influence reproductive outcomes is unclear. Here, we used our trophoblast organoids and primary tissue samples to determine how uNK cells affect placentation. By locating potential interaction axes between trophoblast and uNK cells using single-cell transcriptomics and in vitro modeling of these interactions in organoids, we identify a uNK cell-derived cytokine signal that promotes trophoblast differentiation at the late stage of the invasive pathway. Moreover, it affects transcriptional programs involved in regulating blood flow, nutrients, and inflammatory and adaptive immune responses, as well as gene signatures associated with disorders of pregnancy such as pre-eclampsia. Our findings suggest mechanisms on how optimal immunological interactions between uNK cells and trophoblast enhance reproductive success.
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Affiliation(s)
- Qian Li
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK.
| | - Andrew Sharkey
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Megan Sheridan
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Elisa Magistrati
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Anna Arutyunyan
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Oisin Huhn
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Carmen Sancho-Serra
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Holly Anderson
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Naomi McGovern
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Laura Esposito
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Ridma Fernando
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Lucy Gardner
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Roser Vento-Tormo
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK.
| | | | - Ashley Moffett
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK.
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43
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Ghazanfar S, Guibentif C, Marioni JC. Stabilized mosaic single-cell data integration using unshared features. Nat Biotechnol 2024; 42:284-292. [PMID: 37231260 PMCID: PMC10869270 DOI: 10.1038/s41587-023-01766-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/28/2023] [Indexed: 05/27/2023]
Abstract
Currently available single-cell omics technologies capture many unique features with different biological information content. Data integration aims to place cells, captured with different technologies, onto a common embedding to facilitate downstream analytical tasks. Current horizontal data integration techniques use a set of common features, thereby ignoring non-overlapping features and losing information. Here we introduce StabMap, a mosaic data integration technique that stabilizes mapping of single-cell data by exploiting the non-overlapping features. StabMap first infers a mosaic data topology based on shared features, then projects all cells onto supervised or unsupervised reference coordinates by traversing shortest paths along the topology. We show that StabMap performs well in various simulation contexts, facilitates 'multi-hop' mosaic data integration where some datasets do not share any features and enables the use of spatial gene expression features for mapping dissociated single-cell data onto a spatial transcriptomic reference.
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Affiliation(s)
- Shila Ghazanfar
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
- School of Mathematics and Statistics, The University of Sydney, Camperdown, New South Wales, Australia.
- Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales, Australia.
| | - Carolina Guibentif
- Sahlgrenska Center for Cancer Research, Inst. Biomedicine, Dept. Microbiology and Immunology, University of Gothenburg, Gothenburg, Sweden
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
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44
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Punzon-Jimenez P, Machado-Lopez A, Perez-Moraga R, Llera-Oyola J, Grases D, Galvez-Viedma M, Sibai M, Satorres-Perez E, Lopez-Agullo S, Badenes R, Ferrer-Gomez C, Porta-Pardo E, Roson B, Simon C, Mas A. Effect of aging on the human myometrium at single-cell resolution. Nat Commun 2024; 15:945. [PMID: 38296945 PMCID: PMC10830479 DOI: 10.1038/s41467-024-45143-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: 07/17/2023] [Accepted: 01/17/2024] [Indexed: 02/02/2024] Open
Abstract
Age-associated myometrial dysfunction can prompt complications during pregnancy and labor, which is one of the factors contributing to the 7.8-fold increase in maternal mortality in women over 40. Using single-cell/single-nucleus RNA sequencing and spatial transcriptomics, we have constructed a cellular atlas of the aging myometrium from 186,120 cells across twenty perimenopausal and postmenopausal women. We identify 23 myometrial cell subpopulations, including contractile and venous capillary cells as well as immune-modulated fibroblasts. Myometrial aging leads to fewer contractile capillary cells, a reduced level of ion channel expression in smooth muscle cells, and impaired gene expression in endothelial, smooth muscle, fibroblast, perivascular, and immune cells. We observe altered myometrial cell-to-cell communication as an aging hallmark, which associated with the loss of 25 signaling pathways, including those related to angiogenesis, tissue repair, contractility, immunity, and nervous system regulation. These insights may contribute to a better understanding of the complications faced by older individuals during pregnancy and labor.
