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Whitehead BJ, Corbin D, Alexander ML, Bumgarner J, Zhang N, Karelina K, Weil ZM. Cerebral hypoperfusion exacerbates traumatic brain injury in male but not female mice. Eur J Neurosci 2024; 60:4346-4361. [PMID: 38858126 DOI: 10.1111/ejn.16439] [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: 01/24/2024] [Revised: 05/07/2024] [Accepted: 05/23/2024] [Indexed: 06/12/2024]
Abstract
Mild-moderate traumatic brain injuries (TBIs) are prevalent, and while many individuals recover, there is evidence that a significant number experience long-term health impacts, including increased vulnerability to neurodegenerative diseases. These effects are influenced by other risk factors, such as cardiovascular disease. Our study tested the hypothesis that a pre-injury reduction in cerebral blood flow (CBF), mimicking cardiovascular disease, worsens TBI recovery. We induced bilateral carotid artery stenosis (BCAS) and a mild-moderate closed-head TBI in male and female mice, either alone or in combination, and analyzed CBF, spatial learning, memory, axonal damage, and gene expression. Findings showed that BCAS and TBI independently caused a ~10% decrease in CBF. Mice subjected to both BCAS and TBI experienced more significant CBF reductions, notably affecting spatial learning and memory, particularly in males. Additionally, male mice showed increased axonal damage with both BCAS and TBI compared to either condition alone. Females exhibited spatial memory deficits due to BCAS, but these were not worsened by subsequent TBI. Gene expression analysis in male mice highlighted that TBI and BCAS individually altered neuronal and glial profiles. However, the combination of BCAS and TBI resulted in markedly different transcriptional patterns. Our results suggest that mild cerebrovascular impairments, serving as a stand-in for preexisting cardiovascular conditions, can significantly worsen TBI outcomes in males. This highlights the potential for mild comorbidities to modify TBI outcomes and increase the risk of secondary diseases.
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Affiliation(s)
- Bailey J Whitehead
- Department of Neuroscience and Rockefeller Neuroscience Institute, West Virginia University, Morgantown, West Virginia, USA
| | - Deborah Corbin
- Department of Neuroscience and Rockefeller Neuroscience Institute, West Virginia University, Morgantown, West Virginia, USA
| | - Megan L Alexander
- Department of Neuroscience and Rockefeller Neuroscience Institute, West Virginia University, Morgantown, West Virginia, USA
| | - Jacob Bumgarner
- Department of Neuroscience and Rockefeller Neuroscience Institute, West Virginia University, Morgantown, West Virginia, USA
| | - Ning Zhang
- Department of Neuroscience and Rockefeller Neuroscience Institute, West Virginia University, Morgantown, West Virginia, USA
| | - Kate Karelina
- Department of Neuroscience and Rockefeller Neuroscience Institute, West Virginia University, Morgantown, West Virginia, USA
| | - Zachary M Weil
- Department of Neuroscience and Rockefeller Neuroscience Institute, West Virginia University, Morgantown, West Virginia, USA
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152
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Wang SY, Yang XQ, Wang YX, Shen A, Liang CC, Huang RJ, Cheng UH, Jian R, An N, Xiao YL, Wang LS, Zhao Y, Lin C, Wang CP, Yuan ZP, Yuan SQ. Overexpression of COX7A1 Promotes the Resistance of Gastric Cancer to Oxaliplatin and Weakens the Efficacy of Immunotherapy. J Transl Med 2024; 104:102090. [PMID: 38830579 DOI: 10.1016/j.labinv.2024.102090] [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: 12/19/2023] [Revised: 05/09/2024] [Accepted: 05/28/2024] [Indexed: 06/05/2024] Open
Abstract
Gastric cancer (GC) is one of the most common clinical malignant tumors worldwide, with high morbidity and mortality. Presently, the overall response rate to immunotherapy is low, and current methods for predicting the prognosis of GC are not optimal. Therefore, novel biomarkers with accuracy, efficiency, stability, performance ratio, and wide clinical application are needed. Based on public data sets, the chemotherapy cohort and immunotherapy cohort from Sun Yat-sen University Cancer Center, a series of bioinformatics analyses, such as differential expression analysis, survival analysis, drug sensitivity prediction, enrichment analysis, tumor immune dysfunction and exclusion analysis, single-sample gene set enrichment analysis, stemness index calculation, and immune cell infiltration analysis, were performed for screening and preliminary exploration. Immunohistochemical staining and in vitro experiments were performed for further verification. Overexpression of COX7A1 promoted the resistance of GC cells to Oxaliplatin. COX7A1 may induce immune escape by regulating the number of fibroblasts and their cellular communication with immune cells. In summary, measuring the expression levels of COX7A1 in the clinic may be useful in predicting the prognosis of GC patients, the degree of chemotherapy resistance, and the efficacy of immunotherapy.
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Affiliation(s)
- Si-Yu Wang
- Department of Oncology, The First People's Hospital of Yibin, Yibin, China
| | - Xian-Qi Yang
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yu-Xin Wang
- Department of Nuclear Medicine, The First Hospital of Jilin University, Changchun, China
| | - Ao Shen
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Cheng-Cai Liang
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Run-Jie Huang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Un Hio Cheng
- Department of Urology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Rui Jian
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Nan An
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yu-Long Xiao
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Li-Shuai Wang
- Department of Oncology, The First People's Hospital of Yibin, Yibin, China
| | - Yin Zhao
- Department of Oncology, The First People's Hospital of Yibin, Yibin, China
| | - Chuan Lin
- Department of Oncology, The First People's Hospital of Yibin, Yibin, China
| | - Chang-Ping Wang
- Department of Oncology, The First People's Hospital of Yibin, Yibin, China
| | - Zhi-Ping Yuan
- Department of Oncology, The First People's Hospital of Yibin, Yibin, China
| | - Shu-Qiang Yuan
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
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153
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Dobersalske C, Rauschenbach L, Hua Y, Berliner C, Steinbach A, Grüneboom A, Kokkaliaris KD, Heiland DH, Berger P, Langer S, Tan CL, Stenzel M, Landolsi S, Weber F, Darkwah Oppong M, Werner RA, Gull H, Schröder T, Linsenmann T, Buck AK, Gunzer M, Stuschke M, Keyvani K, Forsting M, Glas M, Kipnis J, Steindler DA, Reinhardt HC, Green EW, Platten M, Tasdogan A, Herrmann K, Rambow F, Cima I, Sure U, Scheffler B. Cranioencephalic functional lymphoid units in glioblastoma. Nat Med 2024:10.1038/s41591-024-03152-x. [PMID: 39085419 DOI: 10.1038/s41591-024-03152-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: 06/26/2023] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
The ecosystem of brain tumors is considered immunosuppressed, but our current knowledge may be incomplete. Here we analyzed clinical cell and tissue specimens derived from patients presenting with glioblastoma or nonmalignant intracranial disease to report that the cranial bone (CB) marrow, in juxtaposition to treatment-naive glioblastoma tumors, harbors active lymphoid populations at the time of initial diagnosis. Clinical and anatomical imaging, single-cell molecular and immune cell profiling and quantification of tumor reactivity identified CD8+ T cell clonotypes in the CB that were also found in the tumor. These were characterized by acute and durable antitumor response rooted in the entire T cell developmental spectrum. In contrast to distal bone marrow, the CB niche proximal to the tumor showed increased frequencies of tumor-reactive CD8+ effector types expressing the lymphoid egress marker S1PR1. In line with this, cranial enhancement of CXCR4 radiolabel may serve as a surrogate marker indicating focal association with improved progression-free survival. The data of this study advocate preservation and further exploitation of these cranioencephalic units for the clinical care of glioblastoma.
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Affiliation(s)
- Celia Dobersalske
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, University Duisburg-Essen, Essen, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- DKFZ Division Translational Neurooncology at the WTZ, University Medicine Essen, Essen, Germany
| | - Laurèl Rauschenbach
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, University Duisburg-Essen, Essen, Germany
- DKFZ Division Translational Neurooncology at the WTZ, University Medicine Essen, Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, Essen, Germany
- Department of Neurosurgery and Spine Surgery, University Hospital Essen, Essen, Germany
- Center for Translational Neuroscience and Behavioral Science (C-TNBS), University of Duisburg-Essen, Essen, Germany
| | - Yichao Hua
- Department of Applied Computational Cancer Research, IKIM, University Hospital Essen, Essen, Germany
| | - Christoph Berliner
- Department of Nuclear Medicine, University Hospital Essen, Essen, Germany
| | - Anita Steinbach
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, University Duisburg-Essen, Essen, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- DKFZ Division Translational Neurooncology at the WTZ, University Medicine Essen, Essen, Germany
| | - Anika Grüneboom
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - Konstantinos D Kokkaliaris
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
- DKTK, German Cancer Consortium, partner site Frankfurt/Mainz, Quantitative Spatial Cancer Biology Laboratory, University Hospital Frankfurt, Frankfurt am Main, Germany
- Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Dieter H Heiland
- DKTK, German Cancer Consortium, partner site Freiburg, Translational Neurosurgery, Microenvironment and Immunology Research Laboratory, University of Freiburg, Freiburg, Germany
- Department of Neurosurgery, University Clinic Erlangen, Erlangen, Germany
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Pia Berger
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, University Duisburg-Essen, Essen, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- DKFZ Division Translational Neurooncology at the WTZ, University Medicine Essen, Essen, Germany
| | - Sarah Langer
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, University Duisburg-Essen, Essen, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- DKFZ Division Translational Neurooncology at the WTZ, University Medicine Essen, Essen, Germany
| | - Chin L Tan
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- DKTK, German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany
| | - Martin Stenzel
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - Somaya Landolsi
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
- DKTK, German Cancer Consortium, partner site Frankfurt/Mainz, Quantitative Spatial Cancer Biology Laboratory, University Hospital Frankfurt, Frankfurt am Main, Germany
- Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Flora Weber
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - Marvin Darkwah Oppong
- Department of Neurosurgery and Spine Surgery, University Hospital Essen, Essen, Germany
- Center for Translational Neuroscience and Behavioral Science (C-TNBS), University of Duisburg-Essen, Essen, Germany
| | - Rudolf A Werner
- Department of Nuclear Medicine, University Hospital Würzburg, Würzburg, Germany
- University Hospital Frankfurt, Department of Nuclear Medicine, Clinic for Radiology and Nuclear Medicine, Frankfurt am Main, Germany
- The Russell H. Morgan Department of Radiology, Division of Nuclear Medicine and Molecular Imaging, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hanah Gull
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, University Duisburg-Essen, Essen, Germany
- DKFZ Division Translational Neurooncology at the WTZ, University Medicine Essen, Essen, Germany
- Department of Neurosurgery and Spine Surgery, University Hospital Essen, Essen, Germany
- Center for Translational Neuroscience and Behavioral Science (C-TNBS), University of Duisburg-Essen, Essen, Germany
| | - Thomas Schröder
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Essen, Germany
| | - Thomas Linsenmann
- Department of Neurosurgery, University Hospital Würzburg, Würzburg, Germany
| | - Andreas K Buck
- Department of Nuclear Medicine, University Hospital Würzburg, Würzburg, Germany
| | - Matthias Gunzer
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, Germany
| | - Martin Stuschke
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, University Duisburg-Essen, Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, Essen, Germany
- Department of Radiation Oncology, University Hospital Essen, Essen, Germany
| | - Kathy Keyvani
- Institute of Neuropathology, University Hospital Essen, Essen, Germany
| | - Michael Forsting
- Department of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Essen, Germany
| | - Martin Glas
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, University Duisburg-Essen, Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, Essen, Germany
- Center for Translational Neuroscience and Behavioral Science (C-TNBS), University of Duisburg-Essen, Essen, Germany
- Department of Neurology, Division of Neurooncology, University Hospital Essen, Essen, Germany
| | - Jonathan Kipnis
- Brain Immunology and Glia (BIG) Center, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Dennis A Steindler
- Steindler Consulting, Boston, MA, USA
- The Eshelman Institute for Innovation, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hans Christian Reinhardt
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, University Duisburg-Essen, Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, Essen, Germany
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Essen, Germany
- Center of Medical Biotechnology (ZMB), University Duisburg-Essen, Essen, Germany
| | - Edward W Green
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- DKTK, German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany
| | - Michael Platten
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- DKTK, German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany
- Immune Monitoring Unit, National Center for Tumor Diseases, Heidelberg, Germany
- Helmholtz Institute for Translational Oncology, Mainz, Germany
- German Cancer Research Center-Hector Cancer Institute at the Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Alpaslan Tasdogan
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, University Duisburg-Essen, Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, Essen, Germany
- Center of Medical Biotechnology (ZMB), University Duisburg-Essen, Essen, Germany
- Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Ken Herrmann
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, University Duisburg-Essen, Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, Essen, Germany
- Department of Nuclear Medicine, University Hospital Essen, Essen, Germany
| | - Florian Rambow
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Department of Applied Computational Cancer Research, IKIM, University Hospital Essen, Essen, Germany
- Center of Medical Biotechnology (ZMB), University Duisburg-Essen, Essen, Germany
| | - Igor Cima
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, University Duisburg-Essen, Essen, Germany
- DKFZ Division Translational Neurooncology at the WTZ, University Medicine Essen, Essen, Germany
| | - Ulrich Sure
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, University Duisburg-Essen, Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, Essen, Germany
- Department of Neurosurgery and Spine Surgery, University Hospital Essen, Essen, Germany
- Center for Translational Neuroscience and Behavioral Science (C-TNBS), University of Duisburg-Essen, Essen, Germany
| | - Björn Scheffler
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, University Duisburg-Essen, Essen, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- DKFZ Division Translational Neurooncology at the WTZ, University Medicine Essen, Essen, Germany.
- West German Cancer Center (WTZ), University Hospital Essen, Essen, Germany.
- Center of Medical Biotechnology (ZMB), University Duisburg-Essen, Essen, Germany.
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154
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Yadav P, Ortega JG, Tamaki W, Chien C, Chang KC, Biswas N, Pan S, Nilsson J, Yin X, Bhattacharyya A, Boostanpour K, Jujaray T, Wang J, Tsukui T, Sheppard D, Li B, Maishan M, Taenaka H, Matthay MA, Muramatsu R, Maliskova L, Ghosh A, Eckalbar WL, Molofsky AB, Wolters PJ, Tamaki SJ, Bivona T, Abate AR, Wagner A, Tharp KM, Bhattacharya M. Macrophage-fibroblast crosstalk drives Arg1-dependent lung fibrosis via ornithine loading. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.06.556606. [PMID: 39211079 PMCID: PMC11360891 DOI: 10.1101/2023.09.06.556606] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Monocyte-derived macrophages recruited to injured tissues induce a maladaptive fibrotic response characterized by excessive production of collagen by local fibroblasts. Macrophages initiate this programming via paracrine factors, but it is unknown whether reciprocal responses from fibroblasts enhance profibrotic polarization of macrophages. We identify macrophage-fibroblast crosstalk necessary for injury-associated fibrosis, in which macrophages induced interleukin 6 ( IL-6 ) expression in fibroblasts via purinergic receptor P2rx4 signaling, and IL-6, in turn, induced arginase 1 ( Arg1 ) expression in macrophages. Arg1 contributed to fibrotic responses by metabolizing arginine to ornithine, which fibroblasts used as a substrate to synthesize proline, a uniquely abundant constituent of collagen. Imaging of idiopathic pulmonary fibrosis (IPF) lung samples confirmed expression of ARG1 in myeloid cells, and arginase inhibition suppressed collagen expression in cultured precision-cut IPF lung slices. Taken together, we define a circuit between macrophages and fibroblasts that facilitates cross-feeding metabolism necessary for injury-associated fibrosis.
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155
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Nath PR, Maclean M, Nagarajan V, Lee JW, Yakin M, Kumar A, Nadali H, Schmidt B, Kaya KD, Kodati S, Young A, Caspi RR, Kuiper JJW, Sen HN. Single-cell profiling identifies a CD8 bright CD244 bright Natural Killer cell subset that reflects disease activity in HLA-A29-positive birdshot chorioretinopathy. Nat Commun 2024; 15:6443. [PMID: 39085199 PMCID: PMC11291632 DOI: 10.1038/s41467-024-50472-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 07/12/2024] [Indexed: 08/02/2024] Open
Abstract
Birdshot chorioretinopathy is an inflammatory eye condition strongly associated with MHC-I allele HLA-A29. The striking association with MHC-I suggests involvement of T cells, whereas natural killer (NK) cell involvement remains largely unstudied. Here we show that HLA-A29-positive birdshot chorioretinopathy patients have a skewed NK cell pool containing expanded CD16 positive NK cells which produce more proinflammatory cytokines. These NK cells contain populations that express CD8A which is involved in MHC-I recognition on target cells, display gene signatures indicative of high cytotoxic activity (GZMB, PRF1 and ISG15), and signaling through NK cell receptor CD244 (SH2D1B). Long-term monitoring of a cohort of birdshot chorioretinopathy patients with active disease identifies a population of CD8bright CD244bright NK cells, which rapidly declines to normal levels upon clinical remission following successful treatment. Collectively, these studies implicate CD8bright CD244bright NK cells in birdshot chorioretinopathy.
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Affiliation(s)
- Pulak R Nath
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA.
