1
|
Liu X, Yuan M, Zhao D, Zeng Q, Li W, Li T, Li Q, Zhuo Y, Luo M, Chen P, Wang L, Feng W, Zhou Z. Single-Nucleus Transcriptomic Atlas of Human Pericoronary Epicardial Adipose Tissue in Normal and Pathological Conditions. Arterioscler Thromb Vasc Biol 2024; 44:1628-1645. [PMID: 38813696 PMCID: PMC11208064 DOI: 10.1161/atvbaha.124.320923] [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: 03/05/2024] [Accepted: 05/15/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND Pericoronary epicardial adipose tissue (EAT) is a unique visceral fat depot that surrounds the adventitia of the coronary arteries without any anatomic barrier. Clinical studies have demonstrated the association between EAT volume and increased risks for coronary artery disease (CAD). However, the cellular and molecular mechanisms underlying the association remain elusive. METHODS We performed single-nucleus RNA sequencing on pericoronary EAT samples collected from 3 groups of subjects: patients undergoing coronary bypass surgery for severe CAD (n=8), patients with CAD with concomitant type 2 diabetes (n=8), and patients with valvular diseases but without concomitant CAD and type 2 diabetes as the control group (n=8). Comparative analyses were performed among groups, including cellular compositional analysis, cell type-resolved transcriptomic changes, gene coexpression network analysis, and intercellular communication analysis. Immunofluorescence staining was performed to confirm the presence of CAD-associated subclusters. RESULTS Unsupervised clustering of 73 386 nuclei identified 15 clusters, encompassing all known cell types in the adipose tissue. Distinct subpopulations were identified within primary cell types, including adipocytes, adipose stem and progenitor cells, and macrophages. CD83high macrophages and FOSBhigh adipocytes were significantly expanded in CAD. In comparison to normal controls, both disease groups exhibited dysregulated pathways and altered secretome in the primary cell types. Nevertheless, minimal differences were noted between the disease groups in terms of cellular composition and transcriptome. In addition, our data highlight a potential interplay between dysregulated circadian clock and altered physiological functions in adipocytes of pericoronary EAT. ANXA1 (annexin A1) and SEMA3B (semaphorin 3B) were identified as important adipokines potentially involved in functional changes of pericoronary EAT and CAD pathogenesis. CONCLUSIONS We built a complete single-nucleus transcriptomic atlas of human pericoronary EAT in normal and diseased conditions of CAD. Our study lays the foundation for developing novel therapeutic strategies for treating CAD by targeting and modifying pericoronary EAT functions.
Collapse
Affiliation(s)
- Xuanyu Liu
- State Key Laboratory of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (X.L., M.Y., D.Z., Q.Z., W.L., T.L., Q.L., Y.Z., M.L., P.C., L.W., W.F., Z.Z.)
- Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine (X.L., M.Y., D.Z., Q.Z., W.L., T.L., Z.Z.), Fuwai Hospital, Beijing, China
| | - Meng Yuan
- State Key Laboratory of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (X.L., M.Y., D.Z., Q.Z., W.L., T.L., Q.L., Y.Z., M.L., P.C., L.W., W.F., Z.Z.)
- Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine (X.L., M.Y., D.Z., Q.Z., W.L., T.L., Z.Z.), Fuwai Hospital, Beijing, China
| | - Danni Zhao
- State Key Laboratory of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (X.L., M.Y., D.Z., Q.Z., W.L., T.L., Q.L., Y.Z., M.L., P.C., L.W., W.F., Z.Z.)
- Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine (X.L., M.Y., D.Z., Q.Z., W.L., T.L., Z.Z.), Fuwai Hospital, Beijing, China
| | - Qingyi Zeng
- State Key Laboratory of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (X.L., M.Y., D.Z., Q.Z., W.L., T.L., Q.L., Y.Z., M.L., P.C., L.W., W.F., Z.Z.)
- Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine (X.L., M.Y., D.Z., Q.Z., W.L., T.L., Z.Z.), Fuwai Hospital, Beijing, China
| | - Wenke Li
- State Key Laboratory of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (X.L., M.Y., D.Z., Q.Z., W.L., T.L., Q.L., Y.Z., M.L., P.C., L.W., W.F., Z.Z.)
- Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine (X.L., M.Y., D.Z., Q.Z., W.L., T.L., Z.Z.), Fuwai Hospital, Beijing, China
| | - Tianjiao Li
- State Key Laboratory of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (X.L., M.Y., D.Z., Q.Z., W.L., T.L., Q.L., Y.Z., M.L., P.C., L.W., W.F., Z.Z.)
- Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine (X.L., M.Y., D.Z., Q.Z., W.L., T.L., Z.Z.), Fuwai Hospital, Beijing, China
| | - Qi Li
- State Key Laboratory of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (X.L., M.Y., D.Z., Q.Z., W.L., T.L., Q.L., Y.Z., M.L., P.C., L.W., W.F., Z.Z.)
- Department of Cardiac Surgery (Q.L., P.C., L.W., W.F.), Fuwai Hospital, Beijing, China
| | - Yue Zhuo
- State Key Laboratory of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (X.L., M.Y., D.Z., Q.Z., W.L., T.L., Q.L., Y.Z., M.L., P.C., L.W., W.F., Z.Z.)
- Center of Vascular Surgery (Y.Z., M.L.), Fuwai Hospital, Beijing, China
| | - Mingyao Luo
- State Key Laboratory of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (X.L., M.Y., D.Z., Q.Z., W.L., T.L., Q.L., Y.Z., M.L., P.C., L.W., W.F., Z.Z.)
- Center of Vascular Surgery (Y.Z., M.L.), Fuwai Hospital, Beijing, China
- Department of Vascular Surgery, Central-China Subcenter of National Center for Cardiovascular Diseases, Henan Cardiovascular Disease Center, Fuwai Central-China Cardiovascular Hospital, Central China Fuwai Hospital of Zhengzhou University, China (M.L.)
- Department of Vascular Surgery, Fuwai Yunnan Cardiovascular Hospital, Affiliated Cardiovascular Hospital of Kunming Medical University, China (M.L.)
| | - Pengfei Chen
- State Key Laboratory of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (X.L., M.Y., D.Z., Q.Z., W.L., T.L., Q.L., Y.Z., M.L., P.C., L.W., W.F., Z.Z.)
- Department of Cardiac Surgery (Q.L., P.C., L.W., W.F.), Fuwai Hospital, Beijing, China
| | - Liqing Wang
- State Key Laboratory of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (X.L., M.Y., D.Z., Q.Z., W.L., T.L., Q.L., Y.Z., M.L., P.C., L.W., W.F., Z.Z.)
- Department of Cardiac Surgery (Q.L., P.C., L.W., W.F.), Fuwai Hospital, Beijing, China
| | - Wei Feng
- State Key Laboratory of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (X.L., M.Y., D.Z., Q.Z., W.L., T.L., Q.L., Y.Z., M.L., P.C., L.W., W.F., Z.Z.)
- Department of Cardiac Surgery (Q.L., P.C., L.W., W.F.), Fuwai Hospital, Beijing, China
| | - Zhou Zhou
- State Key Laboratory of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (X.L., M.Y., D.Z., Q.Z., W.L., T.L., Q.L., Y.Z., M.L., P.C., L.W., W.F., Z.Z.)
- Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine (X.L., M.Y., D.Z., Q.Z., W.L., T.L., Z.Z.), Fuwai Hospital, Beijing, China
| |
Collapse
|
2
|
Narmada BC, Khakpoor A, Shirgaonkar N, Narayanan S, Aw PPK, Singh M, Ong KH, Owino CO, Ng JWT, Yew HC, Binte Mohamed Nasir NS, Au VB, Sng R, Kaliaperumal N, Khine HHTW, di Tocco FC, Masayuki O, Naikar S, Ng HX, Chia SL, Seah CXY, Alnawaz MH, Wai CLY, Tay AYL, Mangat KS, Chew V, Yu W, Connolly JE, Periyasamy G, Plissonnier ML, Levrero M, Lim SG, DasGupta R. Single-cell landscape of functionally cured chronic hepatitis B patients reveals activation of innate and altered CD4-CTL-driven adaptive immunity. J Hepatol 2024; 81:42-61. [PMID: 38423478 DOI: 10.1016/j.jhep.2024.02.017] [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: 12/29/2022] [Revised: 02/05/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND & AIMS Hepatitis B surface antigen (HBsAg) loss or functional cure (FC) is considered the optimal therapeutic outcome for patients with chronic hepatitis B (CHB). However, the immune-pathological biomarkers and underlying mechanisms of FC remain unclear. In this study we comprehensively interrogate disease-associated cell states identified within intrahepatic tissue and matched PBMCs (peripheral blood mononuclear cells) from patients with CHB or after FC, at the resolution of single cells, to provide novel insights into putative mechanisms underlying FC. METHODS We combined single-cell transcriptomics (single-cell RNA sequencing) with multiparametric flow cytometry-based immune phenotyping, and multiplexed immunofluorescence to elucidate the immunopathological cell states associated with CHB vs. FC. RESULTS We found that the intrahepatic environment in CHB and FC displays specific cell identities and molecular signatures that are distinct from those found in matched PBMCs. FC is associated with the emergence of an altered adaptive immune response marked by CD4 cytotoxic T lymphocytes, and an activated innate response represented by liver-resident natural killer cells, specific Kupffer cell subtypes and marginated neutrophils. Surprisingly, we found MHC class II-expressing hepatocytes in patients achieving FC, as well as low but persistent levels of covalently closed circular DNA and pregenomic RNA, which may play an important role in FC. CONCLUSIONS Our study provides conceptually novel insights into the immuno-pathological control of HBV cure, and opens exciting new avenues for clinical management, biomarker discovery and therapeutic development. We believe that the discoveries from this study, as it relates to the activation of an innate and altered immune response that may facilitate sustained, low-grade inflammation, may have broader implications in the resolution of chronic viral hepatitis. IMPACT AND IMPLICATIONS This study dissects the immuno-pathological cell states associated with functionally cured chronic hepatitis B (defined by the loss of HBV surface antigen or HBsAg). We identified the sustained presence of very low viral load, accessory antigen-presenting hepatocytes, adaptive-memory-like natural killer cells, and the emergence of helper CD4 T cells with cytotoxic or effector-like signatures associated with functional cure, suggesting previously unsuspected alterations in the adaptive immune response, as well as a key role for the innate immune response in achieving or maintaining functional cure. Overall, the insights generated from this study may provide new avenues for the development of alternative therapies as well as patient surveillance for better clinical management of chronic hepatitis B.
Collapse
Affiliation(s)
- Balakrishnan Chakrapani Narmada
- Laboratory of Precision Medicine and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), 60 Biopolis St., #02-01 Genome, Singapore 138672; Experimental Drug Development Centre, A∗STAR, 10 Biopolis Way, Chromos, Singapore 138670, Singapore
| | - Atefeh Khakpoor
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Niranjan Shirgaonkar
- Laboratory of Precision Medicine and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), 60 Biopolis St., #02-01 Genome, Singapore 138672
| | - Sriram Narayanan
- Institute of Molecular and Cell Biology, A∗STAR, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Pauline Poh Kim Aw
- Laboratory of Precision Medicine and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), 60 Biopolis St., #02-01 Genome, Singapore 138672
| | - Malay Singh
- Bioinformatics Institute, A∗STAR, 30 Biopolis Street, Matrix, Singapore 138671, Singapore
| | - Kok Haur Ong
- Bioinformatics Institute, A∗STAR, 30 Biopolis Street, Matrix, Singapore 138671, Singapore
| | - Collins Oduor Owino
- Laboratory of Precision Medicine and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), 60 Biopolis St., #02-01 Genome, Singapore 138672; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jane Wei Ting Ng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hui Chuing Yew
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Veonice Bijin Au
- Institute of Molecular and Cell Biology, A∗STAR, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Reina Sng
- Institute of Molecular and Cell Biology, A∗STAR, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Nivashini Kaliaperumal
- Institute of Molecular and Cell Biology, A∗STAR, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Htet Htet Toe Wai Khine
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Otsuka Masayuki
- Translational Immunology Institute (TII), SingHealth-DukeNUS Academic Medical Centre, Singapore 169856, Singapore
| | - Shamita Naikar
- Translational Immunology Institute (TII), SingHealth-DukeNUS Academic Medical Centre, Singapore 169856, Singapore
| | - Hui Xin Ng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Su Li Chia
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Myra Hj Alnawaz
- Department of Medicine, National University Hospital, Singapore
| | - Chris Lee Yoon Wai
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Amy Yuh Ling Tay
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kamarjit Singh Mangat
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Valerie Chew
- Translational Immunology Institute (TII), SingHealth-DukeNUS Academic Medical Centre, Singapore 169856, Singapore
| | - Weimiao Yu
- Institute of Molecular and Cell Biology, A∗STAR, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore; Bioinformatics Institute, A∗STAR, 30 Biopolis Street, Matrix, Singapore 138671, Singapore
| | - John Edward Connolly
- Institute of Molecular and Cell Biology, A∗STAR, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Institute of Biomedical Studies, Baylor University, Waco, TX, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Giridharan Periyasamy
- Experimental Drug Development Centre, A∗STAR, 10 Biopolis Way, Chromos, Singapore 138670, Singapore
| | | | - Massimo Levrero
- Cancer Research Center of Lyon (CRCL), INSERM U1052, CNRS UMR5286, Lyon, France; Department of Hepatology, Hôpital Croix-Rousse, Hospices Civils de Lyon, Lyon, France; University of Lyon Claude Bernard 1 (UCLB1), Lyon, France; Department of Medicine SCIAC and the Italian Institute of Technology (IIT) Center for Life Nanosciences (CLNS), University of Rome La Sapienza, Rome, Italy
| | - Seng Gee Lim
- Institute of Molecular and Cell Biology, A∗STAR, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore; Department of Medicine, National University Hospital, Singapore; Division of Gastroenterology and Hepatology, National University Hospital, National University Health System, Singapore.
| | - Ramanuj DasGupta
- Laboratory of Precision Medicine and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), 60 Biopolis St., #02-01 Genome, Singapore 138672.
| |
Collapse
|
3
|
Zvirblyte J, Nainys J, Juzenas S, Goda K, Kubiliute R, Dasevicius D, Kincius M, Ulys A, Jarmalaite S, Mazutis L. Single-cell transcriptional profiling of clear cell renal cell carcinoma reveals a tumor-associated endothelial tip cell phenotype. Commun Biol 2024; 7:780. [PMID: 38942917 DOI: 10.1038/s42003-024-06478-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 06/21/2024] [Indexed: 06/30/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most prevalent form of renal cancer, accounting for over 75% of cases. The asymptomatic nature of the disease contributes to late-stage diagnoses and poor survival. Highly vascularized and immune infiltrated microenvironment are prominent features of ccRCC, yet the interplay between vasculature and immune cells, disease progression and response to therapy remains poorly understood. Using droplet-based single-cell RNA sequencing we profile 50,236 transcriptomes from paired tumor and healthy adjacent kidney tissues. Our analysis reveals significant heterogeneity and inter-patient variability of the tumor microenvironment. Notably, we discover a previously uncharacterized vasculature subpopulation associated with epithelial-mesenchymal transition. The cell-cell communication analysis reveals multiple modes of immunosuppressive interactions within the tumor microenvironment, including clinically relevant interactions between tumor vasculature and stromal cells with immune cells. The upregulation of the genes involved in these interactions is associated with worse survival in the TCGA KIRC cohort. Our findings demonstrate the role of tumor vasculature and stromal cell populations in shaping the ccRCC microenvironment and uncover a subpopulation of cells within the tumor vasculature that is associated with an angiogenic phenotype.
Collapse
Affiliation(s)
- Justina Zvirblyte
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania
| | - Juozas Nainys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania
- Droplet Genomics, Vilnius, 10257, Lithuania
| | - Simonas Juzenas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania
| | - Karolis Goda
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania
| | - Raimonda Kubiliute
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania
| | - Darius Dasevicius
- National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Klinikos, Vilnius, 08406, Lithuania
| | | | - Albertas Ulys
- National Cancer Institute, Vilnius, 08660, Lithuania
| | - Sonata Jarmalaite
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania.
- National Cancer Institute, Vilnius, 08660, Lithuania.
| | - Linas Mazutis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania.
| |
Collapse
|
4
|
Trsan T, Peng V, Krishna C, Ohara TE, Beatty WL, Sudan R, Kanai M, Krishnamoorthy P, Rodrigues PF, Fachi JL, Grajales-Reyes G, Jaeger N, Fitzpatrick JAJ, Cella M, Gilfillan S, Nakata T, Jaiswal A, Stappenbeck TS, Daly MJ, Xavier RJ, Colonna M. The centrosomal protein FGFR1OP controls myosin function in murine intestinal epithelial cells. Dev Cell 2024:S1534-5807(24)00379-4. [PMID: 38942017 DOI: 10.1016/j.devcel.2024.06.001] [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: 09/04/2023] [Revised: 01/23/2024] [Accepted: 06/05/2024] [Indexed: 06/30/2024]
Abstract
Recent advances in human genetics have shed light on the genetic factors contributing to inflammatory diseases, particularly Crohn's disease (CD), a prominent form of inflammatory bowel disease. Certain risk genes associated with CD directly influence cytokine biology and cell-specific communication networks. Current CD therapies primarily rely on anti-inflammatory drugs, which are inconsistently effective and lack strategies for promoting epithelial restoration and mucosal balance. To understand CD's underlying mechanisms, we investigated the link between CD and the FGFR1OP gene, which encodes a centrosome protein. FGFR1OP deletion in mouse intestinal epithelial cells disrupted crypt architecture, resulting in crypt loss, inflammation, and fatality. FGFR1OP insufficiency hindered epithelial resilience during colitis. FGFR1OP was crucial for preserving non-muscle myosin II activity, ensuring the integrity of the actomyosin cytoskeleton and crypt cell adhesion. This role of FGFR1OP suggests that its deficiency in genetically predisposed individuals may reduce epithelial renewal capacity, heightening susceptibility to inflammation and disease.