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Affiliation(s)
- Paula Punzon-Jimenez
- Carlos Simon Foundation, Valencia, Spain
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, Valencia, Spain
| | - Alba Machado-Lopez
- Carlos Simon Foundation, Valencia, Spain
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain
| | - Raul Perez-Moraga
- Carlos Simon Foundation, Valencia, Spain
- R&D Department, Igenomix, Valencia, Spain
| | | | - Daniela Grases
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | | | - Mustafa Sibai
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | | | | | - Rafael Badenes
- Department of Surgery, University of Valencia, Valencia, Spain
- Hospital Clinico Universitario, Valencia, Spain
| | | | | | - Beatriz Roson
- Carlos Simon Foundation, Valencia, Spain
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain
| | - Carlos Simon
- Carlos Simon Foundation, Valencia, Spain.
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain.
- Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, Valencia, Spain.
- Department of Obstetrics and Gynecology, BIDMC, Harvard University, Boston, MA, USA.
| | - Aymara Mas
- Carlos Simon Foundation, Valencia, Spain.
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain.
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45
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Tadros HJ, Turaga D, Zhao Y, Chang-Ru T, Adachi IA, Li X, Martin JF. Activated fibroblasts drive cellular interactions in end-stage pediatric hypertrophic cardiomyopathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577226. [PMID: 38352607 PMCID: PMC10862753 DOI: 10.1101/2024.01.25.577226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Hypertrophic cardiomyopathy (HCM) is a relatively rare but debilitating diagnosis in the pediatric population and patients with end-stage HCM require heart transplantation. In this study, we performed single-nucleus RNA sequencing on pediatric HCM and control myocardium. We identified distinct underling cellular processes in pediatric, end-stage HCM in cardiomyocytes, fibroblasts, endothelial cells, and myeloid cells, compared to controls. Pediatric HCM was enriched in cardiomyocytes exhibiting "stressed" myocardium gene signatures and underlying pathways associated with cardiac hypertrophy. Cardiac fibroblasts exhibited clear activation signatures and heightened downstream processes associated with fibrosis, more so than adult counterparts. There was notable depletion of tissue-resident macrophages, and increased vascular remodeling in endothelial cells. Our analysis provides the first single nuclei analysis focused on end-stage pediatric HCM.
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Affiliation(s)
- Hanna J Tadros
- Department of Pediatrics, Section of Pediatric Cardiology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Diwakar Turaga
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Division of Critical Care Medicine, Texas Children's Hospital, Houston TX, USA
| | - Yi Zhao
- The Texas Heart Institute, Houston, TX, USA
| | - Tsai Chang-Ru
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
| | - Iki A Adachi
- Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
- Division of Congenital Heart Surgery, Texas Children's Hospital, Houston, TX, USA
| | - Xiao Li
- The Texas Heart Institute, Houston, TX, USA
| | - James F Martin
- The Texas Heart Institute, Houston, TX, USA
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
- Center for Organ Repair and Renewal, Baylor College of Medicine, Houston, TX, USA
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46
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Roux de Bézieux H, Van den Berge K, Street K, Dudoit S. Trajectory inference across multiple conditions with condiments. Nat Commun 2024; 15:833. [PMID: 38280860 PMCID: PMC10821945 DOI: 10.1038/s41467-024-44823-0] [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: 10/13/2023] [Accepted: 01/08/2024] [Indexed: 01/29/2024] Open
Abstract
In single-cell RNA sequencing (scRNA-Seq), gene expression is assessed individually for each cell, allowing the investigation of developmental processes, such as embryogenesis and cellular differentiation and regeneration, at unprecedented resolution. In such dynamic biological systems, cellular states form a continuum, e.g., for the differentiation of stem cells into mature cell types. This process is often represented via a trajectory in a reduced-dimensional representation of the scRNA-Seq dataset. While many methods have been suggested for trajectory inference, it is often unclear how to handle multiple biological groups or conditions, e.g., inferring and comparing the differentiation trajectories of wild-type and knock-out stem cell populations. In this manuscript, we present condiments, a method for the inference and downstream interpretation of cell trajectories across multiple conditions. Our framework allows the interpretation of differences between conditions at the trajectory, cell population, and gene expression levels. We start by integrating datasets from multiple conditions into a single trajectory. By comparing the cell's conditions along the trajectory's path, we can detect large-scale changes, indicative of differential progression or fate selection. We also demonstrate how to detect subtler changes by finding genes that exhibit different behaviors between these conditions along a differentiation path.
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Affiliation(s)
- Hector Roux de Bézieux
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Koen Van den Berge
- Department of Statistics, University of California, Berkeley, CA, USA
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
- Statistics and Decision Sciences, J&J Innovative Medicine, Beerse, Belgium
| | - Kelly Street
- Division of Biostatistics, Department of Population and Public Health Sciences, Keck School of Medicine of USC, Los Angeles, CA, USA.
| | - Sandrine Dudoit
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, CA, USA.