- Lentigen Technology Inc., A Miltenyi Biotec Company, 910 Clopper Road, Gaithersburg, MD, 20878, USA.
| | - Mary Maclean
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
- Translational Immunology Section, Office of Science and Technology, NIAMS, Bethesda, NIH, USA
| | - Vijay Nagarajan
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
- Immunoregulation Section, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Jung Wha Lee
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Mehmet Yakin
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Aman Kumar
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Hadi Nadali
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Brian Schmidt
- NIH Intramural Sequencing Center, NIH, Rockville, USA
| | - Koray D Kaya
- Medical Genetics and Ophthalmic Genomics Unit, NEI, NIH, Bethesda, USA
| | - Shilpa Kodati
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Alice Young
- NIH Intramural Sequencing Center, NIH, Rockville, USA
| | - Rachel R Caspi
- Immunoregulation Section, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Jonas J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands.
| | - H Nida Sen
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
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156
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Katoh M, Nomura S, Yamada S, Ito M, Hayashi H, Katagiri M, Heryed T, Fujiwara T, Takeda N, Nishida M, Sugaya M, Kato M, Osawa T, Abe H, Sakurai Y, Ko T, Fujita K, Zhang B, Hatsuse S, Yamada T, Inoue S, Dai Z, Kubota M, Sawami K, Ono M, Morita H, Kubota Y, Mizuno S, Takahashi S, Nakanishi M, Ushiku T, Nakagami H, Aburatani H, Komuro I. Vaccine Therapy for Heart Failure Targeting the Inflammatory Cytokine Igfbp7. Circulation 2024; 150:374-389. [PMID: 38991046 DOI: 10.1161/circulationaha.123.064719] [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: 03/14/2023] [Accepted: 05/29/2024] [Indexed: 07/13/2024]
Abstract
BACKGROUND The heart comprises many types of cells such as cardiomyocytes, endothelial cells (ECs), fibroblasts, smooth muscle cells, pericytes, and blood cells. Every cell type responds to various stressors (eg, hemodynamic overload and ischemia) and changes its properties and interrelationships among cells. To date, heart failure research has focused mainly on cardiomyocytes; however, other types of cells and their cell-to-cell interactions might also be important in the pathogenesis of heart failure. METHODS Pressure overload was imposed on mice by transverse aortic constriction and the vascular structure of the heart was examined using a tissue transparency technique. Functional and molecular analyses including single-cell RNA sequencing were performed on the hearts of wild-type mice and EC-specific gene knockout mice. Metabolites in heart tissue were measured by capillary electrophoresis-time of flight-mass spectrometry system. The vaccine was prepared by conjugating the synthesized epitope peptides with keyhole limpet hemocyanin and administered to mice with aluminum hydroxide as an adjuvant. Tissue samples from heart failure patients were used for single-nucleus RNA sequencing to examine gene expression in ECs and perform pathway analysis in cardiomyocytes. RESULTS Pressure overload induced the development of intricately entwined blood vessels in murine hearts, leading to the accumulation of replication stress and DNA damage in cardiac ECs. Inhibition of cell proliferation by a cyclin-dependent kinase inhibitor reduced DNA damage in ECs and ameliorated transverse aortic constriction-induced cardiac dysfunction. Single-cell RNA sequencing analysis revealed upregulation of Igfbp7 (insulin-like growth factor-binding protein 7) expression in the senescent ECs and downregulation of insulin signaling and oxidative phosphorylation in cardiomyocytes of murine and human failing hearts. Overexpression of Igfbp7 in the murine heart using AAV9 (adeno-associated virus serotype 9) exacerbated cardiac dysfunction, while EC-specific deletion of Igfbp7 and the vaccine targeting Igfbp7 ameliorated cardiac dysfunction with increased oxidative phosphorylation in cardiomyocytes under pressure overload. CONCLUSIONS Igfbp7 produced by senescent ECs causes cardiac dysfunction and vaccine therapy targeting Igfbp7 may be useful to prevent the development of heart failure.
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Affiliation(s)
- Manami Katoh
- Departments of Cardiovascular Medicine (M.Katoh, S.N., S.Y., M.I., M.Katagiri, T.H., T.F., N.T., T.K., K.F., B.Z., S.H., T.Y., S.I., Z.D., M.Kubota, K.S., H.M., I.K.), The University of Tokyo, Japan
- Frontier Cardiovascular Science (M.Katoh, T.K., S.I., S.N., I.K.), The University of Tokyo, Japan
- Genome Science Division (M.Katoh, S.N., H. Aburatani), The University of Tokyo, Japan
| | - Seitaro Nomura
- Departments of Cardiovascular Medicine (M.Katoh, S.N., S.Y., M.I., M.Katagiri, T.H., T.F., N.T., T.K., K.F., B.Z., S.H., T.Y., S.I., Z.D., M.Kubota, K.S., H.M., I.K.), The University of Tokyo, Japan
- Frontier Cardiovascular Science (M.Katoh, T.K., S.I., S.N., I.K.), The University of Tokyo, Japan
- Genome Science Division (M.Katoh, S.N., H. Aburatani), The University of Tokyo, Japan
| | - Shintaro Yamada
- Departments of Cardiovascular Medicine (M.Katoh, S.N., S.Y., M.I., M.Katagiri, T.H., T.F., N.T., T.K., K.F., B.Z., S.H., T.Y., S.I., Z.D., M.Kubota, K.S., H.M., I.K.), The University of Tokyo, Japan
| | - Masamichi Ito
- Departments of Cardiovascular Medicine (M.Katoh, S.N., S.Y., M.I., M.Katagiri, T.H., T.F., N.T., T.K., K.F., B.Z., S.H., T.Y., S.I., Z.D., M.Kubota, K.S., H.M., I.K.), The University of Tokyo, Japan
| | - Hiroki Hayashi
- Department of Health Development and Medicine, Graduate School of Medicine, Osaka University, Suita, Japan (H.H., H.N.)
| | - Mikako Katagiri
- Departments of Cardiovascular Medicine (M.Katoh, S.N., S.Y., M.I., M.Katagiri, T.H., T.F., N.T., T.K., K.F., B.Z., S.H., T.Y., S.I., Z.D., M.Kubota, K.S., H.M., I.K.), The University of Tokyo, Japan
| | - Tuolisi Heryed
- Departments of Cardiovascular Medicine (M.Katoh, S.N., S.Y., M.I., M.Katagiri, T.H., T.F., N.T., T.K., K.F., B.Z., S.H., T.Y., S.I., Z.D., M.Kubota, K.S., H.M., I.K.), The University of Tokyo, Japan
| | - Takayuki Fujiwara
- Departments of Cardiovascular Medicine (M.Katoh, S.N., S.Y., M.I., M.Katagiri, T.H., T.F., N.T., T.K., K.F., B.Z., S.H., T.Y., S.I., Z.D., M.Kubota, K.S., H.M., I.K.), The University of Tokyo, Japan
| | - Norifumi Takeda
- Departments of Cardiovascular Medicine (M.Katoh, S.N., S.Y., M.I., M.Katagiri, T.H., T.F., N.T., T.K., K.F., B.Z., S.H., T.Y., S.I., Z.D., M.Kubota, K.S., H.M., I.K.), The University of Tokyo, Japan
| | - Miyuki Nishida
- Division of Integrative Nutriomics and Oncology, Research Center for Advanced Science and Technology (M. Nishida, M.S., M.K., T.O.), The University of Tokyo, Japan
| | - Maki Sugaya
- Division of Integrative Nutriomics and Oncology, Research Center for Advanced Science and Technology (M. Nishida, M.S., M.K., T.O.), The University of Tokyo, Japan
| | - Miki Kato
- Division of Integrative Nutriomics and Oncology, Research Center for Advanced Science and Technology (M. Nishida, M.S., M.K., T.O.), The University of Tokyo, Japan
| | - Tsuyoshi Osawa
- Division of Integrative Nutriomics and Oncology, Research Center for Advanced Science and Technology (M. Nishida, M.S., M.K., T.O.), The University of Tokyo, Japan
| | - Hiroyuki Abe
- Pathology (H. Abe, T.U.), The University of Tokyo, Japan
| | - Yoshitaka Sakurai
- Diabetes and Metabolic Diseases, Graduate School of Medicine (Y.S.), The University of Tokyo, Japan
| | - Toshiyuki Ko
- Departments of Cardiovascular Medicine (M.Katoh, S.N., S.Y., M.I., M.Katagiri, T.H., T.F., N.T., T.K., K.F., B.Z., S.H., T.Y., S.I., Z.D., M.Kubota, K.S., H.M., I.K.), The University of Tokyo, Japan
- Frontier Cardiovascular Science (M.Katoh, T.K., S.I., S.N., I.K.), The University of Tokyo, Japan
| | - Kanna Fujita
- Departments of Cardiovascular Medicine (M.Katoh, S.N., S.Y., M.I., M.Katagiri, T.H., T.F., N.T., T.K., K.F., B.Z., S.H., T.Y., S.I., Z.D., M.Kubota, K.S., H.M., I.K.), The University of Tokyo, Japan
| | - Bo Zhang
- Departments of Cardiovascular Medicine (M.Katoh, S.N., S.Y., M.I., M.Katagiri, T.H., T.F., N.T., T.K., K.F., B.Z., S.H., T.Y., S.I., Z.D., M.Kubota, K.S., H.M., I.K.), The University of Tokyo, Japan
| | - Satoshi Hatsuse
- Departments of Cardiovascular Medicine (M.Katoh, S.N., S.Y., M.I., M.Katagiri, T.H., T.F., N.T., T.K., K.F., B.Z., S.H., T.Y., S.I., Z.D., M.Kubota, K.S., H.M., I.K.), The University of Tokyo, Japan
| | - Takanobu Yamada
- Departments of Cardiovascular Medicine (M.Katoh, S.N., S.Y., M.I., M.Katagiri, T.H., T.F., N.T., T.K., K.F., B.Z., S.H., T.Y., S.I., Z.D., M.Kubota, K.S., H.M., I.K.), The University of Tokyo, Japan
| | - Shunsuke Inoue
- Frontier Cardiovascular Science (M.Katoh, T.K., S.I., S.N., I.K.), The University of Tokyo, Japan
| | - Zhehao Dai
- Departments of Cardiovascular Medicine (M.Katoh, S.N., S.Y., M.I., M.Katagiri, T.H., T.F., N.T., T.K., K.F., B.Z., S.H., T.Y., S.I., Z.D., M.Kubota, K.S., H.M., I.K.), The University of Tokyo, Japan
| | - Masayuki Kubota
- Departments of Cardiovascular Medicine (M.Katoh, S.N., S.Y., M.I., M.Katagiri, T.H., T.F., N.T., T.K., K.F., B.Z., S.H., T.Y., S.I., Z.D., M.Kubota, K.S., H.M., I.K.), The University of Tokyo, Japan
| | - Kousuke Sawami
- Departments of Cardiovascular Medicine (M.Katoh, S.N., S.Y., M.I., M.Katagiri, T.H., T.F., N.T., T.K., K.F., B.Z., S.H., T.Y., S.I., Z.D., M.Kubota, K.S., H.M., I.K.), The University of Tokyo, Japan
| | - Minoru Ono
- Cardiothoracic Surgery (M.O.), The University of Tokyo, Japan
| | - Hiroyuki Morita
- Departments of Cardiovascular Medicine (M.Katoh, S.N., S.Y., M.I., M.Katagiri, T.H., T.F., N.T., T.K., K.F., B.Z., S.H., T.Y., S.I., Z.D., M.Kubota, K.S., H.M., I.K.), The University of Tokyo, Japan
| | - Yoshiaki Kubota
- Department of Anatomy, Keio University School of Medicine, Tokyo, Japan (Y.K.)
| | - Seiya Mizuno
- Laboratory Animal Resource Center, Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Ibaraki, Japan (S.M., S.T.)
| | - Satoru Takahashi
- Laboratory Animal Resource Center, Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Ibaraki, Japan (S.M., S.T.)
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science (M. Nakanishi), The University of Tokyo, Japan
| | - Tetsuo Ushiku
- Pathology (H. Abe, T.U.), The University of Tokyo, Japan
| | - Hironori Nakagami
- Departments of Cardiovascular Medicine (M.Katoh, S.N., S.Y., M.I., M.Katagiri, T.H., T.F., N.T., T.K., K.F., B.Z., S.H., T.Y., S.I., Z.D., M.Kubota, K.S., H.M., I.K.), The University of Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Division (M.Katoh, S.N., H. Aburatani), The University of Tokyo, Japan
| | - Issei Komuro
- Frontier Cardiovascular Science (M.Katoh, T.K., S.I., S.N., I.K.), The University of Tokyo, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Ibaraki, Japan (S.M., S.T.)
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157
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Shao W, Lin Z, Xiahou Z, Zhao F, Xu J, Liu X, Cai P. Single-cell RNA sequencing reveals that MYBL2 in malignant epithelial cells is involved in the development and progression of ovarian cancer. Front Immunol 2024; 15:1438198. [PMID: 39136009 PMCID: PMC11317301 DOI: 10.3389/fimmu.2024.1438198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Accepted: 07/12/2024] [Indexed: 08/15/2024] Open
Abstract
Background Ovarian carcinoma (OC) is a prevalent gynecological malignancy associated with high recurrence rates and mortality, often diagnosed at advanced stages. Despite advances in immunotherapy, immune exhaustion remains a significant challenge in achieving optimal tumor control. However, the exploration of intratumoral heterogeneity of malignant epithelial cells and the ovarian cancer tumor microenvironment is still limited, hindering our comprehensive understanding of the disease. Materials and methods Utilizing single-cell RNA sequencing (scRNA-seq), we comprehensively investigated the cellular composition across six ovarian cancer patients with omental metastasis. Our focus centered on analysis of the malignant epithelial cells. Employing CytoTRACE and slingshot pseudotime analyses, we identified critical subpopulations and explored associated transcription factors (TFs) influencing ovarian cancer progression. Furthermore, by integrating clinical factors from a large cohort of bulk RNA sequencing data, we have established a novel prognostic model to investigate the impact of the tumor immune microenvironment on ovarian cancer patients. Furthermore, we have investigated the condition of immunological exhaustion. Results Our study identified a distinct and highly proliferative subgroup of malignant epithelial cells, known as C2 TOP2A+ TCs. This subgroup primarily consisted of patients who hadn't received neoadjuvant chemotherapy. Ovarian cancer patients with elevated TOP2A expression exhibited heightened sensitivity to neoadjuvant chemotherapy (NACT). Moreover, the transcription factor MYBL2 in this subgroup played a critical role in ovarian cancer development. Additionally, we developed an independent prognostic indicator, the TOP2A TCs Risk Score (TTRS), which revealed a correlation between the High TTRS Group and unfavorable outcomes. Furthermore, immune infiltration and drug sensitivity analyses demonstrated increased responsiveness to Paclitaxel, Cisplatin, and Gemcitabine in the Low TTRS Group. Conclusion This research deepens our understanding of malignant epithelial cells in ovarian cancer and enhances our knowledge of the ovarian cancer immune microenvironment and immune exhaustion. We have revealed the heightened susceptibility of the C2 TOP2A+ TCs subgroup to neoadjuvant chemotherapy and emphasized the role of MYBL2 within the C2 subgroup in promoting the occurrence and progression of ovarian cancer. These insights provide valuable guidance for the management of ovarian cancer treatment.
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Affiliation(s)
- Wenwen Shao
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Zhiheng Lin
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Zhikai Xiahou
- China Institute of Sport and Health Science, Beijing Sport University, Beijing, China
| | - Fu Zhao
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Jue Xu
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Xinqi Liu
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Pingping Cai
- Department of Traditional Chinese Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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158
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Salisbury SJ, Daniels RR, Monaghan SJ, Bron JE, Villamayor PR, Gervais O, Fast MD, Sveen L, Houston RD, Robinson N, Robledo D. Keratinocytes drive the epithelial hyperplasia key to sea lice resistance in coho salmon. BMC Biol 2024; 22:160. [PMID: 39075472 PMCID: PMC11287951 DOI: 10.1186/s12915-024-01952-8] [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: 11/15/2023] [Accepted: 06/28/2024] [Indexed: 07/31/2024] Open
Abstract
BACKGROUND Salmonid species have followed markedly divergent evolutionary trajectories in their interactions with sea lice. While sea lice parasitism poses significant economic, environmental, and animal welfare challenges for Atlantic salmon (Salmo salar) aquaculture, coho salmon (Oncorhynchus kisutch) exhibit near-complete resistance to sea lice, achieved through a potent epithelial hyperplasia response leading to rapid louse detachment. The molecular mechanisms underlying these divergent responses to sea lice are unknown. RESULTS We characterized the cellular and molecular responses of Atlantic salmon and coho salmon to sea lice using single-nuclei RNA sequencing. Juvenile fish were exposed to copepodid sea lice (Lepeophtheirus salmonis), and lice-attached pelvic fin and skin samples were collected 12 h, 24 h, 36 h, 48 h, and 60 h after exposure, along with control samples. Comparative analysis of control and treatment samples revealed an immune and wound-healing response that was common to both species, but attenuated in Atlantic salmon, potentially reflecting greater sea louse immunomodulation. Our results revealed unique but complementary roles of three layers of keratinocytes in the epithelial hyperplasia response leading to rapid sea lice rejection in coho salmon. Our results suggest that basal keratinocytes direct the expansion and mobility of intermediate and, especially, superficial keratinocytes, which eventually encapsulate the parasite. CONCLUSIONS Our results highlight the key role of keratinocytes in coho salmon's sea lice resistance and the diverged biological response of the two salmonid host species when interacting with this parasite. This study has identified key pathways and candidate genes that could be manipulated using various biotechnological solutions to improve Atlantic salmon sea lice resistance.
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Affiliation(s)
- S J Salisbury
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
| | - R Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - S J Monaghan
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | - J E Bron
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | - P R Villamayor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
- Department of Genetics, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - O Gervais
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - M D Fast
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada
| | | | - R D Houston
- Benchmark Genetics, 1 Pioneer BuildingMilton Bridge, Edinburgh TechnopolePenicuik, UK
| | - N Robinson
- Nofima AS, Tromsø, Norway.
- Sustainable Aquaculture Laboratory - Temperate and Tropical (SALTT), Deakin University, Melbourne, VIC, 3225, Australia.
| | - D Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
- Department of Genetics, University of Santiago de Compostela, Santiago de Compostela, Spain.
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159
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Lin J, Bai S, He L, Yang Y, Li X, Luo L, Wang Y, Chen YY, Qin J, Zhong Y. Cytotoxic Lymphocyte-Monocyte Complex Reflects the Dynamics of Coronavirus Disease 2019 Systemic Immune Response. J Infect Dis 2024; 230:5-14. [PMID: 39052699 DOI: 10.1093/infdis/jiae048] [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: 07/16/2023] [Revised: 12/01/2023] [Accepted: 01/29/2024] [Indexed: 02/03/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes a variety of clinical manifestations, many of which originate from altered immune responses, either locally or systemically. Immune cell cross-talk occurs mainly in lymphoid organs. However, systemic cell interaction specific to coronavirus disease 2019 has not been well characterized. Here, by employing single-cell RNA sequencing and imaging flow cytometry analysis, we unraveled, in peripheral blood, a heterogeneous group of cell complexes formed by the adherence of CD14+ monocytes to different cytotoxic lymphocytes, including SARS-CoV-2-specific CD8+ T cells, γδ T cells, and natural killer T cells. These lymphocytes attached to CD14+ monocytes that showed enhanced inflammasome activation and pyroptosis-induced cell death in progression stage; in contrast, in the convalescent phase, CD14+ monocytes with elevated antigen presentation potential were targeted by cytotoxic lymphocytes, thereby restricting the excessive immune activation. Collectively, our study reports previously unrecognized cell-cell interplay in the SARS-CoV-2-specific immune response, providing new insight into the intricacy of dynamic immune cell interaction representing antiviral defense.