Collapse
Affiliation(s)
- Tihana Trsan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Vincent Peng
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Chirag Krishna
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Takahiro E Ohara
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Wandy L Beatty
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Raki Sudan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Masahiro Kanai
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Praveen Krishnamoorthy
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Jose L Fachi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gary Grajales-Reyes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Natalia Jaeger
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA; Departments of Cell Biology & Physiology and Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Marina Cella
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Susan Gilfillan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Toru Nakata
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alok Jaiswal
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Mark J Daly
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Ramnik J Xavier
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
5
|
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.
Collapse
|
6
|
Patrick R, Janbandhu V, Tallapragada V, Tan SSM, McKinna EE, Contreras O, Ghazanfar S, Humphreys DT, Murray NJ, Tran YTH, Hume RD, Chong JJH, Harvey RP. Integration mapping of cardiac fibroblast single-cell transcriptomes elucidates cellular principles of fibrosis in diverse pathologies. SCIENCE ADVANCES 2024; 10:eadk8501. [PMID: 38905342 PMCID: PMC11192082 DOI: 10.1126/sciadv.adk8501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
Single-cell technology has allowed researchers to probe tissue complexity and dynamics at unprecedented depth in health and disease. However, the generation of high-dimensionality single-cell atlases and virtual three-dimensional tissues requires integrated reference maps that harmonize disparate experimental designs, analytical pipelines, and taxonomies. Here, we present a comprehensive single-cell transcriptome integration map of cardiac fibrosis, which underpins pathophysiology in most cardiovascular diseases. Our findings reveal similarity between cardiac fibroblast (CF) identities and dynamics in ischemic versus pressure overload models of cardiomyopathy. We also describe timelines for commitment of activated CFs to proliferation and myofibrogenesis, profibrotic and antifibrotic polarization of myofibroblasts and matrifibrocytes, and CF conservation across mouse and human healthy and diseased hearts. These insights have the potential to inform knowledge-based therapies.
Collapse
Affiliation(s)
- Ralph Patrick
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Vaibhao Janbandhu
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia
| | | | - Shannon S. M. Tan
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Emily E. McKinna
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
- Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia
| | - Osvaldo Contreras
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Shila Ghazanfar
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW 2006, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW 2006, Australia
| | - David T. Humphreys
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Nicholas J. Murray
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Yen T. H. Tran
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Robert D. Hume
- Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia
- School of Medical Science, The University of Sydney, Camperdown, NSW 2006, Australia
- Centre for Heart Failure and Diseases of the Aorta, The Baird Institute, Sydney, NSW 2042, Australia
| | - James J. H. Chong
- Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia
- Department of Cardiology, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Richard P. Harvey
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia
- School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington, NSW 2052, Australia
| |
Collapse
|
7
|
Zhang Z, Melzer ME, Arun KM, Sun H, Eriksson CJ, Fabian I, Shaashua S, Kiani K, Oren Y, Goyal Y. Synthetic DNA barcodes identify singlets in scRNA-seq datasets and evaluate doublet algorithms. CELL GENOMICS 2024:100592. [PMID: 38925122 DOI: 10.1016/j.xgen.2024.100592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 03/26/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) datasets contain true single cells, or singlets, in addition to cells that coalesce during the protocol, or doublets. Identifying singlets with high fidelity in scRNA-seq is necessary to avoid false negative and false positive discoveries. Although several methodologies have been proposed, they are typically tested on highly heterogeneous datasets and lack a priori knowledge of true singlets. Here, we leveraged datasets with synthetically introduced DNA barcodes for a hitherto unexplored application: to extract ground-truth singlets. We demonstrated the feasibility of our framework, "singletCode," to evaluate existing doublet detection methods across a range of contexts. We also leveraged our ground-truth singlets to train a proof-of-concept machine learning classifier, which outperformed other doublet detection algorithms. Our integrative framework can identify ground-truth singlets and enable robust doublet detection in non-barcoded datasets.
Collapse
Affiliation(s)
- Ziyang Zhang
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Center for Synthetic Biology, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Madeline E Melzer
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Center for Synthetic Biology, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Keerthana M Arun
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Center for Synthetic Biology, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Hanxiao Sun
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Center for Synthetic Biology, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Carl-Johan Eriksson
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Itai Fabian
- Department of Human Molecular Genetics & Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sagi Shaashua
- Department of Human Molecular Genetics & Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Karun Kiani
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yaara Oren
- Department of Human Molecular Genetics & Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Center for Synthetic Biology, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; CZ Biohub Chicago, Chicago, IL, USA.
| |
Collapse
|
8
|
İş Ö, Wang X, Reddy JS, Min Y, Yilmaz E, Bhattarai P, Patel T, Bergman J, Quicksall Z, Heckman MG, Tutor-New FQ, Can Demirdogen B, White L, Koga S, Krause V, Inoue Y, Kanekiyo T, Cosacak MI, Nelson N, Lee AJ, Vardarajan B, Mayeux R, Kouri N, Deniz K, Carnwath T, Oatman SR, Lewis-Tuffin LJ, Nguyen T, Carrasquillo MM, Graff-Radford J, Petersen RC, Jr Jack CR, Kantarci K, Murray ME, Nho K, Saykin AJ, Dickson DW, Kizil C, Allen M, Ertekin-Taner N. Gliovascular transcriptional perturbations in Alzheimer's disease reveal molecular mechanisms of blood brain barrier dysfunction. Nat Commun 2024; 15:4758. [PMID: 38902234 PMCID: PMC11190273 DOI: 10.1038/s41467-024-48926-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 05/17/2024] [Indexed: 06/22/2024] Open
Abstract
To uncover molecular changes underlying blood-brain-barrier dysfunction in Alzheimer's disease, we performed single nucleus RNA sequencing in 24 Alzheimer's disease and control brains and focused on vascular and astrocyte clusters as main cell types of blood-brain-barrier gliovascular-unit. The majority of the vascular transcriptional changes were in pericytes. Of the vascular molecular targets predicted to interact with astrocytic ligands, SMAD3, upregulated in Alzheimer's disease pericytes, has the highest number of ligands including VEGFA, downregulated in Alzheimer's disease astrocytes. We validated these findings with external datasets comprising 4,730 pericyte and 150,664 astrocyte nuclei. Blood SMAD3 levels are associated with Alzheimer's disease-related neuroimaging outcomes. We determined inverse relationships between pericytic SMAD3 and astrocytic VEGFA in human iPSC and zebrafish models. Here, we detect vast transcriptome changes in Alzheimer's disease at the gliovascular-unit, prioritize perturbed pericytic SMAD3-astrocytic VEGFA interactions, and validate these in cross-species models to provide a molecular mechanism of blood-brain-barrier disintegrity in Alzheimer's disease.
Collapse
Affiliation(s)
- Özkan İş
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Joseph S Reddy
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Yuhao Min
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Elanur Yilmaz
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Prabesh Bhattarai
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Tulsi Patel
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Zachary Quicksall
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Michael G Heckman
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | | | - Birsen Can Demirdogen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey
| | - Launia White
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Shunsuke Koga
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Vincent Krause
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Yasuteru Inoue
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Mehmet Ilyas Cosacak
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, Dresden, Germany
| | - Nastasia Nelson
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Annie J Lee
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Badri Vardarajan
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Richard Mayeux
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Naomi Kouri
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Kaancan Deniz
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Troy Carnwath
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Laura J Lewis-Tuffin
- Mayo Clinic Florida Cytometry and Cell Imaging Laboratory, Mayo Clinic, Jacksonville, FL, USA
| | - Thuy Nguyen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | - Ronald C Petersen
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
- Mayo Clinic Alzheimer's Disease Research Center, Rochester, MN, USA
| | | | - Kejal Kantarci
- Mayo Clinic Alzheimer's Disease Research Center, Rochester, MN, USA
| | | | - Kwangsik Nho
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Caghan Kizil
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA.
| |
Collapse
|
9
|
Serrano G, Berastegui N, Díaz-Mazkiaran A, García-Olloqui P, Rodriguez-Res C, Huerga-Dominguez S, Ainciburu M, Vilas-Zornoza A, Martin-Uriz PS, Aguirre-Ruiz P, Ullate-Agote A, Ariceta B, Lamo-Espinosa JM, Acha P, Calvete O, Jimenez T, Molero A, Montoro MJ, Díez-Campelo M, Valcarcel D, Solé F, Alfonso-Pierola A, Ochoa I, Prósper F, Ezponda T, Hernaez M. Single-cell transcriptional profile of CD34+ hematopoietic progenitor cells from del(5q) myelodysplastic syndromes and impact of lenalidomide. Nat Commun 2024; 15:5272. [PMID: 38902243 PMCID: PMC11189937 DOI: 10.1038/s41467-024-49529-x] [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] [Accepted: 06/06/2024] [Indexed: 06/22/2024] Open
Abstract
While myelodysplastic syndromes with del(5q) (del(5q) MDS) comprises a well-defined hematological subgroup, the molecular basis underlying its origin remains unknown. Using single cell RNA-seq (scRNA-seq) on CD34+ progenitors from del(5q) MDS patients, we have identified cells harboring the deletion, characterizing the transcriptional impact of this genetic insult on disease pathogenesis and treatment response. Interestingly, both del(5q) and non-del(5q) cells present similar transcriptional lesions, indicating that all cells, and not only those harboring the deletion, may contribute to aberrant hematopoietic differentiation. However, gene regulatory network (GRN) analyses reveal a group of regulons showing aberrant activity that could trigger altered hematopoiesis exclusively in del(5q) cells, pointing to a more prominent role of these cells in disease phenotype. In del(5q) MDS patients achieving hematological response upon lenalidomide treatment, the drug reverts several transcriptional alterations in both del(5q) and non-del(5q) cells, but other lesions remain, which may be responsible for potential future relapses. Moreover, lack of hematological response is associated with the inability of lenalidomide to reverse transcriptional alterations. Collectively, this study reveals transcriptional alterations that could contribute to the pathogenesis and treatment response of del(5q) MDS.
Collapse
Affiliation(s)
- Guillermo Serrano
- Computational Biology Program CIMA-Universidad de Navarra, Cancer Center Clínica Universidad de Navarra (CCUN), IdISNA, Pamplona, Spain
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Nerea Berastegui
- Hematology-Oncology Program, CIMA, Cancer Center Clínica Universidad de Navarra (CCUN), IdiSNA, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain
| | - Aintzane Díaz-Mazkiaran
- Computational Biology Program CIMA-Universidad de Navarra, Cancer Center Clínica Universidad de Navarra (CCUN), IdISNA, Pamplona, Spain
- Hematology-Oncology Program, CIMA, Cancer Center Clínica Universidad de Navarra (CCUN), IdiSNA, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain
| | - Paula García-Olloqui
- Hematology-Oncology Program, CIMA, Cancer Center Clínica Universidad de Navarra (CCUN), IdiSNA, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain
| | - Carmen Rodriguez-Res
- Computational Biology Program CIMA-Universidad de Navarra, Cancer Center Clínica Universidad de Navarra (CCUN), IdISNA, Pamplona, Spain
| | - Sofia Huerga-Dominguez
- Hematology and Cell Therapy Service, Cancer Center Clínica Universidad de Navarra (CCUN), IdISNA, Pamplona, Spain
| | - Marina Ainciburu
- Hematology-Oncology Program, CIMA, Cancer Center Clínica Universidad de Navarra (CCUN), IdiSNA, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain
| | - Amaia Vilas-Zornoza
- Hematology-Oncology Program, CIMA, Cancer Center Clínica Universidad de Navarra (CCUN), IdiSNA, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain
| | - Patxi San Martin-Uriz
- Hematology-Oncology Program, CIMA, Cancer Center Clínica Universidad de Navarra (CCUN), IdiSNA, Pamplona, Spain
| | - Paula Aguirre-Ruiz
- Hematology-Oncology Program, CIMA, Cancer Center Clínica Universidad de Navarra (CCUN), IdiSNA, Pamplona, Spain
| | - Asier Ullate-Agote
- Hematology-Oncology Program, CIMA, Cancer Center Clínica Universidad de Navarra (CCUN), IdiSNA, Pamplona, Spain
| | - Beñat Ariceta
- Hematology-Oncology Program, CIMA, Cancer Center Clínica Universidad de Navarra (CCUN), IdiSNA, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain
| | | | - Pamela Acha
- MDS Research Group, Josep Carreras Leukaemia Research Institut, Universitat Autònoma de Barcelona, Barcelona, Spain
- Service of Hematology, Hospital Universitari Vall d'Hebron, Barcelona; Vall d'Hebron Instituto de Oncología (VHIO), Barcelona, Spain
| | - Oriol Calvete
- MDS Research Group, Josep Carreras Leukaemia Research Institut, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Tamara Jimenez
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain
- Department of Hematology, Hospital Universitario de Salamanca-IBSAL, Salamanca, Spain
| | - Antonieta Molero
- Service of Hematology, Hospital Universitari Vall d'Hebron, Barcelona; Vall d'Hebron Instituto de Oncología (VHIO), Barcelona, Spain
| | - Maria Julia Montoro
- Service of Hematology, Hospital Universitari Vall d'Hebron, Barcelona; Vall d'Hebron Instituto de Oncología (VHIO), Barcelona, Spain
| | - Maria Díez-Campelo
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain
- Department of Hematology, Hospital Universitario de Salamanca-IBSAL, Salamanca, Spain
| | - David Valcarcel
- Service of Hematology, Hospital Universitari Vall d'Hebron, Barcelona; Vall d'Hebron Instituto de Oncología (VHIO), Barcelona, Spain
| | - Francisco Solé
- MDS Research Group, Josep Carreras Leukaemia Research Institut, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ana Alfonso-Pierola
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain
- Hematology and Cell Therapy Service, Cancer Center Clínica Universidad de Navarra (CCUN), IdISNA, Pamplona, Spain
| | - Idoia Ochoa
- Instituto de Ciencia de los Datos e Inteligencia Artificial (DATAI), University of Navarra, Pamplona, Spain
- Department of Electrical and Electronics engineering, School of Engineering (Tecnun), University of Navarra, Donostia, Spain
| | - Felipe Prósper
- Hematology-Oncology Program, CIMA, Cancer Center Clínica Universidad de Navarra (CCUN), IdiSNA, Pamplona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain.
- Hematology and Cell Therapy Service, Cancer Center Clínica Universidad de Navarra (CCUN), IdISNA, Pamplona, Spain.
| | - Teresa Ezponda
- Hematology-Oncology Program, CIMA, Cancer Center Clínica Universidad de Navarra (CCUN), IdiSNA, Pamplona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain.
| | - Mikel Hernaez
- Computational Biology Program CIMA-Universidad de Navarra, Cancer Center Clínica Universidad de Navarra (CCUN), IdISNA, Pamplona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain.
- Instituto de Ciencia de los Datos e Inteligencia Artificial (DATAI), University of Navarra, Pamplona, Spain.
| |
Collapse
|
10
|
Huang K, Xu Y, Feng T, Lan H, Ling F, Xiang H, Liu Q. The Advancement and Application of the Single-Cell Transcriptome in Biological and Medical Research. BIOLOGY 2024; 13:451. [PMID: 38927331 PMCID: PMC11200756 DOI: 10.3390/biology13060451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/11/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024]
Abstract
Single-cell RNA sequencing technology (scRNA-seq) has been steadily developing since its inception in 2009. Unlike bulk RNA-seq, scRNA-seq identifies the heterogeneity of tissue cells and reveals gene expression changes in individual cells at the microscopic level. Here, we review the development of scRNA-seq, which has gone through iterations of reverse transcription, in vitro transcription, smart-seq, drop-seq, 10 × Genomics, and spatial single-cell transcriptome technologies. The technology of 10 × Genomics has been widely applied in medicine and biology, producing rich research results. Furthermore, this review presents a summary of the analytical process for single-cell transcriptome data and its integration with other omics analyses, including genomes, epigenomes, proteomes, and metabolomics. The single-cell transcriptome has a wide range of applications in biology and medicine. This review analyzes the applications of scRNA-seq in cancer, stem cell research, developmental biology, microbiology, and other fields. In essence, scRNA-seq provides a means of elucidating gene expression patterns in single cells, thereby offering a valuable tool for scientific research. Nevertheless, the current single-cell transcriptome technology is still imperfect, and this review identifies its shortcomings and anticipates future developments. The objective of this review is to facilitate a deeper comprehension of scRNA-seq technology and its applications in biological and medical research, as well as to identify avenues for its future development in alignment with practical needs.