- Department of Statistics, University of California, Berkeley, CA, USA.
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47
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Lee CYC, Kennedy BC, Richoz N, Dean I, Tuong ZK, Gaspal F, Li Z, Willis C, Hasegawa T, Whiteside SK, Posner DA, Carlesso G, Hammond SA, Dovedi SJ, Roychoudhuri R, Withers DR, Clatworthy MR. Tumour-retained activated CCR7 + dendritic cells are heterogeneous and regulate local anti-tumour cytolytic activity. Nat Commun 2024; 15:682. [PMID: 38267413 PMCID: PMC10808534 DOI: 10.1038/s41467-024-44787-1] [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: 04/27/2023] [Accepted: 01/02/2024] [Indexed: 01/26/2024] Open
Abstract
Tumour dendritic cells (DCs) internalise antigen and upregulate CCR7, which directs their migration to tumour-draining lymph nodes (dLN). CCR7 expression is coupled to an activation programme enriched in regulatory molecule expression, including PD-L1. However, the spatio-temporal dynamics of CCR7+ DCs in anti-tumour immune responses remain unclear. Here, we use photoconvertible mice to precisely track DC migration. We report that CCR7+ DCs are the dominant DC population that migrate to the dLN, but a subset remains tumour-resident despite CCR7 expression. These tumour-retained CCR7+ DCs are phenotypically and transcriptionally distinct from their dLN counterparts and heterogeneous. Moreover, they progressively downregulate the expression of antigen presentation and pro-inflammatory transcripts with more prolonged tumour dwell-time. Tumour-residing CCR7+ DCs co-localise with PD-1+CD8+ T cells in human and murine solid tumours, and following anti-PD-L1 treatment, upregulate stimulatory molecules including OX40L, thereby augmenting anti-tumour cytolytic activity. Altogether, these data uncover previously unappreciated heterogeneity in CCR7+ DCs that may underpin a variable capacity to support intratumoural cytotoxic T cells.
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Affiliation(s)
- Colin Y C Lee
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Bethany C Kennedy
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Nathan Richoz
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
| | - Isaac Dean
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Zewen K Tuong
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Fabrina Gaspal
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Zhi Li
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Claire Willis
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Tetsuo Hasegawa
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
| | | | - David A Posner
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
| | | | | | | | | | - David R Withers
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK.
- Cellular Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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48
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Shahir JA, Stanley N, Purvis JE. Cellograph: a semi-supervised approach to analyzing multi-condition single-cell RNA-sequencing data using graph neural networks. BMC Bioinformatics 2024; 25:25. [PMID: 38221640 PMCID: PMC10788980 DOI: 10.1186/s12859-024-05641-9] [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: 10/31/2023] [Accepted: 01/04/2024] [Indexed: 01/16/2024] Open
Abstract
With the growing number of single-cell datasets collected under more complex experimental conditions, there is an opportunity to leverage single-cell variability to reveal deeper insights into how cells respond to perturbations. Many existing approaches rely on discretizing the data into clusters for differential gene expression (DGE), effectively ironing out any information unveiled by the single-cell variability across cell-types. In addition, DGE often assumes a statistical distribution that, if erroneous, can lead to false positive differentially expressed genes. Here, we present Cellograph: a semi-supervised framework that uses graph neural networks to quantify the effects of perturbations at single-cell granularity. Cellograph not only measures how prototypical cells are of each condition but also learns a latent space that is amenable to interpretable data visualization and clustering. The learned gene weight matrix from training reveals pertinent genes driving the differences between conditions. We demonstrate the utility of our approach on publicly-available datasets including cancer drug therapy, stem cell reprogramming, and organoid differentiation. Cellograph outperforms existing methods for quantifying the effects of experimental perturbations and offers a novel framework to analyze single-cell data using deep learning.