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Affiliation(s)
- Jiajia Lin
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine
- Shanghai Immune Therapy Institute, Renji Hospital and Baoshan Branch of Renji Hospital, Shanghai Jiao Tong University School of Medicine
| | - Shiyu Bai
- Shanghai Immune Therapy Institute, Renji Hospital and Baoshan Branch of Renji Hospital, Shanghai Jiao Tong University School of Medicine
| | - Liheng He
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine
| | - Ye Yang
- Xinhua Hospital, Shanghai Jiao Tong University School of Medicine
| | - Xiyue Li
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine
- Shanghai Immune Therapy Institute, Renji Hospital and Baoshan Branch of Renji Hospital, Shanghai Jiao Tong University School of Medicine
| | - Liulin Luo
- Department of Clinical Laboratory, Yangpu Hospital, Tongji University School of Medicine
| | - Ying Wang
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine
- Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying-Ying Chen
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine
- Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinhong Qin
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine
| | - Yi Zhong
- Shanghai Immune Therapy Institute, Renji Hospital and Baoshan Branch of Renji Hospital, Shanghai Jiao Tong University School of Medicine
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160
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Burtis AEC, DeNicola DMC, Ferguson ME, Santos RG, Pinilla C, Kriss MS, Orlicky DJ, Tamburini BAJ, Gillen AE, Burchill MA. Ag-driven CD8+ T cell clonal expansion is a prominent feature of MASH in humans and mice. Hepatology 2024:01515467-990000000-00978. [PMID: 39047085 DOI: 10.1097/hep.0000000000000971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/31/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND AND AIMS Chronic liver disease due to metabolic dysfunction-associated steatohepatitis (MASH) is a rapidly increasing global epidemic. MASH progression is a consequence of the complex interplay between inflammatory insults and dysregulated hepatic immune responses. T lymphocytes have been shown to accumulate in the liver during MASH, but the cause and consequence of T cell accumulation in the liver remain unclear. Our study aimed to define the phenotype and T cell receptor diversity of T cells from human cirrhotic livers and an animal model of MASH to begin resolving their function in disease. APPROACH AND RESULTS In these studies, we evaluated differences in T cell phenotype in the context of liver disease. Accordingly, we isolated liver resident T cell populations from humans with cirrhosis and from mice with diet-induced MASH. Using both 5' single-cell sequencing and flow cytometry, we defined the phenotype and T cell receptor repertoire of liver resident T cells during health and disease. CONCLUSIONS MASH-induced human cirrhosis and diet-induced MASH in mice resulted in the accumulation of activated and clonally expanded T cells in the liver. The clonally expanded T cells in the liver expressed markers of chronic antigenic stimulation, including PD1, TIGIT, and TOX. Overall, this study establishes for the first time that T cells undergo Ag-dependent clonal expansion and functional differentiation during the progression of MASH. These studies could lead to the identification of antigenic targets that drive T cell activation, clonal expansion, and recruitment to the liver during MASH.
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Affiliation(s)
- Abbigayl E C Burtis
- Division of Gastroenterology and Hepatology, Department of Medicine, Aurora, Colorado, USA
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Destiny M C DeNicola
- Division of Gastroenterology and Hepatology, Department of Medicine, Aurora, Colorado, USA
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Megan E Ferguson
- Division of Gastroenterology and Hepatology, Department of Medicine, Aurora, Colorado, USA
| | - Radleigh G Santos
- Department of Mathematics, Nova Southeastern University, Fort Lauderdale, Florida, USA
| | - Clemencia Pinilla
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Michael S Kriss
- Division of Gastroenterology and Hepatology, Department of Medicine, Aurora, Colorado, USA
| | - David J Orlicky
- Department of Pathology, University of Colorado Anschutz Medical Campus. Aurora, Colorado, USA
| | - Beth A Jirón Tamburini
- Division of Gastroenterology and Hepatology, Department of Medicine, Aurora, Colorado, USA
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Austin E Gillen
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus. Aurora, Colorado, USA
| | - Matthew A Burchill
- Division of Gastroenterology and Hepatology, Department of Medicine, Aurora, Colorado, USA
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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161
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Bormann D, Knoflach M, Poreba E, Riedl CJ, Testa G, Orset C, Levilly A, Cottereau A, Jauk P, Hametner S, Stranzl N, Golabi B, Copic D, Klas K, Direder M, Kühtreiber H, Salek M, Zur Nedden S, Baier-Bitterlich G, Kiechl S, Haider C, Endmayr V, Höftberger R, Ankersmit HJ, Mildner M. Single-nucleus RNA sequencing reveals glial cell type-specific responses to ischemic stroke in male rodents. Nat Commun 2024; 15:6232. [PMID: 39043661 PMCID: PMC11266704 DOI: 10.1038/s41467-024-50465-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 07/09/2024] [Indexed: 07/25/2024] Open
Abstract
Neuroglia critically shape the brain´s response to ischemic stroke. However, their phenotypic heterogeneity impedes a holistic understanding of the cellular composition of the early ischemic lesion. Here we present a single cell resolution transcriptomics dataset of the brain´s acute response to infarction. Oligodendrocyte lineage cells and astrocytes range among the most transcriptionally perturbed populations and exhibit infarction- and subtype-specific molecular signatures. Specifically, we find infarction restricted proliferating oligodendrocyte precursor cells (OPCs), mature oligodendrocytes and reactive astrocytes, exhibiting transcriptional commonalities in response to ischemic injury. OPCs and reactive astrocytes are involved in a shared immuno-glial cross talk with stroke-specific myeloid cells. Within the perilesional zone, osteopontin positive myeloid cells accumulate in close proximity to CD44+ proliferating OPCs and reactive astrocytes. In vitro, osteopontin increases the migratory capacity of OPCs. Collectively, our study highlights molecular cross talk events which might govern the cellular composition of acutely infarcted brain tissue.
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Affiliation(s)
- Daniel Bormann
- Applied Immunology Laboratory, Department of Thoracic Surgery, Medical University of Vienna, 1090, Vienna, Austria
- Aposcience AG, 1200, Vienna, Austria
| | - Michael Knoflach
- Department of Neurology, Medical University of Innsbruck, Anichstraße 35, 6020, Innsbruck, Austria
- VASCage, Centre on Clinical Stroke Research, 6020, Innsbruck, Austria
| | - Emilia Poreba
- Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria
| | - Christian J Riedl
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Giulia Testa
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Cyrille Orset
- Normandie University, UNICAEN, ESR3P, INSERM UMR-S U1237, Physiopathology and Imaging of Neurological Disorders (PhIND), Institut Blood and Brain @ Caen-Normandie (BB@C), GIP Cyceron, Caen, France
- Department of Clinical Research, Caen-Normandie University Hospital, Caen, France
| | - Anthony Levilly
- Normandie University, UNICAEN, ESR3P, INSERM UMR-S U1237, Physiopathology and Imaging of Neurological Disorders (PhIND), Institut Blood and Brain @ Caen-Normandie (BB@C), GIP Cyceron, Caen, France
- Department of Clinical Research, Caen-Normandie University Hospital, Caen, France
| | - Andréa Cottereau
- Normandie University, UNICAEN, ESR3P, INSERM UMR-S U1237, Physiopathology and Imaging of Neurological Disorders (PhIND), Institut Blood and Brain @ Caen-Normandie (BB@C), GIP Cyceron, Caen, France
- Department of Clinical Research, Caen-Normandie University Hospital, Caen, France
| | - Philipp Jauk
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, 1090, Vienna, Austria
| | - Simon Hametner
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Nadine Stranzl
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Bahar Golabi
- Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria
| | - Dragan Copic
- Applied Immunology Laboratory, Department of Thoracic Surgery, Medical University of Vienna, 1090, Vienna, Austria
- Aposcience AG, 1200, Vienna, Austria
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, 1090, Vienna, Austria
| | - Katharina Klas
- Applied Immunology Laboratory, Department of Thoracic Surgery, Medical University of Vienna, 1090, Vienna, Austria
- Aposcience AG, 1200, Vienna, Austria
| | - Martin Direder
- Applied Immunology Laboratory, Department of Thoracic Surgery, Medical University of Vienna, 1090, Vienna, Austria
- Aposcience AG, 1200, Vienna, Austria
- Department of Orthopedics and Trauma Surgery, Medical University of Vienna, 1090, Vienna, Austria
| | - Hannes Kühtreiber
- Applied Immunology Laboratory, Department of Thoracic Surgery, Medical University of Vienna, 1090, Vienna, Austria
- Aposcience AG, 1200, Vienna, Austria
| | - Melanie Salek
- Applied Immunology Laboratory, Department of Thoracic Surgery, Medical University of Vienna, 1090, Vienna, Austria
- Aposcience AG, 1200, Vienna, Austria
| | - Stephanie Zur Nedden
- Institute of Neurobiochemistry, CCB-Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Gabriele Baier-Bitterlich
- Institute of Neurobiochemistry, CCB-Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Stefan Kiechl
- Department of Neurology, Medical University of Innsbruck, Anichstraße 35, 6020, Innsbruck, Austria
- VASCage, Centre on Clinical Stroke Research, 6020, Innsbruck, Austria
| | - Carmen Haider
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Verena Endmayr
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Romana Höftberger
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Hendrik J Ankersmit
- Applied Immunology Laboratory, Department of Thoracic Surgery, Medical University of Vienna, 1090, Vienna, Austria.
- Aposcience AG, 1200, Vienna, Austria.
| | - Michael Mildner
- Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria.
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162
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Zhao J, Shen F, Hu YM, Yin K, Chen Y, Chen YJ, Hu QC, Liang L. Prognostic value and microenvironmental crosstalk of exosome-related signatures in human epidermal growth factor receptor 2 positive breast cancer. Open Life Sci 2024; 19:20220899. [PMID: 39071494 PMCID: PMC11282918 DOI: 10.1515/biol-2022-0899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 07/30/2024] Open
Abstract
This study aimed to determine the prognostic value and microenvironmental crosstalk of exosome-related signatures in human epidermal growth factor receptor 2 positive breast cancer (HER2+ BC). Transcriptome sequencing and clinicopathological data were downloaded from the Cancer Genome Atlas. The 10X single cell sequencing dataset was downloaded from the National Center for Biotechnology Information Gene Expression Omnibus. Exosomes-Related Genes were extracted from the ExoCarta and Gene Set Enrichment Analysis databases. FGF9, SF3B4, and EPCAM were found and deemed the most accurate predictive signatures. Patients with HER2+ BC were subtyped into three groupings by exosome prognostic gene (EPGs). The expression of SF3B4 was positively linked with the infiltration of macrophages, neutrophils, and CD4+ T cells. The expression characteristics of EPGs were associated with the biological process of "response to xenobiotic stimuli." Interactions were relatively high between malignant epithelial cells and fibroblasts, endothelial cells, monocytes, and macrophages. Malignant epithelial cells interact more with fibroblasts and endothelial cells. The migration inhibitory factor pathway was the primary outgoing signaling pattern, while the C-C motif chemokine ligand pathway was the primary incoming signaling pattern for communication between malignant epithelial cells and macrophages. This study described the role of exosome signatures in the prognosis and microenvironment of HER2+ BC and provided a basis for future research.
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Affiliation(s)
- Ji Zhao
- Department of Breast Surgery, Tong Ren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, People’s Republic of China
| | - Feng Shen
- Department of Medical Oncology, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, 361015, People’s Republic of China
| | - Yue-Mei Hu
- Department of Pathology, Tong Ren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, People’s Republic of China
| | - Kai Yin
- Department of Breast Surgery, Tong Ren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, People’s Republic of China
| | - Ying Chen
- Department of Radiation Oncology, Tong Ren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 Xianxia Road, Changning District, Shanghai, 200336, People’s Republic of China
| | - Yan-Jie Chen
- Department of Gastroenterology, Zhongshan Hospital (Xiamen), Fudan University, No. 668, Jinhu Road, Huli District, Xiamen, 361015, People’s Republic of China
- Department of Gastroenterology, Zhongshan Hospital of Fudan University, 180 Fenglin Road, Xuhui District, Shanghai200032, People’s Republic of China
| | - Qun-Chao Hu
- Department of Radiation Oncology, Tong Ren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 Xianxia Road, Changning District, Shanghai, 200336, People’s Republic of China
| | - Li Liang
- Department of Medical Oncology, Zhongshan Hospital Fudan University, No. 180, Fenglin Road, Xuhui District, Shanghai, 200032, People’s Republic of China
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163
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Fazzari E, Azizad DJ, Yu K, Ge W, Li MX, Nano PR, Kan RL, Tum HA, Tse C, Bayley NA, Haka V, Cadet D, Perryman T, Soto JA, Wick B, Raleigh DR, Crouch EE, Patel KS, Liau LM, Deneen B, Nathanson DA, Bhaduri A. Glioblastoma Neurovascular Progenitor Orchestrates Tumor Cell Type Diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.24.604840. [PMID: 39091877 PMCID: PMC11291138 DOI: 10.1101/2024.07.24.604840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Glioblastoma (GBM) is the deadliest form of primary brain tumor with limited treatment options. Recent studies have profiled GBM tumor heterogeneity, revealing numerous axes of variation that explain the molecular and spatial features of the tumor. Here, we seek to bridge descriptive characterization of GBM cell type heterogeneity with the functional role of individual populations within the tumor. Our lens leverages a gene program-centric meta-atlas of published transcriptomic studies to identify commonalities between diverse tumors and cell types in order to decipher the mechanisms that drive them. This approach led to the discovery of a tumor-derived stem cell population with mixed vascular and neural stem cell features, termed a neurovascular progenitor (NVP). Following in situ validation and molecular characterization of NVP cells in GBM patient samples, we characterized their function in vivo. Genetic depletion of NVP cells resulted in altered tumor cell composition, fewer cycling cells, and extended survival, underscoring their critical functional role. Clonal analysis of primary patient tumors in a human organoid tumor transplantation system demonstrated that the NVP has dual potency, generating both neuronal and vascular tumor cells. Although NVP cells comprise a small fraction of the tumor, these clonal analyses demonstrated that they strongly contribute to the total number of cycling cells in the tumor and generate a defined subset of the whole tumor. This study represents a paradigm by which cell type-specific interrogation of tumor populations can be used to study functional heterogeneity and therapeutically targetable vulnerabilities of GBM.
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Affiliation(s)
- Elisa Fazzari
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Daria J Azizad
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Kwanha Yu
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Weihong Ge
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Matthew X Li
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Patricia R Nano
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Ryan L Kan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Hong A Tum
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Christopher Tse
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nicholas A Bayley
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Vjola Haka
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Dimitri Cadet
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Travis Perryman
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Jose A Soto
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Brittney Wick
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - David R Raleigh
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
- Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - Elizabeth E Crouch
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Kunal S Patel
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Linda M Liau
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Benjamin Deneen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - David A Nathanson
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Aparna Bhaduri
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
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164
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Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2561-0. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
Abstract
Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome, proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field, offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.
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Affiliation(s)
- Fengying Sun
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Haoyan Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dongqing Sun
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaliu Fu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Lei Gu
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China
| | - Qinqin Wang
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Dong
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Bin Duan
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Feiyang Xing
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Minmin Xiao
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China.
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Chen Li
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Tieliu Shi
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, 200062, China.
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165
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Ke BJ, Abdurahiman S, Biscu F, Zanella G, Dragoni G, Santhosh S, De Simone V, Zouzaf A, van Baarle L, Stakenborg M, Bosáková V, Van Rymenant Y, Verhulst E, Verstockt S, Klein E, Bislenghi G, Wolthuis A, Frič J, Breynaert C, D’Hoore A, Van der Veken P, De Meester I, Lovisa S, Hawinkels LJ, Verstockt B, De Hertogh G, Vermeire S, Matteoli G. Intercellular interaction between FAP+ fibroblasts and CD150+ inflammatory monocytes mediates fibrostenosis in Crohn's disease. J Clin Invest 2024; 134:e173835. [PMID: 39042469 PMCID: PMC11324301 DOI: 10.1172/jci173835] [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: 07/24/2023] [Accepted: 06/14/2024] [Indexed: 07/25/2024] Open
Abstract
Crohn's disease (CD) is marked by recurring intestinal inflammation and tissue injury, often resulting in fibrostenosis and bowel obstruction, necessitating surgical intervention with high recurrence rates. To elucidate the mechanisms underlying fibrostenosis in CD, we analyzed the transcriptome of cells isolated from the transmural ileum of patients with CD, including a trio of lesions from each patient: non-affected, inflamed, and stenotic ileum samples, and compared them with samples from patients without CD. Our computational analysis revealed that profibrotic signals from a subset of monocyte-derived cells expressing CD150 induced a disease-specific fibroblast population, resulting in chronic inflammation and tissue fibrosis. The transcription factor TWIST1 was identified as a key modulator of fibroblast activation and extracellular matrix (ECM) deposition. Genetic and pharmacological inhibition of TWIST1 prevents fibroblast activation, reducing ECM production and collagen deposition. Our findings suggest that the myeloid-stromal axis may offer a promising therapeutic target to prevent fibrostenosis in CD.
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Affiliation(s)
- Bo-Jun Ke
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Saeed Abdurahiman
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Francesca Biscu
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Gaia Zanella
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Gabriele Dragoni
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Gastroenterology Research Unit, Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Sneha Santhosh
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Veronica De Simone
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Anissa Zouzaf
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Lies van Baarle
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Michelle Stakenborg
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Veronika Bosáková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Brno, Czech Republic
| | - Yentl Van Rymenant
- Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Emile Verhulst
- Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sare Verstockt
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Elliott Klein
- Department of Immunology and Respiratory Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut, USA
| | - Gabriele Bislenghi
- Department of Abdominal Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Albert Wolthuis
- Department of Abdominal Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Jan Frič
- International Clinical Research Center, St. Anne’s University Hospital Brno, Brno, Czech Republic
- International Clinical Research Center, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Christine Breynaert
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Andre D’Hoore
- Department of Abdominal Surgery, University Hospitals Leuven, Leuven, Belgium
| | | | - Ingrid De Meester
- Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sara Lovisa
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Lukas J.A.C. Hawinkels
- Department of Gastroenterology-Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Bram Verstockt
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Gert De Hertogh
- Laboratory of Pathology, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Séverine Vermeire
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Gianluca Matteoli
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium
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166
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Van Drunen R, Dai Y, Wei H, Fekry B, Noori S, Shivshankar S, Bravo R, Zhao Z, Yoo SH, Justice N, Wu JQ, Tong Q, Eckel-Mahan K. Cell-specific regulation of the circadian clock by BMAL1 in the paraventricular nucleus: Implications for regulation of systemic biological rhythms. Cell Rep 2024; 43:114380. [PMID: 38935503 PMCID: PMC11446153 DOI: 10.1016/j.celrep.2024.114380] [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: 09/23/2023] [Revised: 03/28/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024] Open
Abstract
Circadian rhythms are internal biological rhythms driving temporal tissue-specific, metabolic programs. Loss of the circadian transcription factor BMAL1 in the paraventricular nucleus (PVN) of the hypothalamus reveals its importance in metabolic rhythms, but its functions in individual PVN cells are poorly understood. Here, loss of BMAL1 in the PVN results in arrhythmicity of processes controlling energy balance and alters peripheral diurnal gene expression. BMAL1 chromatin immunoprecipitation sequencing (ChIP-seq) and single-nucleus RNA sequencing (snRNA-seq) reveal its temporal regulation of target genes, including oxytocin (OXT), and restoring circulating OXT peaks in BMAL1-PVN knockout (KO) mice rescues absent activity rhythms. While glutamatergic neurons undergo day/night changes in expression of genes involved in cell morphogenesis, astrocytes and oligodendrocytes show gene expression changes in cytoskeletal organization and oxidative phosphorylation. Collectively, our findings show diurnal gene regulation in neuronal and non-neuronal PVN cells and that BMAL1 contributes to diurnal OXT secretion, which is important for systemic diurnal rhythms.