Collapse
Affiliation(s)
- Kongwei Huang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510641, China
| | - Yixue Xu
- Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530005, China;
| | - Tong Feng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Hong Lan
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Fei Ling
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510641, China
| | - Hai Xiang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| |
Collapse
|
11
|
Easter QT, Fernandes Matuck B, Beldorati Stark G, Worth CL, Predeus AV, Fremin B, Huynh K, Ranganathan V, Ren Z, Pereira D, Rupp BT, Weaver T, Miller K, Perez P, Hasuike A, Chen Z, Bush M, Qu X, Lee J, Randell SH, Wallet SM, Sequeira I, Koo H, Tyc KM, Liu J, Ko KI, Teichmann SA, Byrd KM. Single-cell and spatially resolved interactomics of tooth-associated keratinocytes in periodontitis. Nat Commun 2024; 15:5016. [PMID: 38876998 PMCID: PMC11178863 DOI: 10.1038/s41467-024-49037-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: 08/26/2023] [Accepted: 05/20/2024] [Indexed: 06/16/2024] Open
Abstract
Periodontitis affects billions of people worldwide. To address relationships of periodontal niche cell types and microbes in periodontitis, we generated an integrated single-cell RNA sequencing (scRNAseq) atlas of human periodontium (34-sample, 105918-cell), including sulcular and junctional keratinocytes (SK/JKs). SK/JKs displayed altered differentiation states and were enriched for effector cytokines in periodontitis. Single-cell metagenomics revealed 37 bacterial species with cell-specific tropism. Fluorescence in situ hybridization detected intracellular 16 S and mRNA signals of multiple species and correlated with SK/JK proinflammatory phenotypes in situ. Cell-cell communication analysis predicted keratinocyte-specific innate and adaptive immune interactions. Highly multiplexed immunofluorescence (33-antibody) revealed peri-epithelial immune foci, with innate cells often spatially constrained around JKs. Spatial phenotyping revealed immunosuppressed JK-microniches and SK-localized tertiary lymphoid structures in periodontitis. Here, we demonstrate impacts on and predicted interactomics of SK and JK cells in health and periodontitis, which requires further investigation to support precision periodontal interventions in states of chronic inflammation.
Collapse
Affiliation(s)
- Quinn T Easter
- Lab of Oral & Craniofacial Innovation (LOCI), Department of Innovation & Technology Research, ADA Science & Research Institute, Gaithersburg, MD, USA
| | - Bruno Fernandes Matuck
- Lab of Oral & Craniofacial Innovation (LOCI), Department of Innovation & Technology Research, ADA Science & Research Institute, Gaithersburg, MD, USA
| | | | | | | | | | - Khoa Huynh
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | | | - Zhi Ren
- Biofilm Research Laboratories, Center for Innovation & Precision Dentistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Diana Pereira
- Center for Oral Immunobiology and Regenerative Medicine, Barts Centre for Squamous Cancer, Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Brittany T Rupp
- Lab of Oral & Craniofacial Innovation (LOCI), Department of Innovation & Technology Research, ADA Science & Research Institute, Gaithersburg, MD, USA
| | - Theresa Weaver
- Lab of Oral & Craniofacial Innovation (LOCI), Department of Innovation & Technology Research, ADA Science & Research Institute, Gaithersburg, MD, USA
| | | | - Paola Perez
- Salivary Disorders Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Akira Hasuike
- Lab of Oral & Craniofacial Innovation (LOCI), Department of Innovation & Technology Research, ADA Science & Research Institute, Gaithersburg, MD, USA
- Department of Periodontology, Nihon University School of Dentistry, Tokyo, Japan
| | - Zhaoxu Chen
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mandy Bush
- Respiratory TRACTS Core, Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xufeng Qu
- VCU Massey Comprehensive Cancer Center, Bioinformatics Shared Resource Core, Virginia Commonwealth University, Richmond, VA, USA
| | - Janice Lee
- Craniofacial Anomalies & Regeneration Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Scott H Randell
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shannon M Wallet
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Inês Sequeira
- Center for Oral Immunobiology and Regenerative Medicine, Barts Centre for Squamous Cancer, Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Hyun Koo
- Biofilm Research Laboratories, Center for Innovation & Precision Dentistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katarzyna M Tyc
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
- VCU Massey Comprehensive Cancer Center, Bioinformatics Shared Resource Core, Virginia Commonwealth University, Richmond, VA, USA
| | - Jinze Liu
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
- VCU Massey Comprehensive Cancer Center, Bioinformatics Shared Resource Core, Virginia Commonwealth University, Richmond, VA, USA
| | - Kang I Ko
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Physics, Cavendish Laboratory, Cambridge, UK
| | - Kevin M Byrd
- Lab of Oral & Craniofacial Innovation (LOCI), Department of Innovation & Technology Research, ADA Science & Research Institute, Gaithersburg, MD, USA.
- Salivary Disorders Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA.
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| |
Collapse
|
12
|
Rebboah E, Rezaie N, Williams BA, Weimer AK, Shi M, Yang X, Liang HY, Dionne LA, Reese F, Trout D, Jou J, Youngworth I, Reinholdt L, Morabito S, Snyder MP, Wold BJ, Mortazavi A. The ENCODE mouse postnatal developmental time course identifies regulatory programs of cell types and cell states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598567. [PMID: 38915583 PMCID: PMC11195270 DOI: 10.1101/2024.06.12.598567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Postnatal genomic regulation significantly influences tissue and organ maturation but is under-studied relative to existing genomic catalogs of adult tissues or prenatal development in mouse. The ENCODE4 consortium generated the first comprehensive single-nucleus resource of postnatal regulatory events across a diverse set of mouse tissues. The collection spans seven postnatal time points, mirroring human development from childhood to adulthood, and encompasses five core tissues. We identified 30 cell types, further subdivided into 69 subtypes and cell states across adrenal gland, left cerebral cortex, hippocampus, heart, and gastrocnemius muscle. Our annotations cover both known and novel cell differentiation dynamics ranging from early hippocampal neurogenesis to a new sex-specific adrenal gland population during puberty. We used an ensemble Latent Dirichlet Allocation strategy with a curated vocabulary of 2,701 regulatory genes to identify regulatory "topics," each of which is a gene vector, linked to cell type differentiation, subtype specialization, and transitions between cell states. We find recurrent regulatory topics in tissue-resident macrophages, neural cell types, endothelial cells across multiple tissues, and cycling cells of the adrenal gland and heart. Cell-type-specific topics are enriched in transcription factors and microRNA host genes, while chromatin regulators dominate mitosis topics. Corresponding chromatin accessibility data reveal dynamic and sex-specific regulatory elements, with enriched motifs matching transcription factors in regulatory topics. Together, these analyses identify both tissue-specific and common regulatory programs in postnatal development across multiple tissues through the lens of the factors regulating transcription.
Collapse
Affiliation(s)
- Elisabeth Rebboah
- Developmental and Cell Biology, University of California Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, USA
| | - Narges Rezaie
- Developmental and Cell Biology, University of California Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, USA
| | - Brian A. Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Annika K. Weimer
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Minyi Shi
- Department of Next Generation Sequencing and Microchemistry, Proteomics and Lipidomics, Genentech, San Francisco, USA
| | - Xinqiong Yang
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Heidi Yahan Liang
- Developmental and Cell Biology, University of California Irvine, Irvine, USA
| | | | - Fairlie Reese
- Developmental and Cell Biology, University of California Irvine, Irvine, USA
| | - Diane Trout
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Jennifer Jou
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Ingrid Youngworth
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | | | - Samuel Morabito
- Developmental and Cell Biology, University of California Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, USA
| | - Michael P. Snyder
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Barbara J. Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Ali Mortazavi
- Developmental and Cell Biology, University of California Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, USA
| |
Collapse
|
13
|
Mato-Blanco X, Kim SK, Jourdon A, Ma S, Tebbenkamp ATN, Liu F, Duque A, Vaccarino FM, Sestan N, Colantuoni C, Rakic P, Santpere G, Micali N. Early Developmental Origins of Cortical Disorders Modeled in Human Neural Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.598925. [PMID: 38915580 PMCID: PMC11195173 DOI: 10.1101/2024.06.14.598925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The implications of the early phases of human telencephalic development, involving neural stem cells (NSCs), in the etiology of cortical disorders remain elusive. Here, we explored the expression dynamics of cortical and neuropsychiatric disorder-associated genes in datasets generated from human NSCs across telencephalic fate transitions in vitro and in vivo. We identified risk genes expressed in brain organizers and sequential gene regulatory networks across corticogenesis revealing disease-specific critical phases, when NSCs are more vulnerable to gene dysfunctions, and converging signaling across multiple diseases. Moreover, we simulated the impact of risk transcription factor (TF) depletions on different neural cell types spanning the developing human neocortex and observed a spatiotemporal-dependent effect for each perturbation. Finally, single-cell transcriptomics of newly generated autism-affected patient-derived NSCs in vitro revealed recurrent alterations of TFs orchestrating brain patterning and NSC lineage commitment. This work opens new perspectives to explore human brain dysfunctions at the early phases of development. One-sentence summary The temporal analysis of gene regulatory networks in human neural stem cells reveals multiple early critical phases associated with cortical disorders and neuropsychiatric traits.
Collapse
|
14
|
Kim JY, Jung JH, Jung S, Lee S, Lee HA, Ouh YT, Hong SH. Glyoxalase 1: Emerging biomarker and therapeutic target in cervical cancer progression. PLoS One 2024; 19:e0299345. [PMID: 38870176 PMCID: PMC11175447 DOI: 10.1371/journal.pone.0299345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/26/2024] [Indexed: 06/15/2024] Open
Abstract
INTRODUCTION Cervical cancer presents a significant global health challenge, disproportionately impacting underserved populations with limited access to healthcare. Early detection and effective management are vital in addressing this public health concern. This study focuses on Glyoxalase-1 (GLO1), an enzyme crucial for methylglyoxal detoxification, in the context of cervical cancer. METHODS We assessed GLO1 expression in cervical cancer patient samples using immunohistochemistry. In vitro experiments using HeLa cells were conducted to evaluate the impact of GLO1 inhibition on cell viability and migration. Single-cell RNA sequencing (scRNA-seq) and gene set variation analysis were utilized to investigate the role of GLO1 in the metabolism of cervical cancer. Additionally, public microarray data were analyzed to determine GLO1 expression across various stages of cervical cancer. RESULTS Our analysis included 58 cervical cancer patients, and showed that GLO1 is significantly upregulated in cervical cancer tissues compared to normal cervical tissues, independent of pathological findings and disease stage. In vitro experiments indicated that GLO1 inhibition by S-p-bromobenzylglutathione cyclopentyl diester decreased cell viability and migration in cervical cancer cell lines. Analyses of scRNA-seq data and public gene expression datasets corroborated the overexpression of GLO1 and its involvement in cancer metabolism, particularly glycolysis. An examination of expression data from precancerous lesions revealed a progressive increase in GLO1 expression from normal tissue to invasive cervical cancer. CONCLUSIONS This study highlights the critical role of GLO1 in the progression of cervical cancer, presenting it as a potential biomarker and therapeutic target. These findings contribute valuable insights towards personalized treatment approaches and augment the ongoing efforts to combat cervical cancer. Further research is necessary to comprehensively explore GLO1's potential in clinical applications.
Collapse
Affiliation(s)
- Ji-Young Kim
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, Republic of Korea
| | - Ji-Hye Jung
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, Republic of Korea
| | - Soryung Jung
- Department of Life Science, Ewha Womans University, Seoul, Republic of Korea
| | - Sanghyuk Lee
- Department of Life Science, Ewha Womans University, Seoul, Republic of Korea
| | - Hyang Ah Lee
- Department of Obstetrics and Gynecology, School of Medicine, Kangwon National University, Chuncheon, Republic of Korea
| | - Yung-Taek Ouh
- Department of Obstetrics and Gynecology, School of Medicine, Kangwon National University, Chuncheon, Republic of Korea
- Department of Obstetrics and Gynecology, Ansan Hospital, Korea University College of Medicine, Gyeonggi, Republic of Korea
| | - Seok-Ho Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, Republic of Korea
- KW-Bio Co., Ltd, Chuncheon, Republic of Korea
| |
Collapse
|
15
|
Kirk JS, Wang J, Long M, Rosario S, Tracz A, Ji Y, Kumar R, Liu X, Jamroze A, Singh PK, Puzanov I, Chatta G, Cheng Q, Huang J, Wrana JL, Lovell J, Yu H, Liu S, Shen MM, Liu T, Tang DG. Integrated single-cell analysis defines the epigenetic basis of castration-resistant prostate luminal cells. Cell Stem Cell 2024:S1934-5909(24)00185-1. [PMID: 38878775 DOI: 10.1016/j.stem.2024.05.008] [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: 03/13/2023] [Revised: 02/26/2024] [Accepted: 05/20/2024] [Indexed: 06/22/2024]
Abstract
Understanding prostate response to castration and androgen receptor signaling inhibitors (ARSI) is critical to improving long-term prostate cancer (PCa) patient survival. Here, we use a multi-omics approach on 229,794 single cells to create a mouse single-cell reference atlas for interpreting mouse prostate biology and castration response. Our reference atlas refines single-cell annotations and provides a chromatin context, which, when coupled with mouse lineage tracing, demonstrates that castration-resistant luminal cells are distinct from the pre-existent urethra-proximal stem/progenitor cells. Molecular pathway analysis and therapeutic studies further implicate AP1 (JUN/FOS), WNT/β-catenin, FOXQ1, NF-κB, and JAK/STAT pathways as major drivers of castration-resistant luminal populations with relevance to human PCa. Our datasets, which can be explored through an interactive portal (https://visportal.roswellpark.org/data/tang/), can aid in developing combination treatments with ARSI for advanced PCa patients.
Collapse
Affiliation(s)
- Jason S Kirk
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
| | - Jie Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Mark Long
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Spencer Rosario
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Amanda Tracz
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Yibing Ji
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Rahul Kumar
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Xiaozhuo Liu
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Anmbreen Jamroze
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Prashant K Singh
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Igor Puzanov
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Gurkamal Chatta
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Qing Cheng
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jeffrey L Wrana
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X5, Canada
| | - Jonathan Lovell
- Department of Biomedical Engineering, University at Buffalo, Buffalo, NY 14260, USA
| | - Han Yu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Michael M Shen
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tao Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
| | - Dean G Tang
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
| |
Collapse
|
16
|
Sarkozy C, Wu S, Takata K, Aoki T, Neriah SB, Milne K, Goodyear T, Strong C, Rastogi T, Hilton LK, Lai D, Sehn LH, Farinha P, Nelson BH, Weng A, Marra M, Scott DW, Craig JW, Steidl C, Roth A. Integrated single cell analysis reveals co-evolution of malignant B cells and tumor micro-environment in transformed follicular lymphoma. Cancer Cell 2024; 42:1003-1017.e6. [PMID: 38861923 DOI: 10.1016/j.ccell.2024.05.011] [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: 04/04/2023] [Revised: 02/12/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024]
Abstract
Histological transformation of follicular lymphoma (FL) to aggressive forms is associated with poor outcome. Phenotypic consequences of this evolution and its impact on the tumor microenvironment (TME) remain unknown. We perform single-cell whole genome sequencing (scWGS) and transcriptome sequencing (scWTS) of 11 paired pre/post-transformation patient samples and scWTS of additional samples from patients without transformation. Our analysis reveals evolutionary dynamics of transformation at single-cell resolution, highlighting a shifting TME landscape, with an emerging immune-cell exhaustion signature, co-evolving with the shifting malignant B phenotype in a regulatory ecosystem. Integration of scWGS and scWTS identifies malignant cell pathways upregulated during clonal tumor evolution. Using multi-color immunofluorescence, we transfer these findings to a TME-based transformation biomarker, subsequently validated in two independent pretreatment cohorts. Taken together, our results provide a comprehensive view of the combined genomic and phenotypic evolution of malignant cells during transformation and shifting crosstalk between malignant cells and the TME.
Collapse
Affiliation(s)
- Clémentine Sarkozy
- Hematology Department, Institut Curie, Saint Cloud, France; University PSL, Inserm U1288, Laboratoire d'Imagerie Translationnelle en Oncologie, 91400 Orsay, France
| | - Shaocheng Wu
- Department of Molecular Oncology, British Columbia Cancer, Vancouver, BC, Canada
| | - Katsuyoshi Takata
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BC, Canada
| | - Tomohiro Aoki
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Susana B Neriah
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BC, Canada
| | - Katy Milne
- Deeley Research Centre, British Columbia Cancer, Vancouver, BC, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Talia Goodyear
- Deeley Research Centre, British Columbia Cancer, Vancouver, BC, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Celia Strong
- Deeley Research Centre, British Columbia Cancer, Vancouver, BC, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Tashi Rastogi
- Deeley Research Centre, British Columbia Cancer, Vancouver, BC, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Laura K Hilton
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BC, Canada
| | - Daniel Lai
- Department of Molecular Oncology, British Columbia Cancer, Vancouver, BC, Canada
| | - Laurie H Sehn
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BC, Canada
| | - Pedro Farinha
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BC, Canada
| | - Brad H Nelson
- Deeley Research Centre, British Columbia Cancer, Vancouver, BC, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Andrew Weng
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, BC, Canada
| | - Marco Marra
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BC, Canada
| | - Jeffrey W Craig
- Department of Pathology, University of Virginia Health System, Charlottesville, VA, USA
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Andrew Roth
- Department of Molecular Oncology, British Columbia Cancer, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Department of Computer Science, University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|
17
|
Peidli S, Nouailles G, Wyler E, Adler JM, Kunder S, Voß A, Kazmierski J, Pott F, Pennitz P, Postmus D, Teixeira Alves LG, Goffinet C, Gruber AD, Blüthgen N, Witzenrath M, Trimpert J, Landthaler M, Praktiknjo SD. Single-cell-resolved interspecies comparison shows a shared inflammatory axis and a dominant neutrophil-endothelial program in severe COVID-19. Cell Rep 2024; 43:114328. [PMID: 38861386 DOI: 10.1016/j.celrep.2024.114328] [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: 12/15/2023] [Revised: 04/21/2024] [Accepted: 05/22/2024] [Indexed: 06/13/2024] Open
Abstract
A key issue for research on COVID-19 pathogenesis is the lack of biopsies from patients and of samples at the onset of infection. To overcome these hurdles, hamsters were shown to be useful models for studying this disease. Here, we further leverage the model to molecularly survey the disease progression from time-resolved single-cell RNA sequencing data collected from healthy and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected Syrian and Roborovski hamster lungs. We compare our data to human COVID-19 studies, including bronchoalveolar lavage, nasal swab, and postmortem lung tissue, and identify a shared axis of inflammation dominated by macrophages, neutrophils, and endothelial cells, which we show to be transient in Syrian and terminal in Roborovski hamsters. Our data suggest that, following SARS-CoV-2 infection, commitment to a type 1- or type 3-biased immunity determines moderate versus severe COVID-19 outcomes, respectively.