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Affiliation(s)
- Jamshaid A Shahir
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalie Stanley
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeremy E Purvis
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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49
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Ma F, Wang S, Xu L, Huang W, Shi G, Sun Z, Cai W, Wu Z, Huang Y, Meng J, Sun Y, Fang M, Cheng M, Ji Y, Hu T, Zhang Y, Gu B, Zhang J, Song S, Sun Y, Yan W. Single-cell profiling of the microenvironment in human bone metastatic renal cell carcinoma. Commun Biol 2024; 7:91. [PMID: 38216635 PMCID: PMC10786927 DOI: 10.1038/s42003-024-05772-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: 12/10/2022] [Accepted: 01/03/2024] [Indexed: 01/14/2024] Open
Abstract
Bone metastasis is of common occurrence in renal cell carcinoma with poor prognosis, but no optimal treatment approach has been established for bone metastatic renal cell carcinoma. To explore the potential therapeutic targets for bone metastatic renal cell carcinoma, we profile single cell transcriptomes of 6 primary renal cell carcinoma and 9 bone metastatic renal cell carcinoma. We also include scRNA-seq data of early-stage renal cell carcinoma, late-stage renal cell carcinoma, normal kidneys and healthy bone marrow samples in the study to better understand the bone metastasis niche. The molecular properties and dynamic changes of major cell lineages in bone metastatic environment of renal cell carcinoma are characterized. Bone metastatic renal cell carcinoma is associated with multifaceted immune deficiency together with cancer-associated fibroblasts, specifically appearance of macrophages exhibiting malignant and pro-angiogenic features. We also reveal the dominance of immune inhibitory T cells in the bone metastatic renal cell carcinoma which can be partially restored by the treatment. Trajectory analysis showes that myeloid-derived suppressor cells are progenitors of macrophages in the bone metastatic renal cell carcinoma while monocytes are their progenitors in primary tumors and healthy bone marrows. Additionally, the infiltration of immune inhibitory CD47+ T cells is observed in bone metastatic tumors, which may be a result of reduced phagocytosis by SIRPA-expressing macrophages in the bone microenvironment. Together, our results provide a systematic view of various cell types in bone metastatic renal cell carcinoma and suggest avenues for therapeutic solutions.
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Affiliation(s)
- Fen Ma
- Shanghai Key Laboratory of Compound Chinese Medicines, The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, 201203, Shanghai, China
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Shuoer Wang
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Lun Xu
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Wending Huang
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Guohai Shi
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
- Department of Urology, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
| | - Zhengwang Sun
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Weiluo Cai
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Zhiqiang Wu
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Yiming Huang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Juan Meng
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Yining Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Meng Fang
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Mo Cheng
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Yingzheng Ji
- Department of Orthopedic, Naval Medical Center of PLA, Second Military Medical University, 338 Huaihai West Road, Shanghai, China
| | - Tu Hu
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Yunkui Zhang
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
| | - Bingxin Gu
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Jiwei Zhang
- Shanghai Key Laboratory of Compound Chinese Medicines, The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, 201203, Shanghai, China.
| | - Shaoli Song
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China.
| | - Yidi Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China.
| | - Wangjun Yan
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China.
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Munshi RM. Novel ensemble learning approach with SVM-imputed ADASYN features for enhanced cervical cancer prediction. PLoS One 2024; 19:e0296107. [PMID: 38198475 PMCID: PMC10781159 DOI: 10.1371/journal.pone.0296107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/06/2023] [Indexed: 01/12/2024] Open
Abstract
Cervical cancer remains a leading cause of female mortality, particularly in developing regions, underscoring the critical need for early detection and intervention guided by skilled medical professionals. While Pap smear images serve as valuable diagnostic tools, many available datasets for automated cervical cancer detection contain missing data, posing challenges for machine learning models' efficacy. To address these hurdles, this study presents an automated system adept at managing missing information using ADASYN characteristics, resulting in exceptional accuracy. The proposed methodology integrates a voting classifier model harnessing the predictive capacity of three distinct machine learning models. It further incorporates SVM Imputer and ADASYN up-sampled features to mitigate missing value concerns, while leveraging CNN-generated features to augment the model's capabilities. Notably, this model achieves remarkable performance metrics, boasting a 99.99% accuracy, precision, recall, and F1 score. A comprehensive comparative analysis evaluates the proposed model against various machine learning algorithms across four scenarios: original dataset usage, SVM imputation, ADASYN feature utilization, and CNN-generated features. Results indicate the superior efficacy of the proposed model over existing state-of-the-art techniques. This research not only introduces a novel approach but also offers actionable suggestions for refining automated cervical cancer detection systems. Its impact extends to benefiting medical practitioners by enabling earlier detection and improved patient care. Furthermore, the study's findings have substantial societal implications, potentially reducing the burden of cervical cancer through enhanced diagnostic accuracy and timely intervention.
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Affiliation(s)
- Raafat M. Munshi
- Department of Medical Laboratory Technology (MLT), Faculty of Applied Medical Sciences, King Abdulaziz University, Rabigh, Saudi Arabia
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