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Affiliation(s)
- Rachel Van Drunen
- UT Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; MD Anderson Cancer Center/UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Yulin Dai
- Center for Precision Health, McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Haichao Wei
- UT Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Neurosurgery, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Baharan Fekry
- UT Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Sina Noori
- UT Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Samay Shivshankar
- UT Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Rafael Bravo
- UT Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Seung-Hee Yoo
- MD Anderson Cancer Center/UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Biochemistry and Cell Biology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Nicholas Justice
- UT Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; MD Anderson Cancer Center/UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jia Qian Wu
- UT Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; MD Anderson Cancer Center/UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Neurosurgery, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Qingchun Tong
- UT Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; MD Anderson Cancer Center/UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Kristin Eckel-Mahan
- UT Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; MD Anderson Cancer Center/UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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167
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Qian C, Yang Q, Rotinen M, Huang R, Kim H, Gallent B, Yan Y, Cadaneanu R, Zhang B, Kaochar S, Freedland S, Posadas E, Ellis L, Di Vizio D, Morrissey C, Nelson P, Brady L, Murali R, Campbell M, Yang W, Knudsen B, Mostaghel E, Ye H, Garraway I, You S, Freeman M. ONECUT2 acts as a lineage plasticity driver in adenocarcinoma as well as neuroendocrine variants of prostate cancer. Nucleic Acids Res 2024; 52:7740-7760. [PMID: 38932701 PMCID: PMC11260453 DOI: 10.1093/nar/gkae547] [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: 02/02/2024] [Revised: 06/06/2024] [Accepted: 06/26/2024] [Indexed: 06/28/2024] Open
Abstract
Androgen receptor- (AR-) indifference is a mechanism of resistance to hormonal therapy in prostate cancer (PC). Here we demonstrate that ONECUT2 (OC2) activates resistance through multiple drivers associated with adenocarcinoma, stem-like and neuroendocrine (NE) variants. Direct OC2 gene targets include the glucocorticoid receptor (GR; NR3C1) and the NE splicing factor SRRM4, which are key drivers of lineage plasticity. Thus, OC2, despite its previously described NEPC driver function, can indirectly activate a portion of the AR cistrome through epigenetic activation of GR. Mechanisms by which OC2 regulates gene expression include promoter binding, enhancement of genome-wide chromatin accessibility, and super-enhancer reprogramming. Pharmacologic inhibition of OC2 suppresses lineage plasticity reprogramming induced by the AR signaling inhibitor enzalutamide. These results demonstrate that OC2 activation promotes a range of drug resistance mechanisms associated with treatment-emergent lineage variation in PC and support enhanced efforts to therapeutically target OC2 as a means of suppressing treatment-resistant disease.
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Affiliation(s)
- Chen Qian
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Qian Yang
- Departments of Urology and Computational Biomedicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mirja Rotinen
- Department of Health Sciences, Public University of Navarre, Pamplona, Navarra, Spain
| | - Rongrong Huang
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Hyoyoung Kim
- Departments of Urology and Computational Biomedicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Brad Gallent
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Medical Oncology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yiwu Yan
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Radu M Cadaneanu
- Department of Surgical and Perioperative Care, VA Greater Los Angeles; Department of Urology and Jonsson Comprehensive Cancer Center, the David Geffen School of Medicine, UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA 90095, USA
| | - Baohui Zhang
- Department of Surgical and Perioperative Care, VA Greater Los Angeles; Department of Urology and Jonsson Comprehensive Cancer Center, the David Geffen School of Medicine, UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA 90095, USA
| | - Salma Kaochar
- Department of Medicine Section Hematology/Oncology Baylor College of Medicine, Houston, 77030 TX, USA
| | - Stephen J Freedland
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Edwin M Posadas
- Division of Medical Oncology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Leigh Ellis
- Center for Prostate Disease Research, Mutha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and the Walter Reed National Military Medical Center; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20814, USA
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Dolores Di Vizio
- Departments of Urology, Pathology and Laboratory Medicine, and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Lauren Brady
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Ramachandran Murali
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Moray J Campbell
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Wei Yang
- Department of Pathology and Cancer Center, Stony Brook University, NY 11794, USA
| | - Beatrice S Knudsen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84108, USA
- Department of Pathology, University of Utah, Salt Lake City, UT 84108, USA
| | - Elahe A Mostaghel
- Geriatric Research, Education and Clinical Center (GRECC), U.S. Department of Veterans Affairs Puget Sound Health Care System, Seattle, WA 98133, USA
| | - Huihui Ye
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Isla P Garraway
- Department of Surgical and Perioperative Care, VA Greater Los Angeles; Department of Urology and Jonsson Comprehensive Cancer Center, the David Geffen School of Medicine, UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA 90095, USA
| | - Sungyong You
- Departments of Urology and Computational Biomedicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Michael R Freeman
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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Hong X, Zhang X, Jiang R, Qiao S, Wang W, Zhang H, Wang J, Yin B, Li F, Ling C, Wang X, Zhao Y, Wu K, Wu W. A cross-species transcriptomic analysis reveals a novel 2-dimensional classification system explaining the invasiveness heterogeneity of pancreatic neuroendocrine tumor. Cancer Lett 2024:217131. [PMID: 39048044 DOI: 10.1016/j.canlet.2024.217131] [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: 04/16/2024] [Revised: 07/02/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024]
Abstract
Pancreatic neuroendocrine tumors (PanNETs), the second most common type of primary pancreatic tumors, display notable heterogeneity in invasiveness. Current knowledge regarding genomic alterations, including DAXX/ATRX, MEN1 mutations, and copy number variations (CNVs), provides some insights into tumor invasiveness. However, the underlying reasons for the significant variation in invasiveness between insulinoma and other types of PanNETs remain unclear. To construct a comprehensive model for the stratification of prognosis, we employed analysis of both the well-established Rip1-Tag2 (RT2) mouse model of PanNETs and human PanNETs with various functional types. Firstly, by applying single-cell and bulk RNA sequencing in PanNETs from different ages and strains of RT2 mice and human PanNETs, we introduced a 2-dimensional (2D) classification system. Based on the 2-D classification system, human PanNETs were mainly classified as benign insulinomas or non-insulinomas subclusters. Non-insulinomas subtypes mainly included gastrinomas, glucagonomas, VIPomas, and NF-PanNETs, which all exhibited potential invasiveness. In addition, we discovered an enrichment of specific CNV patterns and mutations in corresponding human PanNET subclusters. Then we denoted somatic DAXX/ATRX as the 'second hit' and confounding factors for invasiveness. Finally, by combining the 2D system, DAXX/ATRX mutation status, and tumor diameter, a group of indolent PanNETs with minimal recurrence risk was identified. In conclusion, our current work constructed a comprehensive model to elucidate the heterogeneity of invasiveness in PanNETs and improve prognostic stratification.
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Affiliation(s)
- Xiafei Hong
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Xingwu Zhang
- Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China; School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Rui Jiang
- Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China; Department of General Surgery, Xuanwu hospital capital medical university, Beijing, 100053, China
| | - Sitan Qiao
- BGI-Shenzhen, Shenzhen 518083, China; The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China
| | - Wenze Wang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Hao Zhang
- Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China
| | - Jingqiao Wang
- Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China
| | - Bohui Yin
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | | | - Chao Ling
- The Laboratory of Clinical Genetics, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences& Peking Union Medical, Beijing, 100730, China; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Xianze Wang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Yupei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
| | - Kui Wu
- BGI-Shenzhen, Shenzhen 518083, China.
| | - Wenming Wu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
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169
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McDermott JG, Goodlett BL, Creed HA, Navaneethabalakrishnan S, Rutkowski JM, Mitchell BM. Inflammatory Alterations to Renal Lymphatic Endothelial Cell Gene Expression in Mouse Models of Hypertension. Kidney Blood Press Res 2024; 49:588-604. [PMID: 38972305 PMCID: PMC11345939 DOI: 10.1159/000539721] [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: 10/16/2023] [Accepted: 06/02/2024] [Indexed: 07/09/2024] Open
Abstract
INTRODUCTION Hypertension (HTN) is a major cardiovascular disease that can cause and be worsened by renal damage and inflammation. We previously reported that renal lymphatic endothelial cells (LECs) increase in response to HTN and that augmenting lymphangiogenesis in the kidneys reduces blood pressure and renal pro-inflammatory immune cells in mice with various forms of HTN. Our aim was to evaluate the specific changes that renal LECs undergo in HTN. METHODS We performed single-cell RNA sequencing. Using the angiotensin II-induced and salt-sensitive mouse models of HTN, we isolated renal CD31+ and podoplanin+ cells. RESULTS Sequencing of these cells revealed three distinct cell types with unique expression profiles, including LECs. The number and transcriptional diversity of LECs increased in samples from mice with HTN, as demonstrated by 597 differentially expressed genes (p < 0.01), 274 significantly enriched pathways (p < 0.01), and 331 regulons with specific enrichment in HTN LECs. These changes demonstrate a profound inflammatory response in renal LECs in HTN, leading to an increase in genes and pathways associated with inflammation-driven growth and immune checkpoint activity in LECs. CONCLUSION These results reinforce and help to further explain the benefits of renal LECs and lymphangiogenesis in HTN.
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Affiliation(s)
- Justin G. McDermott
- Department of Medical Physiology, Texas A&M University School of Medicine, Bryan, TX 77807
| | - Bethany L. Goodlett
- Department of Medical Physiology, Texas A&M University School of Medicine, Bryan, TX 77807
| | - Heidi A. Creed
- Department of Medical Physiology, Texas A&M University School of Medicine, Bryan, TX 77807
| | | | - Joseph M. Rutkowski
- Department of Medical Physiology, Texas A&M University School of Medicine, Bryan, TX 77807
| | - Brett M. Mitchell
- Department of Medical Physiology, Texas A&M University School of Medicine, Bryan, TX 77807
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170
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Li W, Pan L, Hong W, Ginhoux F, Zhang X, Xiao C, Li X. A single-cell pan-cancer analysis to show the variability of tumor-infiltrating myeloid cells in immune checkpoint blockade. Nat Commun 2024; 15:6142. [PMID: 39034339 PMCID: PMC11271490 DOI: 10.1038/s41467-024-50478-8] [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: 12/03/2023] [Accepted: 07/12/2024] [Indexed: 07/23/2024] Open
Abstract
Myeloid cells are vital components of the immune system and have pivotal functions in orchestrating immune responses. Understanding their functions within the tumor microenvironment and their interactions with tumor-infiltrating lymphocytes presents formidable challenges across diverse cancer types, particularly with regards to cancer immunotherapies. Here, we explore tumor-infiltrating myeloid cells (TIMs) by conducting a pan-cancer analysis using single-cell transcriptomics across eight distinct cancer types, encompassing a total of 192 tumor samples from 129 patients. By examining gene expression patterns and transcriptional activities of TIMs in different cancer types, we discern notable alterations in abundance of TIMs and kinetic behaviors prior to and following immunotherapy. We also identify specific cell-cell interaction targets in immunotherapy; unique and shared regulatory profiles critical for treatment response; and TIMs associated with survival outcomes. Overall, our study illuminates the heterogeneity of TIMs and improves our understanding of tissue-specific and cancer-specific myeloid subsets within the context of tumor immunotherapies.
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Affiliation(s)
- Weiyuan Li
- School of Medicine, Yunnan University, Kunming, Yunnan, 650091, China
- Department of Reproductive Medicine, The First People's Hospital of Yunnan Province, Kunming, Yunnan, 650032, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, 650031, China
| | - Lu Pan
- Institute of Environmental Medicine, Karolinska Institutet, Solna, 171 65, Sweden
| | - Weifeng Hong
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou, 310005, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310005, China
- Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, 310005, China
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore
- Institut Gustave Roussy, INSERM U1015, Bâtiment de Médecine Moléculaire 114 rue Edouard Vaillant, 94800, Villejuif, France
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xuan Zhang
- Department of Colorectal Surgery, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Chunjie Xiao
- School of Medicine, Yunnan University, Kunming, Yunnan, 650091, China.
| | - Xuexin Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China.
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, Liaoning, China.
- Institute of Health Sciences, China Medical University, Shenyang, 110122, Liaoning, China.
- Department of Physiology and Pharmacology, Karolinska Institute, Solna, 171 65, Sweden.
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171
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Anderson AN, Conley P, Klocke CD, Sengupta SK, Pang A, Farley HC, Gillingham AR, Dawson AD, Fan Y, Jones JA, Gibbs SL, Skalet AH, Wu G, Wong MH. Detection of neoplastic-immune hybrid cells with metastatic properties in uveal melanoma. Biomark Res 2024; 12:67. [PMID: 39030653 PMCID: PMC11264923 DOI: 10.1186/s40364-024-00609-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/18/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND Uveal melanoma is the most common non-cutaneous melanoma and is an intraocular malignancy affecting nearly 7,000 individuals per year worldwide. Of these, approximately 50% will progress to metastatic disease for which there are currently no effective curative therapies. Despite advances in molecular profiling and metastatic stratification of uveal melanoma tumors, little is known regarding their underlying biology of metastasis. Our group has identified a disseminated neoplastic cell population characterized by co-expression of immune and melanoma proteins, circulating hybrid cells (hybrids), in patients with uveal melanoma. Compared to circulating tumor cells, which lack expression of immune proteins, hybrids are detected at an increased prevalence in peripheral blood and can be used as a non-invasive biomarker to predict metastatic progression. METHODS To ascertain mechanisms underlying enhanced hybrid cell dissemination we identified hybrid cells within primary uveal melanoma tumors using single cell RNA sequencing (n = 8) and evaluated their gene expression and predicted ligand-receptor interactions in relation to other melanoma and immune cells within the primary tumor. We then verified expression of upregulated hybrid pathways within patient-matched tumor and peripheral blood hybrids (n = 4) using cyclic immunofluorescence and quantified their protein expression relative to other non-hybrid tumor and disseminated tumor cells. RESULTS Among the top upregulated genes and pathways in hybrid cells were those involved in enhanced cell motility and cytoskeletal rearrangement, immune evasion, and altered cellular metabolism. In patient-matched tumor and peripheral blood, we verified gene expression by examining concordant protein expression for each pathway category: TMSB10 (cell motility), CD74 (immune evasion) and GPX1 (metabolism). Both TMSB10 and GPX1 were expressed on significantly higher numbers of disseminated hybrid cells compared to circulating tumor cells, and CD74 and GPX1 were expressed on more disseminated hybrids than tumor-resident hybrids. Lastly, we identified that hybrid cells express ligand-receptor signaling pathways implicated in promoting metastasis including GAS6-AXL, CXCL12-CXCR4, LGALS9-P4HB and IGF1-IGFR1. CONCLUSION These findings highlight the importance of TMSB10, GPX1 and CD74 for successful hybrid cell dissemination and survival in circulation. Our results contribute to the understanding of uveal melanoma tumor progression and interactions between tumor cells and immune cells in the tumor microenvironment that may promote metastasis.
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Affiliation(s)
- Ashley N Anderson
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University (OHSU), Portland, OR, USA
| | - Patrick Conley
- Department of Medical Informatics and Clinical Epidemiology, OHSU, Portland, OR, USA
| | - Christopher D Klocke
- Department of Medical Informatics and Clinical Epidemiology, OHSU, Portland, OR, USA
| | - Sidharth K Sengupta
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University (OHSU), Portland, OR, USA
| | - Amara Pang
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University (OHSU), Portland, OR, USA
| | - Hannah C Farley
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University (OHSU), Portland, OR, USA
- Department of Biomedical Engineering, OHSU, Portland, OR, USA
| | - Abigail R Gillingham
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University (OHSU), Portland, OR, USA
| | - Aubrey D Dawson
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University (OHSU), Portland, OR, USA
| | - Yichen Fan
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University (OHSU), Portland, OR, USA
| | - Jocelyn A Jones
- Department of Biomedical Engineering, OHSU, Portland, OR, USA
| | - Summer L Gibbs
- Department of Biomedical Engineering, OHSU, Portland, OR, USA
- Knight Cancer Institute, OHSU, Portland, OR, USA
| | - Alison H Skalet
- Casey Eye Institute, OHSU, Portland, OR, USA
- Knight Cancer Institute, OHSU, Portland, OR, USA
| | - Guanming Wu
- Department of Medical Informatics and Clinical Epidemiology, OHSU, Portland, OR, USA
- Knight Cancer Institute, OHSU, Portland, OR, USA
| | - Melissa H Wong
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University (OHSU), Portland, OR, USA.
- Knight Cancer Institute, OHSU, Portland, OR, USA.
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172
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Zheng X, Wu W, Zhao Z, Zhang X, Yu S. Single-cell transcriptomic insights into chemotherapy-induced remodeling of the osteosarcoma tumor microenvironment. J Cancer Res Clin Oncol 2024; 150:356. [PMID: 39033089 PMCID: PMC11271355 DOI: 10.1007/s00432-024-05787-2] [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: 03/22/2024] [Accepted: 05/07/2024] [Indexed: 07/23/2024]
Abstract
PURPOSE Neoadjuvant chemotherapy serves as an effective strategy for treating osteosarcoma (OS) not only by targeting cancerous cells but also by influencing the tumor's immune and stromal elements. Gaining insights into how chemotherapy reshapes the tumor's local environment is crucial for advancing OS treatment protocols. METHODS Using single-cell RNA sequencing, this study analyzed tumor samples from patients with advanced osteosarcoma collected both before and after chemotherapy. RESULTS The results revealed that chemotherapy caused the remaining OS cells to express higher levels of genes associated with stemness. Additionally, this process enhances the presence of cancer-associated fibroblasts, increasing their ability to modify the extracellular matrix (ECM). Chemotherapy also increases the number of endothelial cells, albeit with compromised differentiation capabilities. Importantly, the treatment reduced the immune cell population, including myeloid and T/NK cells, particularly impacting the subpopulations with tumor-fighting capabilities. CONCLUSION These findings highlight the complex reaction of the tumor environment to chemotherapy, providing valuable insights into how chemotherapy influences OS cells and the tumor microenvironment (TME). This knowledge is essential for understanding OS resistance mechanisms to treatments, potentially guiding the development of novel therapies for managing advanced OS.