Collapse
Affiliation(s)
- Stefan Peidli
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Berlin, Germany; Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Geraldine Nouailles
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Julia M Adler
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Sandra Kunder
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Anne Voß
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Julia Kazmierski
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Fabian Pott
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Peter Pennitz
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany
| | - Dylan Postmus
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Luiz Gustavo Teixeira Alves
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Christine Goffinet
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Achim D Gruber
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Nils Blüthgen
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Berlin, Germany; Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Martin Witzenrath
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany; German Center for Lung Research (DZL), Berlin, Germany
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany; Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Markus Landthaler
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany; Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Samantha D Praktiknjo
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
| |
Collapse
|
18
|
Nassiri I, Kwok AJ, Bhandari A, Bull KR, Garner LC, Klenerman P, Webber C, Parkkinen L, Lee AW, Wu Y, Fairfax B, Knight JC, Buck D, Piazza P. Demultiplexing of single-cell RNA-sequencing data using interindividual variation in gene expression. BIOINFORMATICS ADVANCES 2024; 4:vbae085. [PMID: 38911824 PMCID: PMC11193101 DOI: 10.1093/bioadv/vbae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 06/07/2024] [Indexed: 06/25/2024]
Abstract
Motivation Pooled designs for single-cell RNA sequencing, where many cells from distinct samples are processed jointly, offer increased throughput and reduced batch variation. This study describes expression-aware demultiplexing (EAD), a computational method that employs differential co-expression patterns between individuals to demultiplex pooled samples without any extra experimental steps. Results We use synthetic sample pools and show that the top interindividual differentially co-expressed genes provide a distinct cluster of cells per individual, significantly enriching the regulation of metabolism. Our application of EAD to samples of six isogenic inbred mice demonstrated that controlling genetic and environmental effects can solve interindividual variations related to metabolic pathways. We utilized 30 samples from both sepsis and healthy individuals in six batches to assess the performance of classification approaches. The results indicate that combining genetic and EAD results can enhance the accuracy of assignments (Min. 0.94, Mean 0.98, Max. 1). The results were enhanced by an average of 1.4% when EAD and barcoding techniques were combined (Min. 1.25%, Median 1.33%, Max. 1.74%). Furthermore, we demonstrate that interindividual differential co-expression analysis within the same cell type can be used to identify cells from the same donor in different activation states. By analysing single-nuclei transcriptome profiles from the brain, we demonstrate that our method can be applied to nonimmune cells. Availability and implementation EAD workflow is available at https://isarnassiri.github.io/scDIV/ as an R package called scDIV (acronym for single-cell RNA-sequencing data demultiplexing using interindividual variations).
Collapse
Affiliation(s)
- Isar Nassiri
- Nuffield Department of Medicine, Centre for Human Genetics, Oxford-GSK Institute of Molecular and Computational Medicine (IMCM), University of Oxford, Oxford, OX3 7BN, United Kingdom
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, United Kingdom
- Department of Psychiatry, University of Oxford, Oxford, OX3 7JX, United Kingdom
| | - Andrew J Kwok
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, 999077, China
| | - Aneesha Bhandari
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Katherine R Bull
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | - Paul Klenerman
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 9DU, United Kingdom
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, OX1 3SY, United Kingdom
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, United Kingdom
| | - Caleb Webber
- Department of Physiology, Anatomy, Genetics, Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, OX1 3PT, United Kingdom
- UK Dementia Research Institute, Cardiff University, Cardiff, CF24 4HQ, United Kingdom
| | - Laura Parkkinen
- Nuffield Department of Medicine, Centre for Human Genetics, Oxford-GSK Institute of Molecular and Computational Medicine (IMCM), University of Oxford, Oxford, OX3 7BN, United Kingdom
- Nuffield Department of Clinical Neurosciences, Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | - Angela W Lee
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Yanxia Wu
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Benjamin Fairfax
- MRC–Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
- Department of Oncology, University of Oxford & Oxford Cancer Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7DQ, United Kingdom
| | - Julian C Knight
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - David Buck
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Paolo Piazza
- Nuffield Department of Medicine, Centre for Human Genetics, Oxford-GSK Institute of Molecular and Computational Medicine (IMCM), University of Oxford, Oxford, OX3 7BN, United Kingdom
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| |
Collapse
|
19
|
Wang H, Du Y, Huang S, Sun X, Ye Y, Sun H, Chu X, Shan X, Yuan Y, Shen L, Bi Y. Single-cell analysis reveals a subpopulation of adipose progenitor cells that impairs glucose homeostasis. Nat Commun 2024; 15:4827. [PMID: 38844451 PMCID: PMC11156882 DOI: 10.1038/s41467-024-48914-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 05/10/2024] [Indexed: 06/09/2024] Open
Abstract
Adipose progenitor cells (APCs) are heterogeneous stromal cells and help to maintain metabolic homeostasis. However, the influence of obesity on human APC heterogeneity and the role of APC subpopulations on regulating glucose homeostasis remain unknown. Here, we find that APCs in human visceral adipose tissue contain four subsets. The composition and functionality of APCs are altered in patients with type 2 diabetes (T2D). CD9+CD55low APCs are the subset which is significantly increased in T2D patients. Transplantation of these cells from T2D patients into adipose tissue causes glycemic disturbance. Mechanistically, CD9+CD55low APCs promote T2D development through producing bioactive proteins to form a detrimental niche, leading to upregulation of adipocyte lipolysis. Depletion of pathogenic APCs by inducing intracellular diphtheria toxin A expression or using a hunter-killer peptide improves obesity-related glycemic disturbance. Collectively, our data provide deeper insights in human APC functionality and highlights APCs as a potential therapeutic target to combat T2D. All mice utilized in this study are male.
Collapse
Affiliation(s)
- Hongdong Wang
- Department of Endocrinology, Drum Tower Hospital Affiliated to Nanjing University Medical School, Branch of National Clinical Research Centre for Metabolic Diseases, Nanjing, China
| | - Yanhua Du
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shanshan Huang
- Department of Endocrinology, Drum Tower Hospital Affiliated to Nanjing University Medical School, Branch of National Clinical Research Centre for Metabolic Diseases, Nanjing, China
| | - Xitai Sun
- Department of General Surgery, Drum Tower Hospital Affiliated to Nanjing University Medical School, Nanjing, China
| | - Youqiong Ye
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haixiang Sun
- Department of Endocrinology, Drum Tower Hospital Affiliated to Nanjing University Medical School, Branch of National Clinical Research Centre for Metabolic Diseases, Nanjing, China
| | - Xuehui Chu
- Department of General Surgery, Drum Tower Hospital Affiliated to Nanjing University Medical School, Nanjing, China
| | - Xiaodong Shan
- Department of General Surgery, Drum Tower Hospital Affiliated to Nanjing University Medical School, Nanjing, China
| | - Yue Yuan
- Department of Endocrinology, Drum Tower Hospital Affiliated to Nanjing University Medical School, Branch of National Clinical Research Centre for Metabolic Diseases, Nanjing, China
| | - Lei Shen
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yan Bi
- Department of Endocrinology, Drum Tower Hospital Affiliated to Nanjing University Medical School, Branch of National Clinical Research Centre for Metabolic Diseases, Nanjing, China.
| |
Collapse
|
20
|
Malagola E, Vasciaveo A, Ochiai Y, Kim W, Zheng B, Zanella L, Wang ALE, Middelhoff M, Nienhüser H, Deng L, Wu F, Waterbury QT, Belin B, LaBella J, Zamechek LB, Wong MH, Li L, Guha C, Cheng CW, Yan KS, Califano A, Wang TC. Isthmus progenitor cells contribute to homeostatic cellular turnover and support regeneration following intestinal injury. Cell 2024; 187:3056-3071.e17. [PMID: 38848678 PMCID: PMC11164536 DOI: 10.1016/j.cell.2024.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 01/15/2024] [Accepted: 05/01/2024] [Indexed: 06/09/2024]
Abstract
The currently accepted intestinal epithelial cell organization model proposes that Lgr5+ crypt-base columnar (CBC) cells represent the sole intestinal stem cell (ISC) compartment. However, previous studies have indicated that Lgr5+ cells are dispensable for intestinal regeneration, leading to two major hypotheses: one favoring the presence of a quiescent reserve ISC and the other calling for differentiated cell plasticity. To investigate these possibilities, we studied crypt epithelial cells in an unbiased fashion via high-resolution single-cell profiling. These studies, combined with in vivo lineage tracing, show that Lgr5 is not a specific ISC marker and that stemness potential exists beyond the crypt base and resides in the isthmus region, where undifferentiated cells participate in intestinal homeostasis and regeneration following irradiation (IR) injury. Our results provide an alternative model of intestinal epithelial cell organization, suggesting that stemness potential is not restricted to CBC cells, and neither de-differentiation nor reserve ISC are drivers of intestinal regeneration.
Collapse
Affiliation(s)
- Ermanno Malagola
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA
| | | | - Yosuke Ochiai
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Woosook Kim
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Biyun Zheng
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA; Department of Gastroenterology, Fujian Medical University Union Hospital, Fujian 350000, China
| | - Luca Zanella
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Alexander L E Wang
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Moritz Middelhoff
- Klinik und Poliklinik für Innere Medizin II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Henrik Nienhüser
- Department of General, Visceral and Transplant Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Lu Deng
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66107, USA
| | - Feijing Wu
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Quin T Waterbury
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Bryana Belin
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Jonathan LaBella
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Leah B Zamechek
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Melissa H Wong
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, L215, Portland, OR, USA
| | - Linheng Li
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66107, USA
| | - Chandan Guha
- Department of Radiation Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Chia-Wei Cheng
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Kelley S Yan
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA; Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA; Columbia University Digestive and Liver Disease Research Center, New York, NY 10032, USA; Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biochemistry & Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA; Chan Zuckerberg Biohub NY, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Timothy C Wang
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA; Columbia University Digestive and Liver Disease Research Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
| |
Collapse
|
21
|
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.
Collapse
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.
| |
Collapse
|
22
|
Bailey LR, Bugg D, Reichardt IM, Ortaç CD, Nagle A, Gunaje J, Martinson A, Johnson R, MacCoss MJ, Sakamoto T, Kelly DP, Regnier M, Davis JM. MBNL1 Regulates Programmed Postnatal Switching Between Regenerative and Differentiated Cardiac States. Circulation 2024; 149:1812-1829. [PMID: 38426339 PMCID: PMC11147738 DOI: 10.1161/circulationaha.123.066860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND Discovering determinants of cardiomyocyte maturity is critical for deeply understanding the maintenance of differentiated states and potentially reawakening endogenous regenerative programs in adult mammalian hearts as a therapeutic strategy. Forced dedifferentiation paired with oncogene expression is sufficient to drive cardiac regeneration, but elucidation of endogenous developmental regulators of the switch between regenerative and mature cardiomyocyte cell states is necessary for optimal design of regenerative approaches for heart disease. MBNL1 (muscleblind-like 1) regulates fibroblast, thymocyte, and erythroid differentiation and proliferation. Hence, we examined whether MBNL1 promotes and maintains mature cardiomyocyte states while antagonizing cardiomyocyte proliferation. METHODS MBNL1 gain- and loss-of-function mouse models were studied at several developmental time points and in surgical models of heart regeneration. Multi-omics approaches were combined with biochemical, histological, and in vitro assays to determine the mechanisms through which MBNL1 exerts its effects. RESULTS MBNL1 is coexpressed with a maturation-association genetic program in the heart and is regulated by the MEIS1/calcineurin signaling axis. Targeted MBNL1 overexpression early in development prematurely transitioned cardiomyocytes to hypertrophic growth, hypoplasia, and dysfunction, whereas loss of MBNL1 function increased cardiomyocyte cell cycle entry and proliferation through altered cell cycle inhibitor transcript stability. Moreover, MBNL1-dependent stabilization of estrogen-related receptor signaling was essential for maintaining cardiomyocyte maturity in adult myocytes. In accordance with these data, modulating MBNL1 dose tuned the temporal window of neonatal cardiac regeneration, where increased MBNL1 expression arrested myocyte proliferation and regeneration and MBNL1 deletion promoted regenerative states with prolonged myocyte proliferation. However, MBNL1 deficiency was insufficient to promote regeneration in the adult heart because of cell cycle checkpoint activation. CONCLUSIONS Here, MBNL1 was identified as an essential regulator of cardiomyocyte differentiated states, their developmental switch from hyperplastic to hypertrophic growth, and their regenerative potential through controlling an entire maturation program by stabilizing adult myocyte mRNAs during postnatal development and throughout adulthood. Targeting loss of cardiomyocyte maturity and downregulation of cell cycle inhibitors through MBNL1 deletion was not sufficient to promote adult regeneration.
Collapse
Affiliation(s)
- Logan R.J. Bailey
- Lab Medicine and Pathology, University of Washington, Seattle, WA
- Molecular and Cellular Biology, University of Washington, Seattle, WA
- Medical Scientist Training Program, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - Darrian Bugg
- Lab Medicine and Pathology, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - Isabella M. Reichardt
- Bioengineering, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - C. Dessirée Ortaç
- Lab Medicine and Pathology, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - Abigail Nagle
- Bioengineering, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - Jagadambika Gunaje
- Lab Medicine and Pathology, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - Amy Martinson
- Lab Medicine and Pathology, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | | | | | - Tomoya Sakamoto
- Cardiovascular Institute, Medicine, University of Pennsylvania, Philadelphia, PA
| | - Daniel P. Kelly
- Cardiovascular Institute, Medicine, University of Pennsylvania, Philadelphia, PA
| | - Michael Regnier
- Bioengineering, University of Washington, Seattle, WA
- Center for Translational Muscle Research, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - Jennifer M. Davis
- Lab Medicine and Pathology, University of Washington, Seattle, WA
- Bioengineering, University of Washington, Seattle, WA
- Center for Translational Muscle Research, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| |
Collapse
|
23
|
Chien JF, Liu H, Wang BA, Luo C, Bartlett A, Castanon R, Johnson ND, Nery JR, Osteen J, Li J, Altshul J, Kenworthy M, Valadon C, Liem M, Claffey N, O'Connor C, Seeker LA, Ecker JR, Behrens MM, Mukamel EA. Cell-type-specific effects of age and sex on human cortical neurons. Neuron 2024:S0896-6273(24)00360-X. [PMID: 38838671 DOI: 10.1016/j.neuron.2024.05.013] [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: 11/29/2023] [Revised: 03/29/2024] [Accepted: 05/09/2024] [Indexed: 06/07/2024]
Abstract
Altered transcriptional and epigenetic regulation of brain cell types may contribute to cognitive changes with advanced age. Using single-nucleus multi-omic DNA methylation and transcriptome sequencing (snmCT-seq) in frontal cortex from young adult and aged donors, we found widespread age- and sex-related variation in specific neuron types. The proportion of inhibitory SST- and VIP-expressing neurons was reduced in aged donors. Excitatory neurons had more profound age-related changes in their gene expression and DNA methylation than inhibitory cells. Hundreds of genes involved in synaptic activity, including EGR1, were less expressed in aged adults. Genes located in subtelomeric regions increased their expression with age and correlated with reduced telomere length. We further mapped cell-type-specific sex differences in gene expression and X-inactivation escape genes. Multi-omic single-nucleus epigenomes and transcriptomes provide new insight into the effects of age and sex on human neurons.