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Affiliation(s)
- Xuejing Zheng
- Departments of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Nanli, Panjiayuan, Chaoyang District, Beijing, 100021, China
| | - Wence Wu
- Department of Orthopedics, Peking University First Hospital, Beijing, 100021, China
| | - Zhenguo Zhao
- Departments of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Nanli, Panjiayuan, Chaoyang District, Beijing, 100021, China
| | - Xinxin Zhang
- Departments of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Nanli, Panjiayuan, Chaoyang District, Beijing, 100021, China
| | - Shengji Yu
- Departments of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Nanli, Panjiayuan, Chaoyang District, Beijing, 100021, China.
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173
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Hu Q, Zhang B, Jing Y, Ma S, Hu L, Li J, Zheng Y, Xin Z, Peng J, Wang S, Cheng B, Qu J, Zhang W, Liu GH, Wang S. Single-nucleus transcriptomics uncovers a geroprotective role of YAP in primate gingival aging. Protein Cell 2024; 15:612-632. [PMID: 38577810 PMCID: PMC11259548 DOI: 10.1093/procel/pwae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 02/01/2024] [Indexed: 04/06/2024] Open
Abstract
Aging has a profound impact on the gingiva and significantly increases its susceptibility to periodontitis, a worldwide prevalent inflammatory disease. However, a systematic characterization and comprehensive understanding of the regulatory mechanism underlying gingival aging is still lacking. Here, we systematically dissected the phenotypic characteristics of gingiva during aging in primates and constructed the first single-nucleus transcriptomic landscape of gingival aging, by which a panel of cell type-specific signatures were elucidated. Epithelial cells were identified as the most affected cell types by aging in the gingiva. Further analyses pinpointed the crucial role of YAP in epithelial self-renew and homeostasis, which declined during aging in epithelial cells, especially in basal cells. The decline of YAP activity during aging was confirmed in the human gingival tissues, and downregulation of YAP in human primary gingival keratinocytes recapitulated the major phenotypic defects observed in the aged primate gingiva while overexpression of YAP showed rejuvenation effects. Our work provides an in-depth understanding of gingival aging and serves as a rich resource for developing novel strategies to combat aging-associated gingival diseases, with the ultimate goal of advancing periodontal health and promoting healthy aging.
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Affiliation(s)
- Qinchao Hu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510060, China
| | - Bin Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaobin Jing
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- International Center for Aging and Cancer, Hainan Medical University, Haikou 571199, China
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Lei Hu
- Salivary Gland Disease Center and Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Laboratory of Oral Health and Beijing Stomatological Hospital, Capital Medical University, Beijing 100050, China
| | - Jingyi Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Yandong Zheng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zijuan Xin
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Jianmin Peng
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510060, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuan Wu Hospital, Capital Medical University, Beijing 100053, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Bin Cheng
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510060, China
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuan Wu Hospital, Capital Medical University, Beijing 100053, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Songlin Wang
- Salivary Gland Disease Center and Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Laboratory of Oral Health and Beijing Stomatological Hospital, Capital Medical University, Beijing 100050, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
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Brown ME, Thirawatananond P, Peters LD, Kern EJ, Vijay S, Sachs LK, Posgai AL, Brusko MA, Shapiro MR, Mathews CE, Bacher R, Brusko TM. Inhibition of CD226 Co-Stimulation Suppresses Diabetes Development in the NOD Mouse by Augmenting Tregs and Diminishing Effector T Cell Function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603756. [PMID: 39071293 PMCID: PMC11275941 DOI: 10.1101/2024.07.16.603756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Aims/hypothesis Immunotherapeutics targeting T cells are crucial for inhibiting autoimmune disease progression proximal to disease onset in type 1 diabetes. A growing number of T cell-directed therapeutics have demonstrated partial therapeutic efficacy, with anti-CD3 (α-CD3) representing the only regulatory agency-approved drug capable of slowing disease progression through a mechanism involving the induction of partial T cell exhaustion. There is an outstanding need to augment the durability and effectiveness of T cell targeting by directly restraining proinflammatory T helper type 1 (Th1) and type 1 cytotoxic CD8 + T cell (Tc1) subsets, while simultaneously augmenting regulatory T cell (Treg) activity. Here, we present a novel strategy for reducing diabetes incidence in the NOD mouse model using a blocking monoclonal antibody targeting the type 1 diabetes-risk associated T cell co-stimulatory receptor, CD226. Methods Female NOD mice were treated with anti-CD226 between 7-8 weeks of age and then monitored for diabetes incidence and therapeutic mechanism of action. Results Compared to isotype-treated controls, anti-CD226 treated NOD mice showed reduced insulitis severity at 12 weeks and decreased disease incidence at 30 weeks. Flow cytometric analysis performed five weeks post-treatment demonstrated reduced proliferation of CD4 + and CD8 + effector memory T cells in spleens of anti-CD226 treated mice. Phenotyping of pancreatic Tregs revealed increased CD25 expression and STAT5 phosphorylation following anti-CD226, with splenic Tregs displaying augmented suppression of CD4 + T cell responders in vitro. Anti-CD226 treated mice exhibited reduced frequencies of islet-specific glucose-6-phosphatase catalytic subunit related protein (IGRP)-reactive CD8 + T cells in the pancreas, using both ex vivo tetramer staining and single-cell T cell receptor sequencing (scTCR-seq) approaches. 51 Cr-release assays demonstrated reduced cell-mediated lysis of beta-cells by anti-CD226-treated autoreactive cytotoxic T lymphocytes. Conclusions/interpretation CD226 blockade reduces T cell cytotoxicity and improves Treg function, representing a targeted and rational approach for restoring immune regulation in type 1 diabetes. Research in Context What is already known about this subject?: The co-stimulatory receptor CD226 is upregulated upon activation and is highly expressed on NK cell subsets, myeloid cells, and effector T cells. A single nucleotide polymorphism in CD226 ( rs763361 ; C>T) results in a Gly307Ser missense mutation linked to genetic susceptibility for type 1 diabetes. Global knockout of Cd226 and conditional Cd226 knockout in FoxP3 + Tregs reduced insulitis severity and diabetes incidence in NOD mice, indicating a crucial role for CD226 in disease pathogenesis. What is the key question?: Can CD226 blockade reduce T cell cytotoxicity and improve Treg function to diminish diabetes incidence in NOD mice?What are the new findings?: Anti-CD226 treatment reduced insulitis, decreased disease incidence, and inhibited splenic CD4 + and CD8 + effector memory T cell proliferation. Pancreatic Tregs from anti-CD226 treated mice exhibited increased CD25 expression; splenic Tregs displayed augmented STAT5 phosphorylation and suppressive capacity in vitro . Anti-CD226 treatment reduced IGRP-specific pancreatic CD8 + T cell frequencies, and reduced autoreactive CD8 + T cell-mediated lysis of beta-cells in vitro . How might this impact on clinical practice in the foreseeable future?: CD226 blockade could reduce autoreactive T cell cytotoxicity, enhance Treg function, and slow disease progression in high-risk or recent-onset type 1 diabetes cases.
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Song Z, Li S, Shang Z, Lv W, Cheng X, Meng X, Chen R, Zhang S, Zhang R. Integrating multi-omics data to analyze the potential pathogenic mechanism of CTSH gene involved in type 1 diabetes in the exocrine pancreas. Brief Funct Genomics 2024; 23:406-417. [PMID: 38050341 DOI: 10.1093/bfgp/elad052] [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: 06/20/2023] [Revised: 10/19/2023] [Accepted: 11/09/2023] [Indexed: 12/06/2023] Open
Abstract
Type 1 diabetes (T1D) is an autoimmune disease caused by the destruction of insulin-producing pancreatic islet beta cells. Despite significant advancements, the precise pathogenesis of the disease remains unknown. This work integrated data from expression quantitative trait locus (eQTL) studies with Genome wide association study (GWAS) summary data of T1D and single-cell transcriptome data to investigate the potential pathogenic mechanisms of the CTSH gene involved in T1D in exocrine pancreas. Using the summary data-based Mendelian randomization (SMR) approach, we obtained four potential causative genes associated with T1D: BTN3A2, PGAP3, SMARCE1 and CTSH. To further investigate these genes'roles in T1D development, we validated them using a scRNA-seq dataset from pancreatic tissues of both T1D patients and healthy controls. The analysis showed a significantly high expression of the CTSH gene in T1D acinar cells, whereas the other three genes showed no significant changes in the scRNA-seq data. Moreover, single-cell WGCNA analysis revealed the strongest positive correlation between the module containing CTSH and T1D. In addition, we found cellular ligand-receptor interactions between the acinar cells and different cell types, especially ductal cells. Finally, based on functional enrichment analysis, we hypothesized that the CTSH gene in the exocrine pancreas enhances the antiviral response, leading to the overexpression of pro-inflammatory cytokines and the development of an inflammatory microenvironment. This process promotes β cells injury and ultimately the development of T1D. Our findings offer insights into the underlying pathogenic mechanisms of T1D.
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Affiliation(s)
- Zerun Song
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin City, Heilongjiang Province, China
| | - Shuai Li
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin City, Heilongjiang Province, China
| | - Zhenwei Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin City, Heilongjiang Province, China
| | - Wenhua Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin City, Heilongjiang Province, China
| | - Xiangshu Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin City, Heilongjiang Province, China
| | - Xin Meng
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin City, Heilongjiang Province, China
| | - Rui Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin City, Heilongjiang Province, China
| | - Shuhao Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin City, Heilongjiang Province, China
| | - Ruijie Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin City, Heilongjiang Province, China
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Lee GA, Chang YW, Lai JH, Chang TH, Huang SW, Yang CH, Shen TA, Lin WL, Wu YC, Tseng LW, Tseng SH, Chen YC, Chiang YH, Chen CY. CCN1 Is a Therapeutic Target for Reperfused Ischemic Brain Injury. Transl Stroke Res 2024:10.1007/s12975-024-01279-0. [PMID: 39028413 DOI: 10.1007/s12975-024-01279-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/20/2024] [Accepted: 07/03/2024] [Indexed: 07/20/2024]
Abstract
Ischemic stroke can lead to systemic inflammation, which can activate peripheral immune cells, causing neuroinflammation and brain injury. Meningeal lymphatics play a crucial role in transporting solutes and immune cells out of the brain and draining them into cervical lymph nodes (CLNs). However, the role of meningeal lymphatics in regulating systemic inflammation during the reperfusion stage after ischemia is not well understood. In this study, we demonstrated that brain infarct size, neuronal loss, and the effector function of inflammatory macrophage subsets were reduced after ischemia-reperfusion and disruption of meningeal lymphatics. Spatial memory function was improved in the late stage of ischemic stroke following meningeal lymphatic disruption. Brain-infiltrating immune cells, including neutrophils, monocytes, and T and natural killer cells, were reduced after cerebral ischemia-reperfusion and meningeal lymphatic disruption. Single-cell RNA sequencing analysis revealed that meningeal lymphatic disruption reprogrammed the transcriptome profile related to chemotaxis and leukocyte migration in CLN lymphatic endothelial cells (LECs), and it also decreased chemotactic CCN1 expression in floor LECs. Replenishment of CCN1 through intraventricular injection increased brain infarct size and neuronal loss, while restoring numbers of macrophages/microglia in the brains of meningeal lymphatic-disrupted mice after ischemic stroke. Blocking CCN1 in cerebrospinal fluid reduced brain infarcts and improves spatial memory function after ischemia-reperfusion injury. In summary, this study indicates that CCN1-mediated detrimental inflammation was alleviated after cerebral ischemia-reperfusion injury and meningeal lymphatic disruption. CCN1 represents a novel therapeutic target for inhibiting systemic inflammation in the brain-CLN axis after ischemia-reperfusion injury.
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Affiliation(s)
- Gilbert Aaron Lee
- Department of Medical Research, Taipei Medical University Hospital, Taipei, Taiwan
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Child Development Research Center, Taipei Medical University Hospital, Taipei, Taiwan
- TMU Research Center for Digestive Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yu-Wei Chang
- Department of Medical Research, Taipei Medical University Hospital, Taipei, Taiwan
| | - Jing-Huei Lai
- Core Laboratory of Neuroscience, Office of R&D, Taipei Medical University, Taipei, Taiwan
- Center for Neurotrauma and Neuroregeneration, Taipei Medical University, Taipei, Taiwan
| | - Tzu-Hao Chang
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei, Taiwan
| | - Shiu-Wen Huang
- Department of Medical Research, Taipei Medical University Hospital, Taipei, Taiwan
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Pharmacology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chih-Hao Yang
- Department of Pharmacology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ting-An Shen
- Bioinformatics Center, Office of Data Science, Taipei Medical University, Taipei, Taiwan
| | - Wan-Li Lin
- Department of Medical Research, Taipei Medical University Hospital, Taipei, Taiwan
| | - Ying-Chieh Wu
- Department of Medical Research, Taipei Medical University Hospital, Taipei, Taiwan
| | - Li-Wen Tseng
- Department of Medical Research, Taipei Medical University Hospital, Taipei, Taiwan
| | - Sung-Hui Tseng
- Department of Physical Medicine and Rehabilitation, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Physical Medicine and Rehabilitation, Taipei Medical University Hospital, Taipei, Taiwan
| | - Yung-Chieh Chen
- Department of Medical Imaging, Taipei Medical University Hospital, Taipei, Taiwan
| | - Yung-Hsiao Chiang
- Core Laboratory of Neuroscience, Office of R&D, Taipei Medical University, Taipei, Taiwan
- Center for Neurotrauma and Neuroregeneration, Taipei Medical University, Taipei, Taiwan
- Department of Surgery, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Cheng-Yu Chen
- Department of Medical Imaging, Taipei Medical University Hospital, Taipei, Taiwan.
- Department of Radiology, School of Medicine, College of Medicine, Taipei Medical University, No. 250, Wu Hsing Street, Taipei, 110, Taiwan.
- Translational Imaging Research Center, College of Medicine, Taipei Medical University, Taipei, Taiwan.
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177
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Paley MA, Yang X, Hassman LM, Penkava F, Garner LI, Paley GL, Linskey N, Agnew R, Arantes de Faria PH, Feng A, Li SY, Simone D, Roberson ED, Ruzycki PA, Esaulova E, Laurent J, Feigl-Lenzen L, Springer LE, Liu C, Gillespie GM, Bowness P, Garcia KC, Yokoyama WM. Mucosal signatures of pathogenic T cells in HLA-B*27+ anterior uveitis and axial spondyloarthritis. JCI Insight 2024; 9:e174776. [PMID: 39024572 PMCID: PMC11343591 DOI: 10.1172/jci.insight.174776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 07/12/2024] [Indexed: 07/20/2024] Open
Abstract
HLA-B*27 was one of the first HLA alleles associated with an autoimmune disease, i.e., axial spondyloarthritis (axSpA) and acute anterior uveitis (B27AAU), which cause joint and eye inflammation, respectively. Gastrointestinal inflammation has been suggested as a trigger of axSpA. We recently identified a bacterial peptide (YeiH) that can be presented by HLA-B*27 to expanded public T cell receptors in the joint in axSpA and the eye in B27AAU. While YeiH is present in enteric microbiota and pathogens, additional evidence that pathogenic T cells in HLA-B*27-associated autoimmunity may have had a prior antigenic encounter within the gastrointestinal tract remains lacking. Here, we analyzed ocular, synovial, and blood T cells in B27AAU and axSpA, showing that YeiH-specific CD8+ T cells express a mucosal gene set and surface proteins consistent with intestinal differentiation, including CD161, integrin α4β7, and CCR6. In addition, we found an expansion of YeiH-specific CD8+ T cells in axSpA and B27AAU blood compared with that from individuals acting as healthy controls, whereas influenza-specific CD8+ T cells were equivalent across groups. Finally, we demonstrated the dispensability of TRBV9 for antigen recognition. Collectively, our data suggest that, in HLA-B27-associated autoimmunity, early antigen exposure and differentiation of pathogenic CD8+ T cells may occur in enteric organs.
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Affiliation(s)
- Michael A. Paley
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Xinbo Yang
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Lynn M. Hassman
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Frank Penkava
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Science, Botnar Research Center
| | - Lee I. Garner
- NDM Research Building, Nuffield Department of Medicine, and
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Grace L. Paley
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nicole Linskey
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ryan Agnew
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | - Annie Feng
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sophia Y. Li
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Davide Simone
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Science, Botnar Research Center
| | - Elisha D.O. Roberson
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Genetics and
| | - Philip A. Ruzycki
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Genetics and
| | - Ekaterina Esaulova
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jennifer Laurent
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lacey Feigl-Lenzen
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Luke E. Springer
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Chang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Geraldine M. Gillespie
- NDM Research Building, Nuffield Department of Medicine, and
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Paul Bowness
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Science, Botnar Research Center
| | - K. Christopher Garcia
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, California, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Wayne M. Yokoyama
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, Missouri, USA
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178
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Mao X, Shi M, Zhang B, Fu R, Cai M, Yu S, Lin K, Zhang C, Li D, Chen G, Luo W. Integration of single-cell and bulk RNA sequencing revealed immune heterogeneity and its association with disease activity in rheumatoid arthritis patients. Immunol Res 2024:10.1007/s12026-024-09513-5. [PMID: 39009881 DOI: 10.1007/s12026-024-09513-5] [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: 05/22/2024] [Accepted: 06/27/2024] [Indexed: 07/17/2024]
Abstract
Rheumatoid arthritis (RA) is a chronic, inflammatory, systemic autoimmune disease characterized by cartilage, bone damage, synovial inflammation, hyperplasia, autoantibody production, and systemic features. To obtain an overall profile of the immune environment in RA patients and its association with clinical features, we performed single-cell transcriptome and T-cell receptor sequencing of mononuclear cells from peripheral blood (PBMC) and synovial fluid (SF) from RA patients, integrated with two large cohorts with bulk RNA sequencing for further validation and investigation. Dendritic cells (DCs) exhibited relatively high functional heterogeneity and tissue specificity in relation to both antigen presentation and proinflammatory functions. Peripheral helper T cells (TPHs) are likely to originate from synovial tissue, undergo activation and exhaustion, and are subsequently released into the peripheral blood. Notably, among all immune cell types, TPHs were found to have the most intense associations with disease activity. In addition, CD8 effector T cells could be clustered into two groups with different cytokine expressions and play distinct roles in RA development. By integrating single-cell data with bulk sequencing from two large cohorts, we identified interactions among TPHs, CD8 cells, CD16 monocytes, and DCs that strongly contribute to the proinflammatory local environment in RA joints. Of note, the swollen 28-joint counts exhibited a more pronounced association with this immune environment compared to other disease activity indexes. The immune environment alternated significantly from PBMCs to SF, which indicated that a series of immune cells was involved in proinflammatory responses in the local joints of RA patients. By integrating single-cell data with two large cohorts, we have uncovered associations between specific immune cell populations and clinical features. This integration provides a rapid and precise methodology for assessing local immune activation, offering valuable insights into the pathophysiological mechanisms at play in RA.
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Affiliation(s)
- Xiaofan Mao
- Institute of Translational Medicine, The First People's Hospital of Foshan, Foshan, China
| | - Maohua Shi
- Department of Rheumatology, The First People's Hospital of Foshan, Foshan, China
| | - Beiying Zhang
- Institute of Translational Medicine, The First People's Hospital of Foshan, Foshan, China
| | - Rongdang Fu
- Department of Hepatology, The First People's Hospital of Foshan, Foshan, China
| | - Mengyun Cai
- Institute of Translational Medicine, The First People's Hospital of Foshan, Foshan, China
| | - Sifei Yu
- Institute of Translational Medicine, The First People's Hospital of Foshan, Foshan, China
| | - Kairong Lin
- Institute of Translational Medicine, The First People's Hospital of Foshan, Foshan, China
| | - Chuling Zhang
- Institute of Translational Medicine, The First People's Hospital of Foshan, Foshan, China
| | - Dingru Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Guoqiang Chen
- Department of Rheumatology, The First People's Hospital of Foshan, Foshan, China.
| | - Wei Luo
- Institute of Translational Medicine, The First People's Hospital of Foshan, Foshan, China.
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Xu G, Pan T, Li S, Guo J, Zhang Y, Xu Q, Chen R, Ma Y, Li Y. Mapping Single-Cell Transcriptomes of Endometrium Reveals Potential Biomarkers in Endometrial Cancer. Immunotargets Ther 2024; 13:349-366. [PMID: 39050484 PMCID: PMC11268782 DOI: 10.2147/itt.s470994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/03/2024] [Indexed: 07/27/2024] Open
Abstract
Background The heterogeneity and dynamic changes of endometrial cells have a significant impact on health as they determine the normal function of the endometrium during the menstrual cycle. Dysfunction of the endometrium can lead to the occurrence of various gynecological diseases. Therefore, deconvolution of immune microenvironment that drives transcriptional programs throughout the menstrual cycle is key to understand regulatory biology of endometrium. Methods Herein, we comprehensively analyzed single-cell transcriptome of 59,397 cells across ten human endometrium samples and revealed the dynamic cellular heterogeneity throughout the menstrual cycle. Results We identified two perivascular cell subtypes, four epithelial subtypes and four fibroblast cell types in endometrium. Moreover, we inferred the cell type-specific transcription factor (TF) activities and linked critical TFs to transcriptional output of diverse immune cell types, highlighting the importance of transcriptional regulation in endometrium. Dynamic interactions between various types of cells in endometrium contribute to a range of biological pathways regulating differentiation of secretory. Integration of the molecular biomarkers identified in endometrium and bulk transcriptome of 535 endometrial cancers (EC), we revealed five RNA-based molecular subtypes of EC with highly intratumoral heterogeneity and different clinical manifestations. Mechanism analysis uncovered clinically relevant pathways for pathogenesis of EC. Conclusion In summary, our results revealed the dynamic immune microenvironment of endometrium and provided novel insights into future development of RNA-based treatments for endometriosis and endometrial carcinoma.
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Affiliation(s)
- Gang Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China, Harbin, 150081, People’s Republic of China
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, National Center for International Research, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 571199, People’s Republic of China
| | - Tao Pan
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, National Center for International Research, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 571199, People’s Republic of China
| | - Si Li
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, National Center for International Research, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 571199, People’s Republic of China
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, Heilongjiang, 150081, People’s Republic of China
| | - Jing Guo
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, National Center for International Research, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 571199, People’s Republic of China
| | - Ya Zhang
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, National Center for International Research, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 571199, People’s Republic of China
| | - Qi Xu
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, National Center for International Research, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 571199, People’s Republic of China
| | - Renwei Chen
- Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou, Hainan, 571199, People’s Republic of China
| | - Yanlin Ma
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, National Center for International Research, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 571199, People’s Republic of China
| | - Yongsheng Li
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, National Center for International Research, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 571199, People’s Republic of China
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, Heilongjiang, 150081, People’s Republic of China
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180
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Dong Z, Wang F, Liu Y, Li Y, Yu H, Peng S, Sun T, Qu M, Sun K, Wang L, Ma Y, Chen K, Zhao J, Lin Q. Genomic and single-cell analyses reveal genetic signatures of swimming pattern and diapause strategy in jellyfish. Nat Commun 2024; 15:5936. [PMID: 39009560 PMCID: PMC11250803 DOI: 10.1038/s41467-024-49848-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 06/21/2024] [Indexed: 07/17/2024] Open
Abstract
Jellyfish exhibit innovative swimming patterns that contribute to exploring the origins of animal locomotion. However, the genetic and cellular basis of these patterns remains unclear. Herein, we generated chromosome-level genome assemblies of two jellyfish species, Turritopsis rubra and Aurelia coerulea, which exhibit straight and free-swimming patterns, respectively. We observe positive selection of numerous genes involved in statolith formation, hair cell ciliogenesis, ciliary motility, and motor neuron function. The lineage-specific absence of otolith morphogenesis- and ciliary movement-related genes in T. rubra may be associated with homeostatic structural statocyst loss and straight swimming pattern. Notably, single-cell transcriptomic analyses covering key developmental stages reveal the enrichment of diapause-related genes in the cyst during reverse development, suggesting that the sustained diapause state favours the development of new polyps under favourable conditions. This study highlights the complex relationship between genetics, locomotion patterns and survival strategies in jellyfish, thereby providing valuable insights into the evolutionary lineages of movement and adaptation in the animal kingdom.
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Affiliation(s)
- Zhijun Dong
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Fanghan Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Yali Liu
- University of Chinese Academy of Sciences, Beijing, 100101, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yongxue Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Haiyan Yu
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Saijun Peng
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Tingting Sun
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Meng Qu
- University of Chinese Academy of Sciences, Beijing, 100101, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Ke Sun
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Lei Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuanqing Ma
- Shandong Key Laboratory of Marine Ecological Restoration, Shandong Marine Resource and Environment Research Institute, Yantai, Shandong, 264006, China
| | - Kai Chen
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Jianmin Zhao
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Qiang Lin
- University of Chinese Academy of Sciences, Beijing, 100101, China.
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
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181
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Zhang Z, Chen M, Peng X. Integrated analysis of single-cell and bulk RNA-sequencing identifies a signature based on drug response genes to predict prognosis and therapeutic response in ovarian cancer. Heliyon 2024; 10:e33367. [PMID: 39040239 PMCID: PMC11260940 DOI: 10.1016/j.heliyon.2024.e33367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 07/24/2024] Open
Abstract
Ovarian cancer represents a severe gynecological malignancy with a dire prognosis, underscoring the imperative need for dependable biomarkers that can accurately predict drug response and guide therapeutic choices. In this study, we harnessed online single-cell RNA sequencing (scRNAseq) and bulk RNA sequencing (RNAseq) datasets, applying the Scissor algorithm to identify cells responsive to paclitaxel. From these cells, we derived a gene signature, subsequently used to construct a prognostic model that demonstrated high sensitivity and specificity in predicting patient outcomes. Moreover, we conducted pathway and functional enrichment analyses to uncover potential molecular mechanisms driving the prognostic gene signature. This study illustrates the critical role of scRNAseq and bulk RNAseq in developing precise prognostic models for ovarian cancer, potentially transforming clinical decision-making.
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Affiliation(s)
- ZhenWei Zhang
- Jinjiang Municipal Hospital(Shanghai Sixth People's Hospital Fujian Campus), No. 16, Luoshan Section, Jinguang Road, Luoshan Street, Jinjiang City, Quanzhou, Fujian, China
| | - MianMian Chen
- Jinjiang Municipal Hospital(Shanghai Sixth People's Hospital Fujian Campus), No. 16, Luoshan Section, Jinguang Road, Luoshan Street, Jinjiang City, Quanzhou, Fujian, China
| | - XiaoLian Peng
- Jinjiang Municipal Hospital(Shanghai Sixth People's Hospital Fujian Campus), No. 16, Luoshan Section, Jinguang Road, Luoshan Street, Jinjiang City, Quanzhou, Fujian, China
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182
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Wang N, Zhang S, Langfelder P, Ramanathan L, Plascencia M, Gao F, Vaca R, Gu X, Deng L, Dionisio LE, Prasad BC, Vogt T, Horvath S, Aaronson JS, Rosinski J, Yang XW. Msh3 and Pms1 Set Neuronal CAG-repeat Migration Rate to Drive Selective Striatal and Cortical Pathogenesis in HD Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.602815. [PMID: 39026894 PMCID: PMC11257559 DOI: 10.1101/2024.07.09.602815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Modifiers of Huntington's disease (HD) include mismatch repair (MMR) genes; however, their underlying disease-altering mechanisms remain unresolved. Knockout (KO) alleles for 9 HD GWAS modifiers/MMR genes were crossed to the Q140 Huntingtin (mHtt) knock-in mice to probe such mechanisms. Four KO mice strongly ( Msh3 and Pms1 ) or moderately ( Msh2 and Mlh1 ) rescue a triad of adult-onset, striatal medium-spiny-neuron (MSN)-selective phenotypes: somatic Htt DNA CAG-repeat expansion, transcriptionopathy, and mHtt protein aggregation. Comparatively, Q140 cortex also exhibits an analogous, but later-onset, pathogenic triad that is Msh3 -dependent. Remarkably, Q140/homozygous Msh3-KO lacks visible mHtt aggregates in the brain, even at advanced ages (20-months). Moreover, Msh3 -deficiency prevents striatal synaptic marker loss, astrogliosis, and locomotor impairment in HD mice. Purified Q140 MSN nuclei exhibit highly linear age-dependent mHtt DNA repeat expansion (i.e. repeat migration), with modal-CAG increasing at +8.8 repeats/month (R 2 =0.98). This linear rate is reduced to 2.3 and 0.3 repeats/month in Q140 with Msh3 heterozygous and homozygous alleles, respectively. Our study defines somatic Htt CAG-repeat thresholds below which there are no detectable mHtt nuclear or neuropil aggregates. Mild transcriptionopathy can still occur in Q140 mice with stabilized Htt 140-CAG repeats, but the majority of transcriptomic changes are due to somatic repeat expansion. Our analysis reveals 479 genes with expression levels highly correlated with modal-CAG length in MSNs. Thus, our study mechanistically connects HD GWAS genes to selective neuronal vulnerability in HD, in which Msh3 and Pms1 set the linear rate of neuronal mHtt CAG-repeat migration to drive repeat-length dependent pathogenesis; and provides a preclinical platform for targeting these genes for HD suppression across brain regions. One Sentence Summary Msh3 and Pms1 are genetic drivers of sequential striatal and cortical pathogenesis in Q140 mice by mediating selective CAG-repeat migration in HD vulnerable neurons.
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183
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Martínez-Hernández R, Sánchez de la Blanca N, Sacristán-Gómez P, Serrano-Somavilla A, Muñoz De Nova JL, Sánchez Cabo F, Heyn H, Sampedro-Núñez M, Marazuela M. Unraveling the molecular architecture of autoimmune thyroid diseases at spatial resolution. Nat Commun 2024; 15:5895. [PMID: 39003267 PMCID: PMC11246508 DOI: 10.1038/s41467-024-50192-5] [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: 11/08/2023] [Accepted: 06/25/2024] [Indexed: 07/15/2024] Open
Abstract
Autoimmune thyroid diseases (AITD) such as Graves' disease (GD) or Hashimoto's thyroiditis (HT) are organ-specific diseases that involve complex interactions between distinct components of thyroid tissue. Here, we use spatial transcriptomics to explore the molecular architecture, heterogeneity and location of different cells present in the thyroid tissue, including thyroid follicular cells (TFCs), stromal cells such as fibroblasts, endothelial cells, and thyroid infiltrating lymphocytes. We identify damaged antigen-presenting TFCs with upregulated CD74 and MIF expression in thyroid samples from AITD patients. Furthermore, we discern two main fibroblast subpopulations in the connective tissue including ADIRF+ myofibroblasts, mainly enriched in GD, and inflammatory fibroblasts, enriched in HT patients. We also demonstrate an increase of fenestrated PLVAP+ vessels in AITD, especially in GD. Our data unveil stromal and thyroid epithelial cell subpopulations that could play a role in the pathogenesis of AITD.
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Affiliation(s)
- Rebeca Martínez-Hernández
- Department of Endocrinology and Nutrition Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER GCV14/ER/12), Madrid, Spain.
| | - Nuria Sánchez de la Blanca
- Department of Endocrinology and Nutrition Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER GCV14/ER/12), Madrid, Spain
| | - Pablo Sacristán-Gómez
- Department of Endocrinology and Nutrition Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER GCV14/ER/12), Madrid, Spain
| | - Ana Serrano-Somavilla
- Department of Endocrinology and Nutrition Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER GCV14/ER/12), Madrid, Spain
| | - José Luis Muñoz De Nova
- Department of General and Digestive Surgery, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, Madrid, Spain
| | - Fátima Sánchez Cabo
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Miguel Sampedro-Núñez
- Department of Endocrinology and Nutrition Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER GCV14/ER/12), Madrid, Spain
| | - Mónica Marazuela
- Department of Endocrinology and Nutrition Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER GCV14/ER/12), Madrid, Spain.
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184
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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; 4:100592. [PMID: 38925122 PMCID: PMC11293576 DOI: 10.1016/j.xgen.2024.100592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 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.
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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.
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185
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Wang Q, Antone J, Alsop E, Reiman R, Funk C, Bendl J, Dudley JT, Liang WS, Karr TL, Roussos P, Bennett DA, De Jager PL, Serrano GE, Beach TG, Van Keuren-Jensen K, Mastroeni D, Reiman EM, Readhead BP. Single cell transcriptomes and multiscale networks from persons with and without Alzheimer's disease. Nat Commun 2024; 15:5815. [PMID: 38987616 PMCID: PMC11237088 DOI: 10.1038/s41467-024-49790-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 06/13/2024] [Indexed: 07/12/2024] Open
Abstract
The emergence of single nucleus RNA sequencing (snRNA-seq) offers to revolutionize the study of Alzheimer's disease (AD). Integration with complementary multiomics data such as genetics, proteomics and clinical data provides powerful opportunities to link cell subpopulations and molecular networks with a broader disease-relevant context. We report snRNA-seq profiles from superior frontal gyrus samples from 101 well characterized subjects from the Banner Brain and Body Donation Program in combination with whole genome sequences. We report findings that link common AD risk variants with CR1 expression in oligodendrocytes as well as alterations in hematological parameters. We observed an AD-associated CD83(+) microglial subtype with unique molecular networks and which is associated with immunoglobulin IgG4 production in the transverse colon. Our major observations were replicated in two additional, independent snRNA-seq data sets. These findings illustrate the power of multi-tissue molecular profiling to contextualize snRNA-seq brain transcriptomics and reveal disease biology.
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Affiliation(s)
- Qi Wang
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Jerry Antone
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Eric Alsop
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Rebecca Reiman
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Cory Funk
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Jaroslav Bendl
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Joel T Dudley
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Winnie S Liang
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Timothy L Karr
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Philip L De Jager
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Geidy E Serrano
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Thomas G Beach
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | | | - Diego Mastroeni
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Eric M Reiman
- Banner Alzheimer's Institute, Phoenix, AZ, 85006, USA
| | - Benjamin P Readhead
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA.
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186
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Jin H, Zhang C, Nagenborg J, Juhasz P, Ruder AV, Sikkink CJJM, Mees BME, Waring O, Sluimer JC, Neumann D, Goossens P, Donners MMPC, Mardinoglu A, Biessen EAL. Genome-scale metabolic network of human carotid plaque reveals the pivotal role of glutamine/glutamate metabolism in macrophage modulating plaque inflammation and vulnerability. Cardiovasc Diabetol 2024; 23:240. [PMID: 38978031 PMCID: PMC11232311 DOI: 10.1186/s12933-024-02339-3] [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: 10/30/2023] [Accepted: 06/26/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND Metabolism is increasingly recognized as a key regulator of the function and phenotype of the primary cellular constituents of the atherosclerotic vascular wall, including endothelial cells, smooth muscle cells, and inflammatory cells. However, a comprehensive analysis of metabolic changes associated with the transition of plaque from a stable to a hemorrhaged phenotype is lacking. METHODS In this study, we integrated two large mRNA expression and protein abundance datasets (BIKE, n = 126; MaasHPS, n = 43) from human atherosclerotic carotid artery plaque to reconstruct a genome-scale metabolic network (GEM). Next, the GEM findings were linked to metabolomics data from MaasHPS, providing a comprehensive overview of metabolic changes in human plaque. RESULTS Our study identified significant changes in lipid, cholesterol, and inositol metabolism, along with altered lysosomal lytic activity and increased inflammatory activity, in unstable plaques with intraplaque hemorrhage (IPH+) compared to non-hemorrhaged (IPH-) plaques. Moreover, topological analysis of this network model revealed that the conversion of glutamine to glutamate and their flux between the cytoplasm and mitochondria were notably compromised in hemorrhaged plaques, with a significant reduction in overall glutamate levels in IPH+ plaques. Additionally, reduced glutamate availability was associated with an increased presence of macrophages and a pro-inflammatory phenotype in IPH+ plaques, suggesting an inflammation-prone microenvironment. CONCLUSIONS This study is the first to establish a robust and comprehensive GEM for atherosclerotic plaque, providing a valuable resource for understanding plaque metabolism. The utility of this GEM was illustrated by its ability to reliably predict dysregulation in the cholesterol hydroxylation, inositol metabolism, and the glutamine/glutamate pathway in rupture-prone hemorrhaged plaques, a finding that may pave the way to new diagnostic or therapeutic measures.