Collapse
Affiliation(s)
- Jo-Fan Chien
- Department of Physics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Bang-An Wang
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Chongyuan Luo
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Rosa Castanon
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Nicholas D Johnson
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92037, USA; Computational Neurobiology Laboratory, Salk Institute, La Jolla, CA 92037, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Julia Osteen
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Junhao Li
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jordan Altshul
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Mia Kenworthy
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Cynthia Valadon
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Michelle Liem
- Flow Cytometry Core Facility, Salk Institute, La Jolla, CA 92037, USA
| | - Naomi Claffey
- Flow Cytometry Core Facility, Salk Institute, La Jolla, CA 92037, USA
| | - Carolyn O'Connor
- Flow Cytometry Core Facility, Salk Institute, La Jolla, CA 92037, USA
| | - Luise A Seeker
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA.
| | - M Margarita Behrens
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92037, USA; Computational Neurobiology Laboratory, Salk Institute, La Jolla, CA 92037, USA.
| | - Eran A Mukamel
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA.
| |
Collapse
|
24
|
Chen J, Hu X, Zhao J, Yin X, Zheng L, Guo J, Chen J, Wang Y, Sheng X, Dong H, Liu X, Zhang X, Liang J, Liu H, Yao J, Liu J, Shen Y, Chen Z, He Z, Wang Y, Chen N, Nie L, Zhang M, Pan X, Chen Y, Liu H, Zhang Y, Tang Y, Zhu S, Zhao J, Dai J, Wang Z, Zeng Y, Wang Z, Huang H, Liu Z, Shen P, Zeng H, Sun G. Memory/Active T-Cell Activation Is Associated with Immunotherapeutic Response in Fumarate Hydratase-Deficient Renal Cell Carcinoma. Clin Cancer Res 2024; 30:2571-2581. [PMID: 38512114 PMCID: PMC11145163 DOI: 10.1158/1078-0432.ccr-23-2760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/22/2023] [Accepted: 03/19/2024] [Indexed: 03/22/2024]
Abstract
PURPOSE Fumarate hydratase-deficient renal cell carcinoma (FH-deficient RCC) is a rare and lethal subtype of kidney cancer. However, the optimal treatments and molecular correlates of benefits for FH-deficient RCC are currently lacking. EXPERIMENTAL DESIGN A total of 91 patients with FH-deficient RCC from 15 medical centers between 2009 and 2022 were enrolled in this study. Genomic and bulk RNA-sequencing (RNA-seq) were performed on 88 and 45 untreated FH-deficient RCCs, respectively. Single-cell RNA-seq was performed to identify biomarkers for treatment response. Main outcomes included disease-free survival (DFS) for localized patients, objective response rate (ORR), progression-free survival (PFS), and overall survival (OS) for patients with metastasis. RESULTS In the localized setting, we found that a cell-cycle progression signature enabled to predict disease progression. In the metastatic setting, first-line immune checkpoint inhibitor plus tyrosine kinase inhibitor (ICI+TKI) combination therapy showed satisfactory safety and was associated with a higher ORR (43.2% vs. 5.6%), apparently superior PFS (median PFS, 17.3 vs. 9.6 months, P = 0.016) and OS (median OS, not reached vs. 25.7 months, P = 0.005) over TKI monotherapy. Bulk and single-cell RNA-seq data revealed an enrichment of memory and effect T cells in responders to ICI plus TKI combination therapy. Furthermore, we identified a signature of memory and effect T cells that was associated with the effectiveness of ICI plus TKI combination therapy. CONCLUSIONS ICI plus TKI combination therapy may represent a promising treatment option for metastatic FH-deficient RCC. A memory/active T-cell-derived signature is associated with the efficacy of ICI+TKI but necessitates further validation.
Collapse
Affiliation(s)
- Junru Chen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Xu Hu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Junjie Zhao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoxue Yin
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Linmao Zheng
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Jingjing Guo
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jianhui Chen
- Department of Urology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yongquan Wang
- Department of Urology, Southwest Hospital, Army Medical University, Chongqing, China
| | - Xinan Sheng
- Department of Genitourinary Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Haiying Dong
- Department of Urology, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Xiaodong Liu
- Department of Urology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xingming Zhang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiayu Liang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Haolin Liu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Jin Yao
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiyan Liu
- Department of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yali Shen
- Department of Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Zhibin Chen
- Department of Urology, The First People's Hospital of Neijiang, Neijiang, China
| | - Zhengyu He
- Department of Urology, Yaan People's Hospital, Yaan, China
| | - Yaodong Wang
- Department of Urology, Mianyang Central Hospital, Mianyang, China
| | - Ni Chen
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Ling Nie
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Mengni Zhang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Xiuyi Pan
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Yuntian Chen
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
| | - Haoyang Liu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Yaowen Zhang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Yanfeng Tang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Sha Zhu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Jinge Zhao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Jindong Dai
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Zilin Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Yuhao Zeng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Zhipeng Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Haojie Huang
- Institute of Urological Cancer Research, Zhejiang University School of Medicine, The First Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Zhenhua Liu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Pengfei Shen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Zeng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Guangxi Sun
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
25
|
Wang AZ, Mashimo BL, Schaettler MO, Sherpa ND, Leavitt LA, Livingstone AJ, Khan SM, Li M, Anzaldua-Campos MI, Bradley JD, Leuthardt EC, Kim AH, Dowling JL, Chicoine MR, Jones PS, Choi BD, Cahill DP, Carter BS, Petti AA, Johanns TM, Dunn GP. Glioblastoma-Infiltrating CD8+ T Cells Are Predominantly a Clonally Expanded GZMK+ Effector Population. Cancer Discov 2024; 14:1106-1131. [PMID: 38416133 DOI: 10.1158/2159-8290.cd-23-0913] [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: 08/31/2023] [Revised: 12/20/2023] [Accepted: 02/26/2024] [Indexed: 02/29/2024]
Abstract
Recent clinical trials have highlighted the limited efficacy of T cell-based immunotherapy in patients with glioblastoma (GBM). To better understand the characteristics of tumor-infiltrating lymphocytes (TIL) in GBM, we performed cellular indexing of transcriptomes and epitopes by sequencing and single-cell RNA sequencing with paired V(D)J sequencing, respectively, on TILs from two cohorts of patients totaling 15 patients with high-grade glioma, including GBM or astrocytoma, IDH-mutant, grade 4 (G4A). Analysis of the CD8+ TIL landscape reveals an enrichment of clonally expanded GZMK+ effector T cells in the tumor compared with matched blood, which was validated at the protein level. Furthermore, integration with other cancer types highlights the lack of a canonically exhausted CD8+ T-cell population in GBM TIL. These data suggest that GZMK+ effector T cells represent an important T-cell subset within the GBM microenvironment and may harbor potential therapeutic implications. SIGNIFICANCE To understand the limited efficacy of immune-checkpoint blockade in GBM, we applied a multiomics approach to understand the TIL landscape. By highlighting the enrichment of GZMK+ effector T cells and the lack of exhausted T cells, we provide a new potential mechanism of resistance to immunotherapy in GBM. This article is featured in Selected Articles from This Issue, p. 897.
Collapse
Affiliation(s)
- Anthony Z Wang
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bryce L Mashimo
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Maximilian O Schaettler
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Ngima D Sherpa
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Biological and Biomedical Sciences Graduate Program, Harvard University, Cambridge, Massachusetts
| | - Lydia A Leavitt
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Neurosurgery, University of Louisville, Louisville, Kentucky
| | - Alexandra J Livingstone
- Department of Medicine, Division of Medical Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Saad M Khan
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mao Li
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Markus I Anzaldua-Campos
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Neuroscience Undergraduate Program, Harvard University, Cambridge, Massachusetts
| | - Joseph D Bradley
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eric C Leuthardt
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri
- Brain Tumor Center, Washington University School of Medicine/Siteman Cancer Center, St. Louis, Missouri
| | - Albert H Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri
- Brain Tumor Center, Washington University School of Medicine/Siteman Cancer Center, St. Louis, Missouri
| | - Joshua L Dowling
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri
- Brain Tumor Center, Washington University School of Medicine/Siteman Cancer Center, St. Louis, Missouri
| | - Michael R Chicoine
- Department of Neurological Surgery, University of Missouri-Columbia, Columbia, Missouri
| | - Pamela S Jones
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bryan D Choi
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bob S Carter
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Allegra A Petti
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tanner M Johanns
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Brain Tumor Center, Washington University School of Medicine/Siteman Cancer Center, St. Louis, Missouri
| | - Gavin P Dunn
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
26
|
Kubota N, Chen L, Zheng S. Shiba: A unified computational method for robust identification of differential RNA splicing across platforms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596331. [PMID: 38895326 PMCID: PMC11185541 DOI: 10.1101/2024.05.30.596331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Alternative pre-mRNA splicing (AS) is a fundamental regulatory process that generates transcript diversity and cell type variation. We developed Shiba, a robust method integrating transcript assembly, splicing event identification, read counting, and statistical analysis, to efficiently quantify exon splicing levels across various types of RNA-seq datasets. Compared to existing pipelines, Shiba excels in capturing both annotated and unannotated or cryptic differential splicing events with superior accuracy, sensitivity, and reproducibility. Furthermore, Shiba's unique consideration of junction read imbalance and exon-body read coverage reduces false positives, essential for downstream functional analyses. We have further developed scShiba for single-cell/nucleus (sc/sn) RNA-seq data, enabling the exploration of splicing variations in heterogeneous cell populations. Both simulated and real data demonstrate Shiba's robustness across multiple sample sizes, including n=1 datasets and individual cell clusters from scRNA-seq. Application of Shiba on single replicates of RNA-seq identified new AS-NMD targets, and scShiba on snRNA-seq revealed intricate temporal AS regulation in dopaminergic neurons. Both Shiba and scShiba are provided in Docker/Singularity containers and Snakemake pipeline, enhancing accessibility and reproducibility. The comprehensive capabilities of Shiba and scShiba allow systematic and robust quantification of alternative splicing events, laying a solid foundation for mechanistic exploration of functional complexity in RNA splicing.
Collapse
Affiliation(s)
- Naoto Kubota
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA
- Center for RNA Biology and Medicine, University of California, Riverside, CA 92521, USA
| | - Liang Chen
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Sika Zheng
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA
- Center for RNA Biology and Medicine, University of California, Riverside, CA 92521, USA
| |
Collapse
|
27
|
Karlsson F, Kallas T, Thiagarajan D, Karlsson M, Schweitzer M, Navarro JF, Leijonancker L, Geny S, Pettersson E, Rhomberg-Kauert J, Larsson L, van Ooijen H, Petkov S, González-Granillo M, Bunz J, Dahlberg J, Simonetti M, Sathe P, Brodin P, Barrio AM, Fredriksson S. Molecular pixelation: spatial proteomics of single cells by sequencing. Nat Methods 2024; 21:1044-1052. [PMID: 38720062 PMCID: PMC11166577 DOI: 10.1038/s41592-024-02268-9] [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: 07/07/2023] [Accepted: 04/02/2024] [Indexed: 06/13/2024]
Abstract
The spatial distribution of cell surface proteins governs vital processes of the immune system such as intercellular communication and mobility. However, fluorescence microscopy has limited scalability in the multiplexing and throughput needed to drive spatial proteomics discoveries at subcellular level. We present Molecular Pixelation (MPX), an optics-free, DNA sequence-based method for spatial proteomics of single cells using antibody-oligonucleotide conjugates (AOCs) and DNA-based, nanometer-sized molecular pixels. The relative locations of AOCs are inferred by sequentially associating them into local neighborhoods using the sequence-unique DNA pixels, forming >1,000 spatially connected zones per cell in 3D. For each single cell, DNA-sequencing reads are computationally arranged into spatial proteomics networks for 76 proteins. By studying immune cell dynamics using spatial statistics on graph representations of the data, we identify known and new patterns of spatial organization of proteins on chemokine-stimulated T cells, highlighting the potential of MPX in defining cell states by the spatial arrangement of proteins.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Petter Brodin
- Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
- Department of Immunology and Inflammation, Imperial College London, London, UK
- Medical Research Council London Institute of Medical Sciences (LMS), Imperial College Hammersmith Campus, London, UK
| | | | - Simon Fredriksson
- Pixelgen Technologies AB, Stockholm, Sweden.
- Royal Institute of Technology, Department of Protein Science, Stockholm, Sweden.
| |
Collapse
|
28
|
Lalanne JB, Regalado SG, Domcke S, Calderon D, Martin BK, Li X, Li T, Suiter CC, Lee C, Trapnell C, Shendure J. Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters. Nat Methods 2024; 21:983-993. [PMID: 38724692 PMCID: PMC11166576 DOI: 10.1038/s41592-024-02260-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/22/2024] [Indexed: 06/13/2024]
Abstract
The inability to scalably and precisely measure the activity of developmental cis-regulatory elements (CREs) in multicellular systems is a bottleneck in genomics. Here we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. The resulting measurement of reporter expression is accurate over multiple orders of magnitude, with a precision approaching the limit set by Poisson counting noise. Together with RNA barcode stabilization via circularization, these scalable single-cell quantitative expression reporters provide high-contrast readouts, analogous to classic in situ assays but entirely from sequencing. Screening >200 regions of accessible chromatin in a multicellular in vitro model of early mammalian development, we identify 13 (8 previously uncharacterized) autonomous and cell-type-specific developmental CREs. We further demonstrate that chimeric CRE pairs generate cognate two-cell-type activity profiles and assess gain- and loss-of-function multicellular expression phenotypes from CRE variants with perturbed transcription factor binding sites. Single-cell quantitative expression reporters can be applied in developmental and multicellular systems to quantitatively characterize native, perturbed and synthetic CREs at scale, with high sensitivity and at single-cell resolution.
Collapse
Affiliation(s)
| | - Samuel G Regalado
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Silvia Domcke
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Diego Calderon
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Beth K Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Xiaoyi Li
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Tony Li
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Chase C Suiter
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Choli Lee
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
| |
Collapse
|
29
|
Choksi SP, Byrnes LE, Konjikusic MJ, Tsai BWH, Deleon R, Lu Q, Westlake CJ, Reiter JF. An alternative cell cycle coordinates multiciliated cell differentiation. Nature 2024; 630:214-221. [PMID: 38811726 DOI: 10.1038/s41586-024-07476-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 04/26/2024] [Indexed: 05/31/2024]
Abstract
The canonical mitotic cell cycle coordinates DNA replication, centriole duplication and cytokinesis to generate two cells from one1. Some cells, such as mammalian trophoblast giant cells, use cell cycle variants like the endocycle to bypass mitosis2. Differentiating multiciliated cells, found in the mammalian airway, brain ventricles and reproductive tract, are post-mitotic but generate hundreds of centrioles, each of which matures into a basal body and nucleates a motile cilium3,4. Several cell cycle regulators have previously been implicated in specific steps of multiciliated cell differentiation5,6. Here we show that differentiating multiciliated cells integrate cell cycle regulators into a new alternative cell cycle, which we refer to as the multiciliation cycle. The multiciliation cycle redeploys many canonical cell cycle regulators, including cyclin-dependent kinases (CDKs) and their cognate cyclins. For example, cyclin D1, CDK4 and CDK6, which are regulators of mitotic G1-to-S progression, are required to initiate multiciliated cell differentiation. The multiciliation cycle amplifies some aspects of the canonical cell cycle, such as centriole synthesis, and blocks others, such as DNA replication. E2F7, a transcriptional regulator of canonical S-to-G2 progression, is expressed at high levels during the multiciliation cycle. In the multiciliation cycle, E2F7 directly dampens the expression of genes encoding DNA replication machinery and terminates the S phase-like gene expression program. Loss of E2F7 causes aberrant acquisition of DNA synthesis in multiciliated cells and dysregulation of multiciliation cycle progression, which disrupts centriole maturation and ciliogenesis. We conclude that multiciliated cells use an alternative cell cycle that orchestrates differentiation instead of controlling proliferation.
Collapse
Affiliation(s)
- Semil P Choksi
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Lauren E Byrnes
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Mia J Konjikusic
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Benedict W H Tsai
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Rachel Deleon
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Quanlong Lu
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Christopher J Westlake
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| |
Collapse
|
30
|
Fabyanic EB, Hu P, Qiu Q, Berríos KN, Connolly DR, Wang T, Flournoy J, Zhou Z, Kohli RM, Wu H. Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects. Nat Biotechnol 2024; 42:960-974. [PMID: 37640946 DOI: 10.1038/s41587-023-01909-2] [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: 03/08/2021] [Accepted: 07/19/2023] [Indexed: 08/31/2023]
Abstract
Oxidative modification of 5-methylcytosine (5mC) by ten-eleven translocation (TET) DNA dioxygenases generates 5-hydroxymethylcytosine (5hmC), the most abundant form of oxidized 5mC. Existing single-cell bisulfite sequencing methods cannot resolve 5mC and 5hmC, leaving the cell-type-specific regulatory mechanisms of TET and 5hmC largely unknown. Here, we present joint single-nucleus (hydroxy)methylcytosine sequencing (Joint-snhmC-seq), a scalable and quantitative approach that simultaneously profiles 5hmC and true 5mC in single cells by harnessing differential deaminase activity of APOBEC3A toward 5mC and chemically protected 5hmC. Joint-snhmC-seq profiling of single nuclei from mouse brains reveals an unprecedented level of epigenetic heterogeneity of both 5hmC and true 5mC at single-cell resolution. We show that cell-type-specific profiles of 5hmC or true 5mC improve multimodal single-cell data integration, enable accurate identification of neuronal subtypes and uncover context-specific regulatory effects on cell-type-specific genes by TET enzymes.
Collapse
Affiliation(s)
- Emily B Fabyanic
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Peng Hu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Qi Qiu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Kiara N Berríos
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel R Connolly
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Tong Wang
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer Flournoy
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhaolan Zhou
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul M Kohli
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
31
|
Matchett KP, Wilson-Kanamori JR, Portman JR, Kapourani CA, Fercoq F, May S, Zajdel E, Beltran M, Sutherland EF, Mackey JBG, Brice M, Wilson GC, Wallace SJ, Kitto L, Younger NT, Dobie R, Mole DJ, Oniscu GC, Wigmore SJ, Ramachandran P, Vallejos CA, Carragher NO, Saeidinejad MM, Quaglia A, Jalan R, Simpson KJ, Kendall TJ, Rule JA, Lee WM, Hoare M, Weston CJ, Marioni JC, Teichmann SA, Bird TG, Carlin LM, Henderson NC. Multimodal decoding of human liver regeneration. Nature 2024; 630:158-165. [PMID: 38693268 PMCID: PMC11153152 DOI: 10.1038/s41586-024-07376-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/02/2024] [Indexed: 05/03/2024]
Abstract
The liver has a unique ability to regenerate1,2; however, in the setting of acute liver failure (ALF), this regenerative capacity is often overwhelmed, leaving emergency liver transplantation as the only curative option3-5. Here, to advance understanding of human liver regeneration, we use paired single-nucleus RNA sequencing combined with spatial profiling of healthy and ALF explant human livers to generate a single-cell, pan-lineage atlas of human liver regeneration. We uncover a novel ANXA2+ migratory hepatocyte subpopulation, which emerges during human liver regeneration, and a corollary subpopulation in a mouse model of acetaminophen (APAP)-induced liver regeneration. Interrogation of necrotic wound closure and hepatocyte proliferation across multiple timepoints following APAP-induced liver injury in mice demonstrates that wound closure precedes hepatocyte proliferation. Four-dimensional intravital imaging of APAP-induced mouse liver injury identifies motile hepatocytes at the edge of the necrotic area, enabling collective migration of the hepatocyte sheet to effect wound closure. Depletion of hepatocyte ANXA2 reduces hepatocyte growth factor-induced human and mouse hepatocyte migration in vitro, and abrogates necrotic wound closure following APAP-induced mouse liver injury. Together, our work dissects unanticipated aspects of liver regeneration, demonstrating an uncoupling of wound closure and hepatocyte proliferation and uncovering a novel migratory hepatocyte subpopulation that mediates wound closure following liver injury. Therapies designed to promote rapid reconstitution of normal hepatic microarchitecture and reparation of the gut-liver barrier may advance new areas of therapeutic discovery in regenerative medicine.