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Affiliation(s)
- Han Jin
- Central Laboratory, Tianjin Medical University General Hospital, Tianjin, China
- Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht UMC+, Maastricht, the Netherlands
- Science for Life Laboratory (SciLifeLab), KTH-Royal Institute of Technology, Solna, Sweden
| | - Cheng Zhang
- Science for Life Laboratory (SciLifeLab), KTH-Royal Institute of Technology, Solna, Sweden
| | - Jan Nagenborg
- Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht UMC+, Maastricht, the Netherlands
| | | | - Adele V Ruder
- Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht UMC+, Maastricht, the Netherlands
| | | | - Barend M E Mees
- Department of Surgery, Maastricht UMC+, Maastricht, the Netherlands
| | - Olivia Waring
- Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht UMC+, Maastricht, the Netherlands
| | - Judith C Sluimer
- Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht UMC+, Maastricht, the Netherlands
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, Scotland
| | - Dietbert Neumann
- Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht UMC+, Maastricht, the Netherlands
| | - Pieter Goossens
- Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht UMC+, Maastricht, the Netherlands
| | - Marjo M P C Donners
- Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht UMC+, Maastricht, the Netherlands
| | - Adil Mardinoglu
- Science for Life Laboratory (SciLifeLab), KTH-Royal Institute of Technology, Solna, Sweden.
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK.
| | - Erik A L Biessen
- Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht UMC+, Maastricht, the Netherlands.
- Institute for Molecular Cardiovascular Research, RWTH Aachen University, Aachen, Germany.
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187
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Sunusi U, Ziegelmeyer B, Osuji I, Medvedovic M, Todd H, Abou-Khalil J, Zimmermann N. Pathophysiology of hypereosinophilia-associated heart disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601845. [PMID: 39005455 PMCID: PMC11245001 DOI: 10.1101/2024.07.03.601845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Background Cardiac complications in patients with hypereosinophilia cause significant morbidity and mortality. However, mechanisms of how eosinophilic inflammation causes heart damage are poorly understood. Methods We developed a model of hypereosinophilia-associated heart disease by challenging hypereosinophilic mice with peptide from the cardiac myosin heavy chain. Disease outcomes were measured by histology, immunohistochemistry, flow cytometry, and measurement of cells and biomarkers in peripheral blood. Eosinophil dependence was determined by using eosinophil-deficient mice (ΔdblGATA). Single cells from heart were subjected to single cell RNA sequencing to assess cell composition, subtypes and expression profiles. Results Mice challenged with myocarditic and control peptide had peripheral blood leukocytosis, but only those challenged with myocarditic peptide had heart inflammation. Heart tissue was infiltrated by eosinophil-rich inflammatory infiltrates associated with cardiomyocyte damage. Disease penetrance and severity were dependent on the presence of eosinophils. Single cell RNA sequencing showed enrichment of myeloid cells, T-cells and granulocytes (neutrophils and eosinophils) in the myocarditic mice. Macrophages were M2 skewed, and eosinophils had an activated phenotype. Gene enrichment analysis identified several pathways potentially involved in pathophysiology of disease. Conclusion Eosinophils are required for heart damage in hypereosinophilia-associated heart disease. Additionally, myeloid cells, granulocytes and T-cell cooperatively or independently participate in the pathogenesis of hypereosinophilia-associated heart disease.
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188
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Ni Y, You G, Gong Y, Su X, Du Y, Wang X, Ding X, Fu Q, Zhang M, Cheng T, Lan Y, Liu B, Liu C. Human yolk sac-derived innate lymphoid-biased multipotent progenitors emerge prior to hematopoietic stem cell formation. Dev Cell 2024:S1534-5807(24)00388-5. [PMID: 38996461 DOI: 10.1016/j.devcel.2024.06.010] [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: 04/29/2024] [Accepted: 06/17/2024] [Indexed: 07/14/2024]
Abstract
Hematopoietic stem cell (HSC)-independent lymphopoiesis has been elucidated in murine embryos. However, our understanding regarding human embryonic counterparts remains limited. Here, we demonstrated the presence of human yolk sac-derived lymphoid-biased progenitors (YSLPs) expressing CD34, IL7R, LTB, and IRF8 at Carnegie stage 10, much earlier than the first HSC emergence. The number and lymphopoietic potential of these progenitors were both significantly higher in the yolk sac than the embryo proper at this early stage. Importantly, single-cell/bulk culture and CITE-seq have elucidated the tendency of YSLP to differentiate into innate lymphoid cells and dendritic cells. Notably, lymphoid progenitors in fetal liver before and after HSC seeding displayed distinct transcriptional features, with the former closely resembling those of YSLPs. Overall, our data identified the origin, potential, and migratory dynamics of innate lymphoid-biased multipotent progenitors in human yolk sac before HSC emergence, providing insights for understanding the stepwise establishment of innate immune system in humans.
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Affiliation(s)
- Yanli Ni
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing 100071, China
| | - Guoju You
- School of Medicine, Tsinghua University, Beijing 100080, China
| | - Yandong Gong
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing 100071, China
| | - Xiaoyu Su
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang 212013, China
| | - Yuan Du
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650031, China
| | - Xiaoshuang Wang
- Department of Biochemistry and Molecular Biology, State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Xiaochen Ding
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing 100071, China
| | - Qingfeng Fu
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing 100071, China
| | - Man Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing 100071, China
| | - Tao Cheng
- Department of Biochemistry and Molecular Biology, State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China; State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China.
| | - Yu Lan
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 510632, China.
| | - Bing Liu
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing 100071, China; State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650031, China; Department of Physiology and Pathophysiology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.
| | - Chen Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China.
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189
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Howe JR, Chan CL, Lee D, Blanquart M, Romero HK, Zadina AN, Lemieux ME, Mills F, Desplats PA, Tye KM, Root CM. Control of innate olfactory valence by segregated cortical amygdala circuits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600895. [PMID: 38979308 PMCID: PMC11230396 DOI: 10.1101/2024.06.26.600895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Animals perform innate behaviors that are stereotyped responses to specific evolutionarily relevant stimuli in the absence of prior learning or experience. These behaviors can be reduced to an axis of valence, whereby specific odors evoke approach or avoidance. The cortical amygdala (plCoA) mediates innate attraction and aversion to odor. However, little is known about how this brain area gives rise to behaviors of opposing motivational valence. Here, we sought to define the circuit features of plCoA that give rise to innate olfactory behaviors of valence. We characterized the physiology, gene expression, and projections of this structure, identifying a divergent, topographic organization that selectively controls innate attraction and avoidance to odor. First, we examined odor-evoked responses in these areas and found sparse encoding of odor identity, but not valence. We next considered a topographic organization and found that optogenetic stimulation of the anterior and posterior domains of plCoA elicits attraction and avoidance, respectively, suggesting a functional axis for valence. Using single cell and spatial RNA sequencing, we identified the molecular cell types in plCoA, revealing an anteroposterior gradient in cell types, whereby anterior glutamatergic neurons preferentially express Slc17a6 and posterior neurons express Slc17a7. Activation of these respective cell types recapitulates appetitive and aversive valence behaviors, and chemogenetic inhibition reveals partial necessity for valence responses to innate appetitive or aversive odors. Finally, we identified topographically organized circuits defined by projections, whereby anterior neurons preferentially project to medial amygdala, and posterior neurons preferentially project to nucleus accumbens, which are respectively sufficient and necessary for innate negative and positive olfactory valence. Together, these data advance our understanding of how the olfactory system generates stereotypic, hardwired attraction and avoidance, and supports a model whereby distinct, topographically distributed plCoA populations direct innate olfactory valence responses by signaling to divergent valence-specific targets, linking upstream olfactory identity to downstream valence behaviors, through a population code. This represents a novel circuit motif in which valence encoding is represented not by the firing properties of individual neurons, but by population level identity encoding that is routed through divergent targets to mediate distinct valence.
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Affiliation(s)
- James R. Howe
- Department of Biological Sciences, Section of Neuroscience, University of California, San Diego, La Jolla, CA 92093, USA
- Neurosciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- These authors contributed equally
| | - Chung-Lung Chan
- Department of Biological Sciences, Section of Neuroscience, University of California, San Diego, La Jolla, CA 92093, USA
- These authors contributed equally
| | - Donghyung Lee
- Department of Biological Sciences, Section of Neuroscience, University of California, San Diego, La Jolla, CA 92093, USA
| | - Marlon Blanquart
- Department of Biological Sciences, Section of Neuroscience, University of California, San Diego, La Jolla, CA 92093, USA
| | - Haylie K. Romero
- Neurosciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Abigail N. Zadina
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, 10027, USA
| | | | - Fergil Mills
- Salk Institute for Biological Sciences, La Jolla, CA 92037, USA
| | - Paula A. Desplats
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kay M. Tye
- Department of Biological Sciences, Section of Neuroscience, University of California, San Diego, La Jolla, CA 92093, USA
- Salk Institute for Biological Sciences, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, La Jolla, CA 92037, USA
| | - Cory M. Root
- Department of Biological Sciences, Section of Neuroscience, University of California, San Diego, La Jolla, CA 92093, USA
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Wu C, Yu H, Liang F, Huang X, Jiang B, Lou Z, Liu Y, Wu Z, Wang Q, Shen H, Chen M, Wu P, Wu M. Hypoxia inhibits the iMo/cDC2/CD8+ TRMs immune axis in the tumor microenvironment of human esophageal cancer. J Immunother Cancer 2024; 12:e008889. [PMID: 38964786 PMCID: PMC11227851 DOI: 10.1136/jitc-2024-008889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Esophageal cancer (ESCA) is a form of malignant tumor associated with chronic inflammation and immune dysregulation. However, the specific immune status and key mechanisms of immune regulation in this disease require further exploration. METHODS To investigate the features of the human ESCA tumor immune microenvironment and its possible regulation, we performed mass cytometry by time of flight, single-cell RNA sequencing, multicolor fluorescence staining of tissue, and flow cytometry analyses on tumor and paracancerous tissue from treatment-naïve patients. RESULTS We depicted the immune landscape of the ESCA and revealed that CD8+ (tissue-resident memory CD8+ T cells (CD8+ TRMs) were closely related to disease progression. We also revealed the heterogeneity of CD8+ TRMs in the ESCA tumor microenvironment (TME), which was associated with their differentiation and function. Moreover, the subset of CD8+ TRMs in tumor (called tTRMs) that expressed high levels of granzyme B and immune checkpoints was markedly decreased in the TME of advanced ESCA. We showed that tTRMs are tumor effector cells preactivated in the TME. We then demonstrated that conventional dendritic cells (cDC2s) derived from intermediate monocytes (iMos) are essential for maintaining the proliferation of CD8+ TRMs in the TME. Our preliminary study showed that hypoxia can promote the apoptosis of iMos and impede the maturation of cDC2s, which in turn reduces the proliferative capacity of CD8+ TRMs, thereby contributing to the progression of cancer. CONCLUSIONS Our study revealed the essential antitumor roles of CD8+ TRMs and preliminarily explored the regulation of the iMo/cDC2/CD8+ TRM immune axis in the human ESCA TME.
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Affiliation(s)
- Chuanqiang Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
- Laboratory of Clinical Research Center of Zhejiang Province, The Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Huan Yu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Fuxiang Liang
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Xiancong Huang
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang Province, People's Republic of China
| | - Bin Jiang
- Department of Thoracic Surgery, Shandong Provincial Hospital, Jinan, Shandong Province, People's Republic of China
| | - Zhiling Lou
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Yafei Liu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Zixiang Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Qi Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Hong Shen
- Department of Medical Oncology, The Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Pin Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Ming Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
- Laboratory of Clinical Research Center of Zhejiang Province, The Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
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Zhu Y, Zhang Y, He S, Yi S, Feng H, Xia X, Fang X, Gong X, Zhao P. Integrating single-nucleus RNA sequencing and spatial transcriptomics to elucidate a specialized subpopulation of astrocytes, microglia and vascular cells in brains of mouse model of lipopolysaccharide-induced sepsis-associated encephalopathy. J Neuroinflammation 2024; 21:169. [PMID: 38961424 PMCID: PMC11223438 DOI: 10.1186/s12974-024-03161-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND Understanding the mechanism behind sepsis-associated encephalopathy (SAE) remains a formidable task. This study endeavors to shed light on the complex cellular and molecular alterations that occur in the brains of a mouse model with SAE, ultimately unraveling the underlying mechanisms of this condition. METHODS We established a murine model using intraperitoneal injection of lipopolysaccharide (LPS) in wild type and Anxa1-/- mice and collected brain tissues for analysis at 0-hour, 12-hour, 24-hour, and 72-hour post-injection. Utilizing advanced techniques such as single-nucleus RNA sequencing (snRNA-seq) and Stereo-seq, we conducted a comprehensive characterization of the cellular responses and molecular patterns within the brain. RESULTS Our study uncovered notable temporal differences in the response to LPS challenge between Anxa1-/- (annexin A1 knockout) and wild type mice, specifically at the 12-hour and 24-hour time points following injection. We observed a significant increase in the proportion of Astro-2 and Micro-2 cells in these mice. These cells exhibited a colocalization pattern with the vascular subtype Vas-1, forming a distinct region known as V1A2M2, where Astro-2 and Micro-2 cells surrounded Vas-1. Moreover, through further analysis, we discovered significant upregulation of ligands and receptors such as Timp1-Cd63, Timp1-Itgb1, Timp1-Lrp1, as well as Ccl2-Ackr1 and Cxcl2-Ackr1 within this region. In addition, we observed a notable increase in the expression of Cd14-Itgb1, Cd14-Tlr2, and Cd14-C3ar1 in regions enriched with Micro-2 cells. Additionally, Cxcl10-Sdc4 showed broad upregulation in brain regions containing both Micro-2 and Astro-2 cells. Notably, upon LPS challenge, there was an observed increase in Anxa1 expression in the mouse brain. Furthermore, our study revealed a noteworthy increase in mortality rates following Anxa1 knockdown. However, we did not observe substantial differences in the types, numbers, or distribution of other brain cells between Anxa1-/- and wildtype mice over time. Nevertheless, when comparing the 24-hour post LPS injection time point, we observed a significant decrease in the proportion and distribution of Micro-2 and Astro-2 cells in the vicinity of blood vessels in Anxa1-/- mice. Additionally, we noted reduced expression levels of several ligand-receptor pairs including Cd14-Tlr2, Cd14-C3ar1, Cd14-Itgb1, Cxcl10-Sdc4, Ccl2-Ackr1, and Cxcl2-Ackr1. CONCLUSIONS By combining snRNA-seq and Stereo-seq techniques, our study successfully identified a distinctive cellular colocalization, referred to as a special pathological niche, comprising Astro-2, Micro-2, and Vas-1 cells. Furthermore, we observed an upregulation of ligand-receptor pairs within this niche. These findings suggest a potential association between this cellular arrangement and the underlying mechanisms contributing to SAE or the increased mortality observed in Anxa1 knockdown mice.
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Grants
- 2021A1515012429 Natural Science Foundation of Guangdong Province, China
- 211102114530659 Shaoguan Municipal Science and Technology Program, China
- 20221807 Shaoguan Engineering Research Center for Research and Development of Molecular and Cellular Technology in Rapid Diagnosis of Infectious Diseases and Cancer Program, China
- KEYANSHEN (2023) 01 Research Fund for Joint Laboratory for Digital and Precise Detection of Clinical Pathogens, Yuebei People's Hospital Affiliated to Shantou University Medical College, China
- RS202001 Research Project for Outstanding Scholar of Yuebei People's Hospital, Shantou University Medical College, China
- Research Fund for Joint Laboratory for Digital and Precise Detection of Clinical Pathogens, Yuebei People’s Hospital Affiliated to Shantou University Medical College, China
- Research Project for Outstanding Scholar of Yuebei People’s Hospital, Shantou University Medical College, China
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Affiliation(s)
- Yanyan Zhu
- Department of Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, No 133, Huimin Road South, Wujiang District, Shaoguan, 512025, China
- Laboratory for Diagnosis of Clinical Microbiology and Infection, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China
- Research Center for Interdisciplinary & High-quality Innovative Development in Laboratory Medicine, Shaoguan, 512025, China
- Shaoguan Municipal Quality Control Center for Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China
- Shaoguan Municipal Quality Control Center for Surveillance of Bacterial Resistance, Shaoguan, 512025, China
- Shaoguan Engineering Research Center for Research and Development of Molecular and Cellular Technology in Rapid Diagnosis of Infectious Diseases and Cancer, Shaoguan, 512025, China
| | - Yin Zhang
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Sheng He
- Department of Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, No 133, Huimin Road South, Wujiang District, Shaoguan, 512025, China
- Laboratory for Diagnosis of Clinical Microbiology and Infection, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China
- Research Center for Interdisciplinary & High-quality Innovative Development in Laboratory Medicine, Shaoguan, 512025, China
- Shaoguan Municipal Quality Control Center for Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China
- Shaoguan Municipal Quality Control Center for Surveillance of Bacterial Resistance, Shaoguan, 512025, China
- Shaoguan Engineering Research Center for Research and Development of Molecular and Cellular Technology in Rapid Diagnosis of Infectious Diseases and Cancer, Shaoguan, 512025, China
| | - Sanjun Yi
- Department of Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, No 133, Huimin Road South, Wujiang District, Shaoguan, 512025, China
- Laboratory for Diagnosis of Clinical Microbiology and Infection, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China
- Research Center for Interdisciplinary & High-quality Innovative Development in Laboratory Medicine, Shaoguan, 512025, China
- Shaoguan Municipal Quality Control Center for Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China
- Shaoguan Municipal Quality Control Center for Surveillance of Bacterial Resistance, Shaoguan, 512025, China
- Shaoguan Engineering Research Center for Research and Development of Molecular and Cellular Technology in Rapid Diagnosis of Infectious Diseases and Cancer, Shaoguan, 512025, China
| | - Hao Feng
- Jiaxing University Master Degree Cultivation Base, Zhejiang Chinese Medical University, Jiaxing, 314001, China
| | - Xianzhu Xia
- Department of Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, No 133, Huimin Road South, Wujiang District, Shaoguan, 512025, China
- Laboratory for Diagnosis of Clinical Microbiology and Infection, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China
- Research Center for Interdisciplinary & High-quality Innovative Development in Laboratory Medicine, Shaoguan, 512025, China
| | | | - Xiaoqian Gong
- Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China.
| | - Pingsen Zhao
- Department of Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, No 133, Huimin Road South, Wujiang District, Shaoguan, 512025, China.
- Laboratory for Diagnosis of Clinical Microbiology and Infection, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China.
- Research Center for Interdisciplinary & High-quality Innovative Development in Laboratory Medicine, Shaoguan, 512025, China.
- Shaoguan Municipal Quality Control Center for Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China.
- Shaoguan Municipal Quality Control Center for Surveillance of Bacterial Resistance, Shaoguan, 512025, China.
- Shaoguan Engineering Research Center for Research and Development of Molecular and Cellular Technology in Rapid Diagnosis of Infectious Diseases and Cancer, Shaoguan, 512025, China.