Collapse
Affiliation(s)
- K P Matchett
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - J R Wilson-Kanamori
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - J R Portman
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - C A Kapourani
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
- MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- School of Informatics, University of Edinburgh, Edinburgh, UK
| | - F Fercoq
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - S May
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - E Zajdel
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - M Beltran
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - E F Sutherland
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - J B G Mackey
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - M Brice
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - G C Wilson
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - S J Wallace
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - L Kitto
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - N T Younger
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - R Dobie
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - D J Mole
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
- University Department of Clinical Surgery, University of Edinburgh, Edinburgh, UK
| | - G C Oniscu
- Edinburgh Transplant Centre, Royal Infirmary of Edinburgh, Edinburgh, UK
- Division of Transplant Surgery, CLINTEC, Karolinska Institutet, Stockholm, Sweden
| | - S J Wigmore
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
- University Department of Clinical Surgery, University of Edinburgh, Edinburgh, UK
| | - P Ramachandran
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - C A Vallejos
- MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- The Alan Turing Institute, London, UK
| | - N O Carragher
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - M M Saeidinejad
- Institute for Liver and Digestive Health, University College London, London, UK
| | - A Quaglia
- Department of Cellular Pathology, Royal Free London NHS Foundation Trust, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - R Jalan
- Institute for Liver and Digestive Health, University College London, London, UK
- European Foundation for the Study of Chronic Liver Failure, Barcelona, Spain
| | - K J Simpson
- Department of Hepatology, University of Edinburgh and Scottish Liver Transplant Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - T J Kendall
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - J A Rule
- Department of Internal Medicine, University of Texas, Southwestern Medical Center, Dallas, TX, USA
| | - W M Lee
- Department of Internal Medicine, University of Texas, Southwestern Medical Center, Dallas, TX, USA
| | - M Hoare
- Early Cancer Institute, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - C J Weston
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - J C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
- Wellcome Genome Campus, Wellcome Sanger Institute, Cambridge, UK
| | - S A Teichmann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
- Wellcome Genome Campus, Wellcome Sanger Institute, Cambridge, UK
- Department of Physics, Cavendish Laboratory, Cambridge, UK
| | - T G Bird
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - L M Carlin
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - N C Henderson
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
32
|
Tang SY, Lordan R, Meng H, Auerbach BJ, Hennessy EJ, Sengupta A, Das US, Joshi R, Marcos-Contreras OA, McConnell R, Grant GR, Ricciotti E, Muzykantov VR, Grosser T, Weiljie AM, FitzGerald GA. Differential Impact In Vivo of Pf4-ΔCre-Mediated and Gp1ba-ΔCre-Mediated Depletion of Cyclooxygenase-1 in Platelets in Mice. Arterioscler Thromb Vasc Biol 2024; 44:1393-1406. [PMID: 38660804 PMCID: PMC11138953 DOI: 10.1161/atvbaha.123.320295] [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: 10/26/2023] [Accepted: 04/12/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND Low-dose aspirin is widely used for the secondary prevention of cardiovascular disease. The beneficial effects of low-dose aspirin are attributable to its inhibition of platelet Cox (cyclooxygenase)-1-derived thromboxane A2. Until recently, the use of the Pf4 (platelet factor 4) Cre has been the only genetic approach to generating megakaryocyte/platelet ablation of Cox-1 in mice. However, Pf4-ΔCre displays ectopic expression outside the megakaryocyte/platelet lineage, especially during inflammation. The use of the Gp1ba (glycoprotein 1bα) Cre promises a more specific, targeted approach. METHODS To evaluate the role of Cox-1 in platelets, we crossed Pf4-ΔCre or Gp1ba-ΔCre mice with Cox-1flox/flox mice to generate platelet Cox-1-/- mice on normolipidemic and hyperlipidemic (Ldlr-/-; low-density lipoprotein receptor) backgrounds. RESULTS Ex vivo platelet aggregation induced by arachidonic acid or adenosine diphosphate in platelet-rich plasma was inhibited to a similar extent in Pf4-ΔCre Cox-1-/-/Ldlr-/- and Gp1ba-ΔCre Cox-1-/-/Ldlr-/- mice. In a mouse model of tail injury, Pf4-ΔCre-mediated and Gp1ba-ΔCre-mediated deletions of Cox-1 were similarly efficient in suppressing platelet prostanoid biosynthesis. Experimental thrombogenesis and attendant blood loss were similar in both models. However, the impact on atherogenesis was divergent, being accelerated in the Pf4-ΔCre mice while restrained in the Gp1ba-ΔCres. In the former, accelerated atherogenesis was associated with greater suppression of PGI2 biosynthesis, a reduction in the lipopolysaccharide-evoked capacity to produce PGE2 (prostaglandin E) and PGD2 (prostanglandin D), activation of the inflammasome, elevated plasma levels of IL-1β (interleukin), reduced plasma levels of HDL-C (high-density lipoprotein receptor-cholesterol), and a reduction in the capacity for reverse cholesterol transport. By contrast, in the latter, plasma HDL-C and α-tocopherol were elevated, and MIP-1α (macrophage inflammatory protein-1α) and MCP-1 (monocyte chemoattractant protein 1) were reduced. CONCLUSIONS Both approaches to Cox-1 deletion similarly restrain thrombogenesis, but a differential impact on Cox-1-dependent prostanoid formation by the vasculature may contribute to an inflammatory phenotype and accelerated atherogenesis in Pf4-ΔCre mice.
Collapse
Affiliation(s)
- Soon Yew Tang
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania
| | - Ronan Lordan
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania
| | - Hu Meng
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania
| | - Benjamin J. Auerbach
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania
| | - Elizabeth J. Hennessy
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania
| | - Arjun Sengupta
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania
| | - Ujjalkumar S. Das
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania
| | - Robin Joshi
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania
| | | | - Ryan McConnell
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania
| | - Gregory R. Grant
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania
- Department of Genetics, University of Pennsylvania
| | - Emanuela Ricciotti
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania
| | - Vladimir R. Muzykantov
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania
| | - Tilo Grosser
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania
- Department of Medicine Perelman School of Medicine, University of Pennsylvania
| | - Aalim M. Weiljie
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania
| | - Garret A. FitzGerald
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania
- Department of Genetics, University of Pennsylvania
| |
Collapse
|
33
|
De Rop FV, Hulselmans G, Flerin C, Soler-Vila P, Rafels A, Christiaens V, González-Blas CB, Marchese D, Caratù G, Poovathingal S, Rozenblatt-Rosen O, Slyper M, Luo W, Muus C, Duarte F, Shrestha R, Bagdatli ST, Corces MR, Mamanova L, Knights A, Meyer KB, Mulqueen R, Taherinasab A, Maschmeyer P, Pezoldt J, Lambert CLG, Iglesias M, Najle SR, Dossani ZY, Martelotto LG, Burkett Z, Lebofsky R, Martin-Subero JI, Pillai S, Sebé-Pedrós A, Deplancke B, Teichmann SA, Ludwig LS, Braun TP, Adey AC, Greenleaf WJ, Buenrostro JD, Regev A, Aerts S, Heyn H. Systematic benchmarking of single-cell ATAC-sequencing protocols. Nat Biotechnol 2024; 42:916-926. [PMID: 37537502 PMCID: PMC11180611 DOI: 10.1038/s41587-023-01881-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/22/2023] [Indexed: 08/05/2023]
Abstract
Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity. However, an exploration of systemic biases among scATAC-seq technologies has remained absent. In this study, we benchmark the performance of eight scATAC-seq methods across 47 experiments using human peripheral blood mononuclear cells (PBMCs) as a reference sample and develop PUMATAC, a universal preprocessing pipeline, to handle the various sequencing data formats. Our analyses reveal significant differences in sequencing library complexity and tagmentation specificity, which impact cell-type annotation, genotype demultiplexing, peak calling, differential region accessibility and transcription factor motif enrichment. Our findings underscore the importance of sample extraction, method selection, data processing and total cost of experiments, offering valuable guidance for future research. Finally, our data and analysis pipeline encompasses 169,000 PBMC scATAC-seq profiles and a best practices code repository for scATAC-seq data analysis, which are freely available to extend this benchmarking effort to future protocols.
Collapse
Grants
- R01 DA047237 NIDA NIH HHS
- R00 AG059918 NIA NIH HHS
- U19 AI057266 NIAID NIH HHS
- G0B5619N Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)
- RF1 MH128842 NIMH NIH HHS
- UM1 HG009436 NHGRI NIH HHS
- 1S80920N Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)
- UM1 HG012076 NHGRI NIH HHS
- RM1 HG007735 NHGRI NIH HHS
- G094121N Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)
- R35 GM124704 NIGMS NIH HHS
- UM1 HG009442 NHGRI NIH HHS
- Wellcome Trust
- H.H. received support for the project PID2020-115439GB-I00- funded by MCIN/AEI/ 10.13039/501100011033. This publication is also supported as part of a project (BCLLATLAS and ESPACE) that has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement No 810287 and 874710).
- M.R.C. is supported by the National Institutes on Aging K99/R00AG059918.
- K.B.M. is supported by Wellcome (WT211276/Z/18/Z and Sanger core grant WT206194).
- S.A.T. is supported by Wellcome (WT211276/Z/18/Z and Sanger core grant WT206194).
- This work was supported by funding from the Rita Allen Foundation (W.J.G.), the Human Frontiers Science (RGY006S) (W.J.G.). W.J.G. is a Chan Zuckerberg Biohub investigator and acknowledges grants 2017-174468 and 2018-182817 from the Chan Zuckerberg Initiative, and the National Institutes of Health grants RM1-HG007735, UM1-HG009442, UM1-HG009436, R01- HG00990901, and U19- AI057266 (to W.J.G.). W.J.G. acknowledges funding from Emerson Collective.
- This work was supported by an ERC Consolidator Grant to S.A. (no. 724226_cis- CONTROL), KU Leuven (grant no. C14/22/125 to S.A.), Foundation Against Cancer (grant no, F/2020/1396 to S.A.), F.W.O. (grants G0I2722N, G0B5619N and G094121N to S.A.), Aligning Science Across Parkinson’s (ASAP, grant no. ASAP-000430 to S.A.)
Collapse
Affiliation(s)
- Florian V De Rop
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Chris Flerin
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Paula Soler-Vila
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Albert Rafels
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Valerie Christiaens
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Carmen Bravo González-Blas
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Domenica Marchese
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ginevra Caratù
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | | | | | - Wendy Luo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Fabiana Duarte
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rojesh Shrestha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - M Ryan Corces
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | | | | | | | - Ryan Mulqueen
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Akram Taherinasab
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA
- Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA
| | - Patrick Maschmeyer
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Jörn Pezoldt
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Camille Lucie Germaine Lambert
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Marta Iglesias
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sebastián R Najle
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Zain Y Dossani
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Luciano G Martelotto
- Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- University of Melbourne Centre for Cancer Research, Victoria Comprehensive Cancer Centre, Melbourne, Victoria, Australia
| | - Zach Burkett
- Digital Biology Group, Bio-Rad, Pleasanton, CA, USA
| | | | - José Ignacio Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Satish Pillai
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Arnau Sebé-Pedrós
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Cambridge, UK
- Department of Physics/Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Leif S Ludwig
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Theodore P Braun
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA
- Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA
| | - Andrew C Adey
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jason D Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute of Integrative Cancer Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Stein Aerts
- VIB Center for Brain and Disease Research, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| |
Collapse
|
34
|
Ye Y, Zeng S, Hu X. Unveiling the hidden role of disulfidptosis in kidney renal clear cell carcinoma: a prognostic signature for personalized treatment. Apoptosis 2024; 29:693-708. [PMID: 38296888 DOI: 10.1007/s10495-023-01933-2] [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] [Accepted: 12/19/2023] [Indexed: 02/02/2024]
Abstract
The role of disulfidptosis in kidney renal clear cell carcinoma (KIRC) remains unknown. This study investigated disulfidptosis-related biomarkers for KIRC prognosis prediction and individualized treatment. KIRC patients were clustered by disulfidptosis profiles. Differential expression analysis, survival models, and machine learning were used to construct the disulfidptosis-related prognostic signature (DRPS). Characterizations of the tumor immune microenvironment, genetic drivers, drug sensitivity, and immunotherapy response were explored according to the DRPS risk stratification. Markers included in the signature were validated using single-cell, spatial transcriptomics, quantitative RT-qPCR, and immunohistochemistry. In the discovery cohort, we unveiled two clusters of KIRC patients that differed significantly in disulfidptosis regulator expressions and overall survival (OS). After multiple feature selection steps, a DRPS prognostic model with four features (CHAC1, COL7A1, FOXM1, SHOX2) was constructed and validated. Combined with clinical factors, the model demonstrated robust performance in the discovery and external validation cohorts (5-year AUC = 0.793 and 0.846, respectively). KIRC patients with high-risk scores are characterized by inferior OS, less tumor purity, and increased infiltrations of fibroblasts, M1 macrophages, and B cells. High-risk patients also have higher frequencies of BAP1 and AHNAK2 mutation. Besides, the correlation between the DRPS score and the chemotherapy-response signature indicated the potential effect of Gefitinib for high-risk patients. Among the signature genes, FOXM1 is highly expressed in cycling tumor cells and exhibits spatial aggregation, while others are expressed sparsely within tumor samples. The DRPS model enables improved clinical management and personalized KIRC therapy. The identified biomarkers and immune characteristics offer new mechanistic insight into disulfidptosis in KIRC.
Collapse
Affiliation(s)
- Yang Ye
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, NO.8 GongTi South Road, Beijing, 100020, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Song Zeng
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, NO.8 GongTi South Road, Beijing, 100020, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Xiaopeng Hu
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, NO.8 GongTi South Road, Beijing, 100020, China.
- Institute of Urology, Capital Medical University, Beijing, China.
| |
Collapse
|
35
|
Weinand K, Sakaue S, Nathan A, Jonsson AH, Zhang F, Watts GFM, Al Suqri M, Zhu Z, Rao DA, Anolik JH, Brenner MB, Donlin LT, Wei K, Raychaudhuri S. The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis. Nat Commun 2024; 15:4650. [PMID: 38821936 PMCID: PMC11143375 DOI: 10.1038/s41467-024-48620-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/02/2024] [Indexed: 06/02/2024] Open
Abstract
Synovial tissue inflammation is a hallmark of rheumatoid arthritis (RA). Recent work has identified prominent pathogenic cell states in inflamed RA synovial tissue, such as T peripheral helper cells; however, the epigenetic regulation of these states has yet to be defined. Here, we examine genome-wide open chromatin at single-cell resolution in 30 synovial tissue samples, including 12 samples with transcriptional data in multimodal experiments. We identify 24 chromatin classes and predict their associated transcription factors, including a CD8 + GZMK+ class associated with EOMES and a lining fibroblast class associated with AP-1. By integrating with an RA tissue transcriptional atlas, we propose that these chromatin classes represent 'superstates' corresponding to multiple transcriptional cell states. Finally, we demonstrate the utility of this RA tissue chromatin atlas through the associations between disease phenotypes and chromatin class abundance, as well as the nomination of classes mediating the effects of putatively causal RA genetic variants.
Collapse
Affiliation(s)
- Kathryn Weinand
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Saori Sakaue
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aparna Nathan
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anna Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Fan Zhang
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine Division of Rheumatology and Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Gerald F M Watts
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Majd Al Suqri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zhu Zhu
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jennifer H Anolik
- Division of Allergy, Immunology and Rheumatology, Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Michael B Brenner
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Laura T Donlin
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
| |
Collapse
|
36
|
Shuldiner EG, Karmakar S, Tsai MK, Hebert JD, Tang YJ, Andrejka L, Wang M, Detrick CR, Cai H, Tang R, Petrov DA, Winslow MM. Aging represses lung tumorigenesis and alters tumor suppression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596319. [PMID: 38853826 PMCID: PMC11160591 DOI: 10.1101/2024.05.28.596319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Most cancers are diagnosed in persons over the age of sixty, but little is known about how age impacts tumorigenesis. While aging is accompanied by mutation accumulation - widely understood to contribute to cancer risk - it is also associated with numerous other cellular and molecular changes likely to impact tumorigenesis. Moreover, cancer incidence decreases in the oldest part of the population, suggesting that very old age may reduce carcinogenesis. Here we show that aging represses tumor initiation and growth in genetically engineered mouse models of human lung cancer. Moreover, aging dampens the impact of inactivating many, but not all, tumor suppressor genes with the impact of inactivating PTEN, a negative regulator of the PI3K/AKT pathway, weakened to a disproportionate extent. Single-cell transcriptomic analysis revealed that neoplastic cells from tumors in old mice retain many age-related transcriptomic changes, showing that age has an enduring impact that persists through oncogenic transformation. Furthermore, the consequences of PTEN inactivation were strikingly age-dependent, with PTEN deficiency reducing signatures of aging in cancer cells and the tumor microenvironment. Our findings suggest that the relationship between age and lung cancer incidence may reflect an integration of the competing effects of driver mutation accumulation and tumor suppressive effects of aging.
Collapse
|
37
|
Mallach A, Zielonka M, van Lieshout V, An Y, Khoo JH, Vanheusden M, Chen WT, Moechars D, Arancibia-Carcamo IL, Fiers M, De Strooper B. Microglia-astrocyte crosstalk in the amyloid plaque niche of an Alzheimer's disease mouse model, as revealed by spatial transcriptomics. Cell Rep 2024; 43:114216. [PMID: 38819990 DOI: 10.1016/j.celrep.2024.114216] [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: 06/20/2023] [Revised: 02/02/2024] [Accepted: 04/25/2024] [Indexed: 06/02/2024] Open
Abstract
The amyloid plaque niche is a pivotal hallmark of Alzheimer's disease (AD). Here, we employ two high-resolution spatial transcriptomics (ST) platforms, CosMx and Spatial Enhanced Resolution Omics-sequencing (Stereo-seq), to characterize the transcriptomic alterations, cellular compositions, and signaling perturbations in the amyloid plaque niche in an AD mouse model. We discover heterogeneity in the cellular composition of plaque niches, marked by an increase in microglial accumulation. We profile the transcriptomic alterations of glial cells in the vicinity of plaques and conclude that the microglial response to plaques is consistent across different brain regions, while the astrocytic response is more heterogeneous. Meanwhile, as the microglial density of plaque niches increases, astrocytes acquire a more neurotoxic phenotype and play a key role in inducing GABAergic signaling and decreasing glutamatergic signaling in hippocampal neurons. We thus show that the accumulation of microglia around hippocampal plaques disrupts astrocytic signaling, in turn inducing an imbalance in neuronal synaptic signaling.
Collapse
Affiliation(s)
- Anna Mallach
- UK Dementia Research Institute at UCL, University College London, London WC1E 6BT, UK; The Francis Crick Institute, London NW1 1AT, UK; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Magdalena Zielonka
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium
| | - Veerle van Lieshout
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium
| | - Yanru An
- BGI Research, 49276 Riga, Latvia
| | | | - Marisa Vanheusden
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium; Discovery Biology, Muna Therapeutics, Leuven, Belgium
| | - Wei-Ting Chen
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium; Discovery Biology, Muna Therapeutics, Leuven, Belgium
| | - Daan Moechars
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium
| | - I Lorena Arancibia-Carcamo
- UK Dementia Research Institute at UCL, University College London, London WC1E 6BT, UK; The Francis Crick Institute, London NW1 1AT, UK
| | - Mark Fiers
- UK Dementia Research Institute at UCL, University College London, London WC1E 6BT, UK; The Francis Crick Institute, London NW1 1AT, UK; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium; Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | - Bart De Strooper
- UK Dementia Research Institute at UCL, University College London, London WC1E 6BT, UK; The Francis Crick Institute, London NW1 1AT, UK; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium.
| |
Collapse
|
38
|
Lin P, Gan YB, He J, Lin SE, Xu JK, Chang L, Zhao LM, Zhu J, Zhang L, Huang S, Hu O, Wang YB, Jin HJ, Li YY, Yan PL, Chen L, Jiang JX, Liu P. Advancing skeletal health and disease research with single-cell RNA sequencing. Mil Med Res 2024; 11:33. [PMID: 38816888 PMCID: PMC11138034 DOI: 10.1186/s40779-024-00538-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 05/15/2024] [Indexed: 06/01/2024] Open
Abstract
Orthopedic conditions have emerged as global health concerns, impacting approximately 1.7 billion individuals worldwide. However, the limited understanding of the underlying pathological processes at the cellular and molecular level has hindered the development of comprehensive treatment options for these disorders. The advent of single-cell RNA sequencing (scRNA-seq) technology has revolutionized biomedical research by enabling detailed examination of cellular and molecular diversity. Nevertheless, investigating mechanisms at the single-cell level in highly mineralized skeletal tissue poses technical challenges. In this comprehensive review, we present a streamlined approach to obtaining high-quality single cells from skeletal tissue and provide an overview of existing scRNA-seq technologies employed in skeletal studies along with practical bioinformatic analysis pipelines. By utilizing these methodologies, crucial insights into the developmental dynamics, maintenance of homeostasis, and pathological processes involved in spine, joint, bone, muscle, and tendon disorders have been uncovered. Specifically focusing on the joint diseases of degenerative disc disease, osteoarthritis, and rheumatoid arthritis using scRNA-seq has provided novel insights and a more nuanced comprehension. These findings have paved the way for discovering novel therapeutic targets that offer potential benefits to patients suffering from diverse skeletal disorders.
Collapse
Grants
- 2022YFA1103202 National Key Research and Development Program of China
- 82272507 National Natural Science Foundation of China
- 32270887 National Natural Science Foundation of China
- 32200654 National Natural Science Foundation of China
- CSTB2023NSCQ-ZDJO008 Natural Science Foundation of Chongqing
- BX20220397 Postdoctoral Innovative Talent Support Program
- SFLKF202201 Independent Research Project of State Key Laboratory of Trauma and Chemical Poisoning
- 2021-XZYG-B10 General Hospital of Western Theater Command Research Project
- 14113723 University Grants Committee, Research Grants Council of Hong Kong, China
- N_CUHK472/22 University Grants Committee, Research Grants Council of Hong Kong, China
- C7030-18G University Grants Committee, Research Grants Council of Hong Kong, China
- T13-402/17-N University Grants Committee, Research Grants Council of Hong Kong, China
- AoE/M-402/20 University Grants Committee, Research Grants Council of Hong Kong, China
Collapse
Affiliation(s)
- Peng Lin
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Yi-Bo Gan
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Jian He
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
- Pancreatic Injury and Repair Key Laboratory of Sichuan Province, the General Hospital of Western Theater Command, Chengdu, 610031, China
| | - Si-En Lin
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, Faculty of Medicine, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, 999077, China
| | - Jian-Kun Xu
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, Faculty of Medicine, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, 999077, China
| | - Liang Chang
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, Faculty of Medicine, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, 999077, China
| | - Li-Ming Zhao
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Sacramento, CA, 94305, USA
| | - Jun Zhu
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Liang Zhang
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Sha Huang
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Ou Hu
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Ying-Bo Wang
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Huai-Jian Jin
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Yang-Yang Li
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Pu-Lin Yan
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Lin Chen
- Center of Bone Metabolism and Repair, State Key Laboratory of Trauma and Chemical Poisoning, Trauma Center, Research Institute of Surgery, Laboratory for the Prevention and Rehabilitation of Military Training Related Injuries, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Jian-Xin Jiang
- Wound Trauma Medical Center, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China.
| | - Peng Liu
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China.
| |
Collapse
|
39
|
Li XC, Gandara L, Ekelöf M, Richter K, Alexandrov T, Crocker J. Rapid response of fly populations to gene dosage across development and generations. Nat Commun 2024; 15:4551. [PMID: 38811562 PMCID: PMC11137061 DOI: 10.1038/s41467-024-48960-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
Although the effects of genetic and environmental perturbations on multicellular organisms are rarely restricted to single phenotypic layers, our current understanding of how developmental programs react to these challenges remains limited. Here, we have examined the phenotypic consequences of disturbing the bicoid regulatory network in early Drosophila embryos. We generated flies with two extra copies of bicoid, which causes a posterior shift of the network's regulatory outputs and a decrease in fitness. We subjected these flies to EMS mutagenesis, followed by experimental evolution. After only 8-15 generations, experimental populations have normalized patterns of gene expression and increased survival. Using a phenomics approach, we find that populations were normalized through rapid increases in embryo size driven by maternal changes in metabolism and ovariole development. We extend our results to additional populations of flies, demonstrating predictability. Together, our results necessitate a broader view of regulatory network evolution at the systems level.
Collapse
Affiliation(s)
- Xueying C Li
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- College of Life Sciences, Beijing Normal University, Beijing, China.
| | - Lautaro Gandara
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Måns Ekelöf
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Kerstin Richter
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Theodore Alexandrov
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Medicine Partnership Unit between EMBL and Heidelberg University, Heidelberg, Germany
- BioInnovation Institute, Copenhagen, Denmark
| | - Justin Crocker
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
| |
Collapse
|
40
|
Liu Y, Guo J, Matoga M, Korotkova M, Jakobsson PJ, Aguzzi A. NG2 glia protect against prion neurotoxicity by inhibiting microglia-to-neuron prostaglandin E2 signaling. Nat Neurosci 2024:10.1038/s41593-024-01663-x. [PMID: 38802591 DOI: 10.1038/s41593-024-01663-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 04/22/2024] [Indexed: 05/29/2024]
Abstract
Oligodendrocyte-lineage cells, including NG2 glia, undergo prominent changes in various neurodegenerative disorders. Here, we identify a neuroprotective role for NG2 glia against prion toxicity. NG2 glia were activated after prion infection in cerebellar organotypic cultured slices (COCS) and in brains of prion-inoculated mice. In both model systems, depletion of NG2 glia exacerbated prion-induced neurodegeneration and accelerated prion pathology. Loss of NG2 glia enhanced the biosynthesis of prostaglandin E2 (PGE2) by microglia, which augmented prion neurotoxicity through binding to the EP4 receptor. Pharmacological or genetic inhibition of PGE2 biosynthesis attenuated prion-induced neurodegeneration in COCS and mice, reduced the enhanced neurodegeneration in NG2-glia-depleted COCS after prion infection, and dampened the acceleration of prion disease in NG2-glia-depleted mice. These data unveil a non-cell-autonomous interaction between NG2 glia and microglia in prion disease and suggest that PGE2 signaling may represent an actionable target against prion diseases.
Collapse
Affiliation(s)
- Yingjun Liu
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland.
| | - Jingjing Guo
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Maja Matoga
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Marina Korotkova
- Karolinska Institutet, Department of Medicine Solna, Division of Rheumatology, Stockholm, Sweden
- Karolinska University Hospital at Solna, Stockholm, Sweden
| | - Per-Johan Jakobsson
- Karolinska Institutet, Department of Medicine Solna, Division of Rheumatology, Stockholm, Sweden
- Karolinska University Hospital at Solna, Stockholm, Sweden
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
41
|
Yuan F, Zhang R, Li J, Lei Q, Wang S, Jiang F, Guo Y, Xiang M. CCR5-overexpressing mesenchymal stem cells protect against experimental autoimmune uveitis: insights from single-cell transcriptome analysis. J Neuroinflammation 2024; 21:136. [PMID: 38802924 PMCID: PMC11131209 DOI: 10.1186/s12974-024-03134-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 05/17/2024] [Indexed: 05/29/2024] Open
Abstract
Autoimmune uveitis is a leading cause of severe vision loss, and animal models provide unique opportunities for studying its pathogenesis and therapeutic strategies. Here we employ scRNA-seq, RNA-seq and various molecular and cellular approaches to characterize mouse models of classical experimental autoimmune uveitis (EAU), revealing that EAU causes broad retinal neuron degeneration and marker downregulation, and that Müller glia may act as antigen-presenting cells. Moreover, EAU immune response is primarily driven by Th1 cells, and results in dramatic upregulation of CC chemokines, especially CCL5, in the EAU retina. Accordingly, overexpression of CCR5, a CCL5 receptor, in mesenchymal stem cells (MSCs) enhances their homing capacity and improves their immunomodulatory outcomes in preventing EAU, by reducing infiltrating T cells and activated microglia and suppressing Nlrp3 inflammasome activation. Taken together, our data not only provide valuable insights into the molecular characteristics of EAU but also open an avenue for innovative MSC-based therapy.
Collapse
Affiliation(s)
- Fa Yuan
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Rong Zhang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Jiani Li
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Qiannan Lei
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Shuyi Wang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Fanying Jiang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Yanan Guo
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Mengqing Xiang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China.
- Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| |
Collapse
|
42
|
Li X, Poire A, Jeong KJ, Zhang D, Ozmen TY, Chen G, Sun C, Mills GB. C5aR1 inhibition reprograms tumor associated macrophages and reverses PARP inhibitor resistance in breast cancer. Nat Commun 2024; 15:4485. [PMID: 38802355 PMCID: PMC11130309 DOI: 10.1038/s41467-024-48637-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: 11/21/2022] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
Although Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) have been approved in multiple diseases, including BRCA1/2 mutant breast cancer, responses are usually transient requiring the deployment of combination therapies for optimal efficacy. Here we thus explore mechanisms underlying sensitivity and resistance to PARPi using two intrinsically PARPi sensitive (T22) and resistant (T127) syngeneic murine breast cancer models in female mice. We demonstrate that tumor associated macrophages (TAM) potentially contribute to the differential sensitivity to PARPi. By single-cell RNA-sequencing, we identify a TAM_C3 cluster, expressing genes implicated in anti-inflammatory activity, that is enriched in PARPi resistant T127 tumors and markedly decreased by PARPi in T22 tumors. Rps19/C5aR1 signaling is selectively elevated in TAM_C3. C5aR1 inhibition or transferring C5aR1hi cells increases and decreases PARPi sensitivity, respectively. High C5aR1 levels in human breast cancers are associated with poor responses to immune checkpoint blockade. Thus, targeting C5aR1 may selectively deplete pro-tumoral macrophages and engender sensitivity to PARPi and potentially other therapies.
Collapse
Affiliation(s)
- Xi Li
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Alfonso Poire
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Kang Jin Jeong
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Dong Zhang
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Tugba Yildiran Ozmen
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chaoyang Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Gordon B Mills
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| |
Collapse
|
43
|
Ruzicka WB, Mohammadi S, Fullard JF, Davila-Velderrain J, Subburaju S, Tso DR, Hourihan M, Jiang S, Lee HC, Bendl J, Voloudakis G, Haroutunian V, Hoffman GE, Roussos P, Kellis M. Single-cell multi-cohort dissection of the schizophrenia transcriptome. Science 2024; 384:eadg5136. [PMID: 38781388 DOI: 10.1126/science.adg5136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/21/2023] [Indexed: 05/25/2024]
Abstract
The complexity and heterogeneity of schizophrenia have hindered mechanistic elucidation and the development of more effective therapies. Here, we performed single-cell dissection of schizophrenia-associated transcriptomic changes in the human prefrontal cortex across 140 individuals in two independent cohorts. Excitatory neurons were the most affected cell group, with transcriptional changes converging on neurodevelopment and synapse-related molecular pathways. Transcriptional alterations included known genetic risk factors, suggesting convergence of rare and common genomic variants on neuronal population-specific alterations in schizophrenia. Based on the magnitude of schizophrenia-associated transcriptional change, we identified two populations of individuals with schizophrenia marked by expression of specific excitatory and inhibitory neuronal cell states. This single-cell atlas links transcriptomic changes to etiological genetic risk factors, contextualizing established knowledge within the human cortical cytoarchitecture and facilitating mechanistic understanding of schizophrenia pathophysiology and heterogeneity.
Collapse
Affiliation(s)
- W Brad Ruzicka
- Laboratory for Epigenomics in Human Psychopathology, McLean Hospital, Belmont, MA 02478, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shahin Mohammadi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jose Davila-Velderrain
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Neurogenomics Research Center, Human Technopole, 20157 Milan, Italy
| | - Sivan Subburaju
- Laboratory for Epigenomics in Human Psychopathology, McLean Hospital, Belmont, MA 02478, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Reed Tso
- Laboratory for Epigenomics in Human Psychopathology, McLean Hospital, Belmont, MA 02478, USA
| | - Makayla Hourihan
- Laboratory for Epigenomics in Human Psychopathology, McLean Hospital, Belmont, MA 02478, USA
| | - Shan Jiang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hao-Chih Lee
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Georgios Voloudakis
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vahram Haroutunian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research, Education and Clinical Centers, James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Neurogenomics Research Center, Human Technopole, 20157 Milan, Italy
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| |
Collapse
|
44
|
Cai A, Meng Y, Zhou H, Cai H, Shao X, Wang Q, Xu Y, Zhou Y, Zhou W, Chen L, Mou S. Podocyte Pathogenic Bone Morphogenetic Protein-2 Pathway and Immune Cell Behaviors in Primary Membranous Nephropathy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2404151. [PMID: 38785168 DOI: 10.1002/advs.202404151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Indexed: 05/25/2024]
Abstract
Primary membranous nephropathy (PMN) is one of the leading causes of end-stage renal disease, and the most frequent cause of massive proteinuria in nondiabetic adults, resulting in fatal complications. However, the underlying pathomechanisms of PMN remain largely unclear. Here, single-cell RNA sequencing is employed to analyze kidney biopsies from eleven PMN patients and seven healthy subjects. Profiling 44 060 cells from patients allowed us to characterize the cellular composition and cell-type-specific gene expression in the PMN kidney. The complement-induced BMP2/pSMAD1/COL4 pathway is identified as the pathogenic pathway in podocytes, bridging two key events, i.e., complement system activation and glomerular basement membrane thickening in PMN. Augmented infiltration and activation of myeloid leukocytes and B lymphocytes are found, profiling delicate crosstalk of immune cells in PMN kidneys. Overall, these results provide valuable insights into the roles of podocytes and immune cells in PMN, and comprehensive resources toward the complete understanding of PMN pathophysiology.
Collapse
Affiliation(s)
- Anxiang Cai
- Department of Nephrology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yiwei Meng
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- Institute of Molecular Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Hang Zhou
- Department of Nephrology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Hong Cai
- Department of Nephrology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xinghua Shao
- Department of Nephrology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Qin Wang
- Department of Nephrology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yao Xu
- Department of Nephrology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yin Zhou
- Department of Nephrology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Wenyan Zhou
- Department of Nephrology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China
| | - Shan Mou
- Department of Nephrology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| |
Collapse
|
45
|
Emani PS, Liu JJ, Clarke D, Jensen M, Warrell J, Gupta C, Meng R, Lee CY, Xu S, Dursun C, Lou S, Chen Y, Chu Z, Galeev T, Hwang A, Li Y, Ni P, Zhou X, Bakken TE, Bendl J, Bicks L, Chatterjee T, Cheng L, Cheng Y, Dai Y, Duan Z, Flaherty M, Fullard JF, Gancz M, Garrido-Martín D, Gaynor-Gillett S, Grundman J, Hawken N, Henry E, Hoffman GE, Huang A, Jiang Y, Jin T, Jorstad NL, Kawaguchi R, Khullar S, Liu J, Liu J, Liu S, Ma S, Margolis M, Mazariegos S, Moore J, Moran JR, Nguyen E, Phalke N, Pjanic M, Pratt H, Quintero D, Rajagopalan AS, Riesenmy TR, Shedd N, Shi M, Spector M, Terwilliger R, Travaglini KJ, Wamsley B, Wang G, Xia Y, Xiao S, Yang AC, Zheng S, Gandal MJ, Lee D, Lein ES, Roussos P, Sestan N, Weng Z, White KP, Won H, Girgenti MJ, Zhang J, Wang D, Geschwind D, Gerstein M. Single-cell genomics and regulatory networks for 388 human brains. Science 2024; 384:eadi5199. [PMID: 38781369 DOI: 10.1126/science.adi5199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 04/05/2024] [Indexed: 05/25/2024]
Abstract
Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multiomics datasets into a resource comprising >2.8 million nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550,000 cell type-specific regulatory elements and >1.4 million single-cell expression quantitative trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized ~250 disease-risk genes and drug targets with associated cell types.
Collapse
Affiliation(s)
- Prashant S Emani
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Jason J Liu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Declan Clarke
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Matthew Jensen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Jonathan Warrell
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Chirag Gupta
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ran Meng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Che Yu Lee
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Siwei Xu
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Cagatay Dursun
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Shaoke Lou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Yuhang Chen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Zhiyuan Chu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Timur Galeev
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Ahyeon Hwang
- Department of Computer Science, University of California, Irvine, CA 92697, USA
- Mathematical, Computational and Systems Biology, University of California, Irvine, CA 92697, USA
| | - Yunyang Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Pengyu Ni
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Xiao Zhou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lucy Bicks
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Tanima Chatterjee
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Yuyan Cheng
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi Dai
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Ziheng Duan
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | | | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael Gancz
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Diego Garrido-Martín
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona 08028, Spain
| | - Sophia Gaynor-Gillett
- Tempus Labs, Chicago, IL 60654, USA
- Department of Biology, Cornell College, Mount Vernon, IA 52314, USA
| | - Jennifer Grundman
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Natalie Hawken
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Ella Henry
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY 10468, USA
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Ao Huang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Yunzhe Jiang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Ting Jin
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | | | - Riki Kawaguchi
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, CA 90095, USA
| | - Saniya Khullar
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jianyin Liu
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Junhao Liu
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Shuang Liu
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | | | - Samantha Mazariegos
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Jill Moore
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | | | - Eric Nguyen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Nishigandha Phalke
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Milos Pjanic
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Henry Pratt
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Diana Quintero
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | | | - Tiernon R Riesenmy
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Nicole Shedd
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | | | | | - Rosemarie Terwilliger
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06520, USA
| | | | - Brie Wamsley
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Gaoyuan Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Yan Xia
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Shaohua Xiao
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Andrew C Yang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Suchen Zheng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Michael J Gandal
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles CA, 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Donghoon Lee
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY 10468, USA
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Zhiping Weng
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Kevin P White
- Yong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew J Girgenti
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06520, USA
- Wu Tsai Institute, Yale University, New Haven, CT 06520, USA
- Clinical Neuroscience Division, National Center for Posttraumatic Stress Disorder, Veterans Affairs Connecticut Healthcare System, West Haven, CT 06516, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Daifeng Wang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Daniel Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, CA 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
- Department of Biomedical Informatics & Data Science, Yale University, New Haven, CT 06520, USA
| |
Collapse
|
46
|
De Zuani M, Xue H, Park JS, Dentro SC, Seferbekova Z, Tessier J, Curras-Alonso S, Hadjipanayis A, Athanasiadis EI, Gerstung M, Bayraktar O, Cvejic A. Single-cell and spatial transcriptomics analysis of non-small cell lung cancer. Nat Commun 2024; 15:4388. [PMID: 38782901 PMCID: PMC11116453 DOI: 10.1038/s41467-024-48700-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Lung cancer is the second most frequently diagnosed cancer and the leading cause of cancer-related mortality worldwide. Tumour ecosystems feature diverse immune cell types. Myeloid cells, in particular, are prevalent and have a well-established role in promoting the disease. In our study, we profile approximately 900,000 cells from 25 treatment-naive patients with adenocarcinoma and squamous-cell carcinoma by single-cell and spatial transcriptomics. We note an inverse relationship between anti-inflammatory macrophages and NK cells/T cells, and with reduced NK cell cytotoxicity within the tumour. While we observe a similar cell type composition in both adenocarcinoma and squamous-cell carcinoma, we detect significant differences in the co-expression of various immune checkpoint inhibitors. Moreover, we reveal evidence of a transcriptional "reprogramming" of macrophages in tumours, shifting them towards cholesterol export and adopting a foetal-like transcriptional signature which promotes iron efflux. Our multi-omic resource offers a high-resolution molecular map of tumour-associated macrophages, enhancing our understanding of their role within the tumour microenvironment.
Collapse
Affiliation(s)
- Marco De Zuani
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- OpenTargets, Wellcome Genome Campus, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Haoliang Xue
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- OpenTargets, Wellcome Genome Campus, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Jun Sung Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- OpenTargets, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Stefan C Dentro
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
- Division of Artificial Intelligence in Oncology, DKFZ, Heidelberg, Germany
| | - Zaira Seferbekova
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Julien Tessier
- Precision Medicine and Computational Biology, Sanofi, Cambridge, MA, USA
| | | | | | - Emmanouil I Athanasiadis
- OpenTargets, Wellcome Genome Campus, Hinxton, UK
- Medical Image and Signal Processing Laboratory (MEDISP), Department of Biomedical Engineering, University of West Attica, Athens, Greece
| | - Moritz Gerstung
- OpenTargets, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
- Division of Artificial Intelligence in Oncology, DKFZ, Heidelberg, Germany
| | - Omer Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- OpenTargets, Wellcome Genome Campus, Hinxton, UK
| | - Ana Cvejic
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
- OpenTargets, Wellcome Genome Campus, Hinxton, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
47
|
Deng E, Shen Q, Zhang J, Fang Y, Chang L, Luo G, Fan X. Systematic evaluation of single-cell RNA-seq analyses performance based on long-read sequencing platforms. J Adv Res 2024:S2090-1232(24)00210-8. [PMID: 38782298 DOI: 10.1016/j.jare.2024.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 04/23/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024] Open
Abstract
INTRODUCTION The rapid development of next-generation sequencing (NGS)-based single-cell RNA sequencing (scRNA-seq) allows for detecting and quantifying gene expression in a high-throughput manner, providing a powerful tool for comprehensively understanding cellular function in various biological processes. However, the NGS-based scRNA-seq only quantifies gene expression and cannot reveal the exact transcript structures (isoforms) of each gene due to the limited read length. On the other hand, the long read length of third-generation sequencing (TGS) technologies, including Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), enable direct reading of intact cDNA molecules. OBJECTIVES Both ONT and PacBio have been used in conjunction with scRNA-seq, but their performance in single-cell analyses has not been systematically evaluated. METHODS To address this, we generated ONT and PacBio data from the same single-cell cDNA libraries containing different amount of cells. RESULTS Using NGS as a control, we assessed the performance of each platform in cell type identification. Additionally, the reliability in identifying novel isoforms and allele-specific gene/isoform expression by both platforms was verified, providing a systematic evaluation to design the sequencing strategies in single-cell transcriptome studies. CONCLUSION Beyond gene expression analysis, which the NGS-based scRNA-seq only affords, TGS-based scRNA-seq achieved gene splicing analyses, identifying novel isoforms. Attribute to higher sequencing quality of PacBio, it outperforms ONT in accuracy of novel transcripts identification and allele-specific gene/isoform expression.
Collapse
Affiliation(s)
- Enze Deng
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Qingmei Shen
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China; GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510005, China
| | - Jingna Zhang
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Yaowei Fang
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Lei Chang
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510005, China
| | - Guanzheng Luo
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xiaoying Fan
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China; GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510005, China.
| |
Collapse
|
48
|
Li X, Turaga D, Li RG, Tsai CR, Quinn JN, Zhao Y, Wilson R, Carlson K, Wang J, Spinner JA, Hickey EJ, Adachi I, Martin JF. The Macrophage Landscape Across the Lifespan of a Human Cardiac Allograft. Circulation 2024; 149:1650-1666. [PMID: 38344825 PMCID: PMC11105989 DOI: 10.1161/circulationaha.123.065294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 01/16/2024] [Indexed: 05/22/2024]
Abstract
BACKGROUND Much of our knowledge of organ rejection after transplantation is derived from rodent models. METHODS We used single-nucleus RNA sequencing to investigate the inflammatory myocardial microenvironment in human pediatric cardiac allografts at different stages after transplantation. We distinguished donor- from recipient-derived cells using naturally occurring genetic variants embedded in single-nucleus RNA sequencing data. RESULTS Donor-derived tissue resident macrophages, which accompany the allograft into the recipient, are lost over time after transplantation. In contrast, monocyte-derived macrophages from the recipient populate the heart within days after transplantation and form 2 macrophage populations: recipient MP1 and recipient MP2. Recipient MP2s have cell signatures similar to donor-derived resident macrophages; however, they lack signatures of pro-reparative phagocytic activity typical of donor-derived resident macrophages and instead express profibrotic genes. In contrast, recipient MP1s express genes consistent with hallmarks of cellular rejection. Our data suggest that recipient MP1s activate a subset of natural killer cells, turning them into a cytotoxic cell population through feed-forward signaling between recipient MP1s and natural killer cells. CONCLUSIONS Our findings reveal an imbalance of donor-derived and recipient-derived macrophages in the pediatric cardiac allograft that contributes to allograft failure.
Collapse
Affiliation(s)
- Xiao Li
- The Texas Heart Institute, 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
| | - Rich G. Li
- The Texas Heart Institute, Houston, TX, USA
| | - Chang-Ru Tsai
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
| | - Julianna N. Quinn
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, TX, USA
| | - Yi Zhao
- The Texas Heart Institute, Houston, TX, USA
| | | | - Katherine Carlson
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
| | - Jun Wang
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, TX, USA
| | - Joseph A. Spinner
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Division of Cardiology, Texas Children’s Hospital, Houston, TX, USA
| | - Edward J. Hickey
- Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
- Division of Congenital Heart Surgery, Texas Children’s Hospital, Houston, TX, USA
| | - Iki Adachi
- Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
- Division of Congenital Heart Surgery, Texas Children’s Hospital, 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
| |
Collapse
|
49
|
Linna-Kuosmanen S, Schmauch E, Galani K, Ojanen J, Boix CA, Örd T, Toropainen A, Singha PK, Moreau PR, Harju K, Blazeski A, Segerstolpe Å, Lahtinen V, Hou L, Kang K, Meibalan E, Agudelo LZ, Kokki H, Halonen J, Jalkanen J, Gunn J, MacRae CA, Hollmén M, Hartikainen JEK, Kaikkonen MU, García-Cardeña G, Tavi P, Kiviniemi T, Kellis M. Transcriptomic and spatial dissection of human ex vivo right atrial tissue reveals proinflammatory microvascular changes in ischemic heart disease. Cell Rep Med 2024; 5:101556. [PMID: 38776872 PMCID: PMC11148807 DOI: 10.1016/j.xcrm.2024.101556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 11/27/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024]
Abstract
Cardiovascular disease plays a central role in the electrical and structural remodeling of the right atrium, predisposing to arrhythmias, heart failure, and sudden death. Here, we dissect with single-nuclei RNA sequencing (snRNA-seq) and spatial transcriptomics the gene expression changes in the human ex vivo right atrial tissue and pericardial fluid in ischemic heart disease, myocardial infarction, and ischemic and non-ischemic heart failure using asymptomatic patients with valvular disease who undergo preventive surgery as the control group. We reveal substantial differences in disease-associated gene expression in all cell types, collectively suggesting inflammatory microvascular dysfunction and changes in the right atrial tissue composition as the valvular and vascular diseases progress into heart failure. The data collectively suggest that investigation of human cardiovascular disease should expand to all functionally important parts of the heart, which may help us to identify mechanisms promoting more severe types of the disease.
Collapse
Affiliation(s)
- Suvi Linna-Kuosmanen
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland.
| | - Eloi Schmauch
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Kyriakitsa Galani
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Johannes Ojanen
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Carles A Boix
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tiit Örd
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Anu Toropainen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Prosanta K Singha
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Pierre R Moreau
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Kristiina Harju
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Adriana Blazeski
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Excellence in Vascular Biology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Åsa Segerstolpe
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Veikko Lahtinen
- Heart Center, Turku University Hospital, 20521 Turku, Finland; MediCity Research Laboratories and InFLAMES Flagship, University of Turku, 20500 Turku, Finland
| | - Lei Hou
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kai Kang
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Elamaran Meibalan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Excellence in Vascular Biology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Leandro Z Agudelo
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hannu Kokki
- School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Jari Halonen
- School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland; Heart Center, Kuopio University Hospital, 70200 Kuopio, Finland
| | - Juho Jalkanen
- MediCity Research Laboratories and InFLAMES Flagship, University of Turku, 20500 Turku, Finland
| | - Jarmo Gunn
- Heart Center, Turku University Hospital, 20521 Turku, Finland; Department of Medicine, University of Turku, 20500 Turku, Finland
| | - Calum A MacRae
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Cardiovascular Medicine and Network Medicine Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Maija Hollmén
- MediCity Research Laboratories and InFLAMES Flagship, University of Turku, 20500 Turku, Finland
| | - Juha E K Hartikainen
- School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland; Heart Center, Kuopio University Hospital, 70200 Kuopio, Finland
| | - Minna U Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Guillermo García-Cardeña
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Excellence in Vascular Biology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Pasi Tavi
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Tuomas Kiviniemi
- Heart Center, Turku University Hospital, 20521 Turku, Finland; Department of Medicine, University of Turku, 20500 Turku, Finland; Cardiovascular Medicine and Network Medicine Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| |
Collapse
|
50
|
Liu H, Sima X, Xiao B, Gulizeba H, Zhao S, Zhou T, Huang Y. Integrated analysis of single-cell and bulk RNA sequencing data reveals a myeloid cell-related regulon predicting neoadjuvant immunotherapy response across cancers. J Transl Med 2024; 22:486. [PMID: 38773508 PMCID: PMC11110189 DOI: 10.1186/s12967-024-05123-9] [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: 12/20/2023] [Accepted: 03/20/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Immunotherapy has brought about a paradigm shift in the treatment of cancer. However, the majority of patients exhibit resistance or become refractory to immunotherapy, and the underlying mechanisms remain to be explored. METHODS Sing-cell RNA sequencing (scRNA‑seq) datasets derived from 1 pretreatment and 1 posttreatment achieving pathological complete response (pCR) patient with lung adenocarcinoma (LUAD) who received neoadjuvant immunotherapy were collected, and pySCENIC was used to find the gene regulatory network (GRN) between cell types and immune checkpoint inhibitor (ICI) response. A regulon predicting ICI response was identified and validated using large‑scale pan-cancer data, including a colorectal cancer scRNA‑seq dataset, a breast cancer scRNA‑seq dataset, The Cancer Genome Atlas (TCGA) pan-cancer cohort, and 5 ICI transcriptomic cohorts. Symphony reference mapping was performed to construct the myeloid cell map. RESULTS Thirteen major cluster cell types were identified by comparing pretreatment and posttreatment patients, and the fraction of myeloid cells was higher in the posttreatment group (19.0% vs. 11.8%). A PPARG regulon (containing 23 target genes) was associated with ICI response, and its function was validated by a colorectal cancer scRNA‑seq dataset, a breast cancer scRNA‑seq dataset, TCGA pan-cancer cohort, and 5 ICI transcriptomic cohorts. Additionally, a myeloid cell map was developed, and cluster I, II, and III myeloid cells with high expression of PPARG were identified. Moreover, we constructed a website called PPARG ( https://pparg.online/PPARG/ or http://43.134.20.130:3838/PPARG/ ), which provides a powerful discovery tool and resource value for researchers. CONCLUSIONS The PPARG regulon is a predictor of ICI response. The myeloid cell map enables the identification of PPARG subclusters in public scRNA-seq datasets and provides a powerful discovery tool and resource value.
Collapse
Affiliation(s)
- Hong Liu
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, P. R. China
| | - Xiaoxian Sima
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, P. R. China
| | - Bijing Xiao
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, P. R. China
| | - Haimiti Gulizeba
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, P. R. China
| | - Shen Zhao
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, P. R. China.
| | - Ting Zhou
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, P. R. China.
| | - Yan Huang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, P. R. China.
| |
Collapse
|