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Qadir MMF, Elgamal RM, Song K, Kudtarkar P, Sakamuri SS, Katakam PV, El-Dahr SS, Kolls JK, Gaulton KJ, Mauvais-Jarvis F. Single cell regulatory architecture of human pancreatic islets suggests sex differences in β cell function and the pathogenesis of type 2 diabetes. RESEARCH SQUARE 2024:rs.3.rs-4607352. [PMID: 39011095 PMCID: PMC11247939 DOI: 10.21203/rs.3.rs-4607352/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Type 2 and type 1 diabetes (T2D, T1D) exhibit sex differences in insulin secretion, the mechanisms of which are unknown. We examined sex differences in human pancreatic islets from 52 donors with and without T2D combining single cell RNA-seq (scRNA-seq), single nucleus assay for transposase-accessible chromatin sequencing (snATAC-seq), hormone secretion, and bioenergetics. In nondiabetic (ND) donors, sex differences in islet cells gene accessibility and expression predominantly involved sex chromosomes. Islets from T2D donors exhibited similar sex differences in sex chromosomes differentially expressed genes (DEGs), but also exhibited sex differences in autosomal genes. Comparing β cells from T2D vs. ND donors, gene enrichment of female β cells showed suppression in mitochondrial respiration, while male β cells exhibited suppressed insulin secretion. Thus, although sex differences in gene accessibility and expression of ND β cells predominantly affect sex chromosomes, the transition to T2D reveals sex differences in autosomes highlighting mitochondrial failure in females.
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Affiliation(s)
- Mirza Muhammad Fahd Qadir
- Section of Endocrinology and Metabolism, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
- Southeast Louisiana Veterans Health Care System, New Orleans, LA, USA
- Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA
| | - Ruth M. Elgamal
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Keijing Song
- Center for Translational Research in Infection and Inflammation, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Parul Kudtarkar
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Siva S.V.P Sakamuri
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Prasad V. Katakam
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Samir S. El-Dahr
- Department of Pediatrics, Tulane University, School of Medicine, New Orleans, LA, USA
| | - Jay K. Kolls
- Center for Translational Research in Infection and Inflammation, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Kyle J. Gaulton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Franck Mauvais-Jarvis
- Section of Endocrinology and Metabolism, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
- Southeast Louisiana Veterans Health Care System, New Orleans, LA, USA
- Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA
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Praharaj M, Shen F, Lee AJ, Zhao L, Nirschl TR, Theodros D, Singh AK, Wang X, Adusei KM, Lombardo KA, Williams RA, Sena LA, Thompson EA, Tam A, Yegnasubramanian S, Pearce EJ, Leone RD, Alt J, Rais R, Slusher BS, Pardoll DM, Powell JD, Zarif JC. Metabolic Reprogramming of Tumor-Associated Macrophages Using Glutamine Antagonist JHU083 Drives Tumor Immunity in Myeloid-Rich Prostate and Bladder Cancers. Cancer Immunol Res 2024; 12:854-875. [PMID: 38701369 PMCID: PMC11217738 DOI: 10.1158/2326-6066.cir-23-1105] [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: 12/27/2023] [Revised: 04/10/2024] [Accepted: 04/30/2024] [Indexed: 05/05/2024]
Abstract
Glutamine metabolism in tumor microenvironments critically regulates antitumor immunity. Using the glutamine-antagonist prodrug JHU083, we report potent tumor growth inhibition in urologic tumors by JHU083-reprogrammed tumor-associated macrophages (TAMs) and tumor-infiltrating monocytes. We show JHU083-mediated glutamine antagonism in tumor microenvironments induced by TNF, proinflammatory, and mTORC1 signaling in intratumoral TAM clusters. JHU083-reprogrammed TAMs also exhibited increased tumor cell phagocytosis and diminished proangiogenic capacities. In vivo inhibition of TAM glutamine consumption resulted in increased glycolysis, a broken tricarboxylic acid (TCA) cycle, and purine metabolism disruption. Although the antitumor effect of glutamine antagonism on tumor-infiltrating T cells was moderate, JHU083 promoted a stem cell-like phenotype in CD8+ T cells and decreased the abundance of regulatory T cells. Finally, JHU083 caused a global shutdown in glutamine-utilizing metabolic pathways in tumor cells, leading to reduced HIF-1α, c-MYC phosphorylation, and induction of tumor cell apoptosis, all key antitumor features. Altogether, our findings demonstrate that targeting glutamine with JHU083 led to suppressed tumor growth as well as reprogramming of immunosuppressive TAMs within prostate and bladder tumors that promoted antitumor immune responses. JHU083 can offer an effective therapeutic benefit for tumor types that are enriched in immunosuppressive TAMs.
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Affiliation(s)
- Monali Praharaj
- Pathobiology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Fan Shen
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Alex J. Lee
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Graduate Program in Immunology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Liang Zhao
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Thomas R. Nirschl
- Pathobiology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Debebe Theodros
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Graduate Program in Immunology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Alok K. Singh
- Department of Medicine, Center for Tuberculosis Research, School of Medicine, Johns Hopkins University, Baltimore, Maryland.
| | - Xiaoxu Wang
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Graduate Program in Immunology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Kenneth M. Adusei
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Graduate Program in Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Kara A. Lombardo
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Raekwon A. Williams
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Laura A. Sena
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Elizabeth A. Thompson
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Ada Tam
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Srinivasan Yegnasubramanian
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Edward J. Pearce
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Robert D. Leone
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Jesse Alt
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland.
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, Maryland.
| | - Rana Rais
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland.
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, Maryland.
| | - Barbara S. Slusher
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland.
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, Maryland.
| | - Drew M. Pardoll
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Jonathan D. Powell
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Jelani C. Zarif
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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Hu H, Wang X, Feng S, Xu Z, Liu J, Heidrich-O'Hare E, Chen Y, Yue M, Zeng L, Rong Z, Chen T, Billiar T, Ding Y, Huang H, Duerr RH, Chen W. A unified model-based framework for doublet or multiplet detection in single-cell multiomics data. Nat Commun 2024; 15:5562. [PMID: 38956023 PMCID: PMC11220103 DOI: 10.1038/s41467-024-49448-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: 11/30/2023] [Accepted: 06/03/2024] [Indexed: 07/04/2024] Open
Abstract
Droplet-based single-cell sequencing techniques rely on the fundamental assumption that each droplet encapsulates a single cell, enabling individual cell omics profiling. However, the inevitable issue of multiplets, where two or more cells are encapsulated within a single droplet, can lead to spurious cell type annotations and obscure true biological findings. The issue of multiplets is exacerbated in single-cell multiomics settings, where integrating cross-modality information for clustering can inadvertently promote the aggregation of multiplet clusters and increase the risk of erroneous cell type annotations. Here, we propose a compound Poisson model-based framework for multiplet detection in single-cell multiomics data. Leveraging experimental cell hashing results as the ground truth for multiplet status, we conducted trimodal DOGMA-seq experiments and generated 17 benchmarking datasets from two tissues, involving a total of 280,123 droplets. We demonstrated that the proposed method is an essential tool for integrating cross-modality multiplet signals, effectively eliminating multiplet clusters in single-cell multiomics data-a task at which the benchmarked single-omics methods proved inadequate.
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Affiliation(s)
- Haoran Hu
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Xinjun Wang
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Site Feng
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Zhongli Xu
- School of Medicine, Tsinghua University, 100084, Beijing, China
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, 15224, USA
| | - Jing Liu
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, 15224, USA
| | | | - Yanshuo Chen
- Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
- Center of Bioinformatics and Computational Biology, College Park, MD, 20740, USA
| | - Molin Yue
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Lang Zeng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Ziqi Rong
- School of Information, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Tianmeng Chen
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Timothy Billiar
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Ying Ding
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Heng Huang
- Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
- Center of Bioinformatics and Computational Biology, College Park, MD, 20740, USA
| | - Richard H Duerr
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| | - Wei Chen
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, 15224, USA.
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
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195
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Liu P, Ren X, Zhang B, Guo S, Fu Q. Investigating the characteristics of mild intervertebral disc degeneration at various age stages using single-cell genomics. Front Cell Dev Biol 2024; 12:1409287. [PMID: 39015652 PMCID: PMC11250600 DOI: 10.3389/fcell.2024.1409287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/03/2024] [Indexed: 07/18/2024] Open
Abstract
Introduction: Intervertebral disc degeneration often occurs in the elderly population, but in recent years, there has been an increasing incidence of disc degeneration in younger individuals, primarily with mild degeneration. Methods: In order to explore the underlying mechanisms of disc degeneration in both young and aging individuals, we collected four types of nucleus pulposus (NP) single-cell sequencing samples for analysis based on Pfirrmann grading: normal-young (NY) (Grade I), normal-old (NO) (Grade I), mild degenerative-young (MY) (Grade II-III), and mild degenerative-old (MO) (Grade II-III). Results: We found that most NP cells in NO and MY samples exhibited oxidative stress, which may be important pathogenic factors in NO and MY groups. On the other hand, NP cells in MO group exhibited endoplasmic reticulum stress. In terms of inflammation, myeloid cells were mainly present in the degenerative group, with the MY group showing a stronger immune response compared to the MO group. Interestingly, dendritic cells in the myeloid lineage played a critical role in the process of mild degeneration. Discussion: Our study investigated the molecular mechanisms of intervertebral disc degeneration from an age perspective, providing insights for improving treatment strategies for patients with disc degeneration at different age groups.
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Affiliation(s)
- Pengcheng Liu
- Department of Orthopedics Surgery, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Ren
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Beiting Zhang
- Department of Orthopedics Surgery, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Song Guo
- Department of Orthopedics Surgery, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qiang Fu
- Department of Orthopedics Surgery, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
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196
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Liu M, Wang C, Huo L, Cao J, Mao X, He Z, Hu C, Sun H, Deng W, He W, Chen Y, Gu M, Liao J, Guo N, He X, Wu Q, Chen J, Zhang L, Wang X, Shang C, Dong J. Complexin-1 enhances ultrasound neurotransmission in the mammalian auditory pathway. Nat Genet 2024; 56:1503-1515. [PMID: 38834904 DOI: 10.1038/s41588-024-01781-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: 11/19/2022] [Accepted: 04/25/2024] [Indexed: 06/06/2024]
Abstract
Unlike megabats, which rely on well-developed vision, microbats use ultrasonic echolocation to navigate and locate prey. To study ultrasound perception, here we compared the auditory cortices of microbats and megabats by constructing reference genomes and single-nucleus atlases for four species. We found that parvalbumin (PV)+ neurons exhibited evident cross-species differences and could respond to ultrasound signals, whereas their silencing severely affected ultrasound perception in the mouse auditory cortex. Moreover, megabat PV+ neurons expressed low levels of complexins (CPLX1-CPLX4), which can facilitate neurotransmitter release, while microbat PV+ neurons highly expressed CPLX1, which improves neurotransmission efficiency. Further perturbation of Cplx1 in PV+ neurons impaired ultrasound perception in the mouse auditory cortex. In addition, CPLX1 functioned in other parts of the auditory pathway in microbats but not megabats and exhibited convergent evolution between echolocating microbats and whales. Altogether, we conclude that CPLX1 expression throughout the entire auditory pathway can enhance mammalian ultrasound neurotransmission.
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Affiliation(s)
- Meiling Liu
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Changliang Wang
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Lifang Huo
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Jie Cao
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Ziqing He
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Chuanxia Hu
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Haijian Sun
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Wenjun Deng
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Weiya He
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Yifu Chen
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Meifeng Gu
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Jiayu Liao
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Ning Guo
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Xiangyang He
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qian Wu
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China.
| | - Xiaoqun Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China.
| | - Congping Shang
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.
| | - Ji Dong
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.
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197
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Lecoutre S, Maqdasy S, Rizo-Roca D, Renzi G, Vlassakev I, Alaeddine LM, Higos R, Jalkanen J, Zhong J, Zareifi DS, Frendo-Cumbo S, Massier L, Hodek O, Juvany M, Moritz T, de Castro Barbosa T, Omar-Hmeadi M, López-Yus M, Merabtene F, Abatan JB, Marcelin G, El Hachem EJ, Rouault C, Bergo MO, Petrus P, Zierath JR, Clément K, Krook A, Mejhert N, Rydén M. Reduced adipocyte glutaminase activity promotes energy expenditure and metabolic health. Nat Metab 2024; 6:1329-1346. [PMID: 39009762 PMCID: PMC11272588 DOI: 10.1038/s42255-024-01083-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 06/14/2024] [Indexed: 07/17/2024]
Abstract
Glutamine and glutamate are interconverted by several enzymes and alterations in this metabolic cycle are linked to cardiometabolic traits. Herein, we show that obesity-associated insulin resistance is characterized by decreased plasma and white adipose tissue glutamine-to-glutamate ratios. We couple these stoichiometric changes to perturbed fat cell glutaminase and glutamine synthase messenger RNA and protein abundance, which together promote glutaminolysis. In human white adipocytes, reductions in glutaminase activity promote aerobic glycolysis and mitochondrial oxidative capacity via increases in hypoxia-inducible factor 1α abundance, lactate levels and p38 mitogen-activated protein kinase signalling. Systemic glutaminase inhibition in male and female mice, or genetically in adipocytes of male mice, triggers the activation of thermogenic gene programs in inguinal adipocytes. Consequently, the knockout mice display higher energy expenditure and improved glucose tolerance compared to control littermates, even under high-fat diet conditions. Altogether, our findings highlight white adipocyte glutamine turnover as an important determinant of energy expenditure and metabolic health.
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Affiliation(s)
- Simon Lecoutre
- Department of Medicine (Huddinge), Karolinska Institutet, ME Endokrinologi, Karolinska University Hospital Huddinge, Huddinge, Sweden
- Nutrition and Obesities: Systemic Approaches Research Group, NutriOmics, Sorbonne Université, INSERM, Paris, France
| | - Salwan Maqdasy
- Department of Medicine (Huddinge), Karolinska Institutet, ME Endokrinologi, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - David Rizo-Roca
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Gianluca Renzi
- Department of Medicine (Huddinge), Karolinska Institutet, ME Endokrinologi, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Ivan Vlassakev
- Department of Medicine (Huddinge), Karolinska Institutet, ME Endokrinologi, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Lynn M Alaeddine
- Department of Medicine (Huddinge), Karolinska Institutet, ME Endokrinologi, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Romane Higos
- Department of Medicine (Huddinge), Karolinska Institutet, ME Endokrinologi, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Jutta Jalkanen
- Department of Medicine (Huddinge), Karolinska Institutet, ME Endokrinologi, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Jiawei Zhong
- Department of Medicine (Huddinge), Karolinska Institutet, ME Endokrinologi, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Danae S Zareifi
- Department of Medicine (Huddinge), Karolinska Institutet, ME Endokrinologi, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Scott Frendo-Cumbo
- Department of Medicine (Huddinge), Karolinska Institutet, ME Endokrinologi, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Lucas Massier
- Department of Medicine (Huddinge), Karolinska Institutet, ME Endokrinologi, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Ondrej Hodek
- Swedish Metabolomics Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Marta Juvany
- Swedish Metabolomics Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Thomas Moritz
- Swedish Metabolomics Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
- The Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thais de Castro Barbosa
- Department of Medicine (Huddinge), Karolinska Institutet, ME Endokrinologi, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Muhmmad Omar-Hmeadi
- Department of Medicine (Huddinge), Karolinska Institutet, ME Endokrinologi, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Marta López-Yus
- Adipocyte and Fat Biology Laboratory (AdipoFat), Translational Research Unit, University Hospital Miguel Servet, Zaragoza, Spain
- Instituto Aragonés de Ciencias de La Salud (IACS), Zaragoza, Spain
- Instituto de Investigación Sanitaria (IIS)-Aragón, Zaragoza, Spain
| | - Fatiha Merabtene
- Nutrition and Obesities: Systemic Approaches Research Group, NutriOmics, Sorbonne Université, INSERM, Paris, France
| | - Jimon Boniface Abatan
- Nutrition and Obesities: Systemic Approaches Research Group, NutriOmics, Sorbonne Université, INSERM, Paris, France
| | - Geneviève Marcelin
- Nutrition and Obesities: Systemic Approaches Research Group, NutriOmics, Sorbonne Université, INSERM, Paris, France
| | - Elie-Julien El Hachem
- Nutrition and Obesities: Systemic Approaches Research Group, NutriOmics, Sorbonne Université, INSERM, Paris, France
| | - Christine Rouault
- Nutrition and Obesities: Systemic Approaches Research Group, NutriOmics, Sorbonne Université, INSERM, Paris, France
| | - Martin O Bergo
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Paul Petrus
- Department of Medicine (Huddinge), Karolinska Institutet, ME Endokrinologi, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Juleen R Zierath
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Karine Clément
- Nutrition and Obesities: Systemic Approaches Research Group, NutriOmics, Sorbonne Université, INSERM, Paris, France
- Nutrition Department, Assistance Publique Hôpitaux de Paris, CRNH Ile-de-France, Pitié-Salpêtrière Hospital, Paris, France
| | - Anna Krook
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Niklas Mejhert
- Department of Medicine (Huddinge), Karolinska Institutet, ME Endokrinologi, Karolinska University Hospital Huddinge, Huddinge, Sweden.
| | - Mikael Rydén
- Department of Medicine (Huddinge), Karolinska Institutet, ME Endokrinologi, Karolinska University Hospital Huddinge, Huddinge, Sweden.
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198
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Chen H, Peng L, Wang Z, He Y, Zhang X. Influence of METTL3 knockdown on PDLSC osteogenesis in E. coli LPS-induced inflammation. Oral Dis 2024; 30:3225-3238. [PMID: 37807890 DOI: 10.1111/odi.14763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/15/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023]
Abstract
OBJECTIVE This study aimed to investigate the effect of METTL3 knockdown on osteogenic differentiation of human periodontal ligament stem cells (PDLSCs) in the weak inflammation microenvironments, as well as the underlying mechanisms. MATERIALS AND METHODS PDLSCs were stimulated by lipopolysaccharide from Escherichia coli (E. coli LPS), followed by quantification of METTL3. METTL3 expression was assessed using RT-qPCR and Western blot analysis in periodontitis. METTL3 knockdown PDLSCs were stimulated with or without E. coli LPS. The evaluation included proinflammatory cytokines, osteogenic markers, ALP activity, and mineralized nodules. Bioinformatics analysis and Western blot determined the association between METTL3 and the PI3K/Akt pathway. RESULTS METTL3 was overexpressed in periodontitis. METTL3 knockdown in PDLSCs reduced proinflammatory cytokines, osteogenic markers, ALP activity, and mineralized nodules in both environments. Bioinformatics analysis suggested a link between METTL3 and the PI3K/Akt pathway. METTL3 knockdown inhibited PI3K/Akt signaling pathway activation. CONCLUSION METTL3 knockdown might inhibit osteogenesis in PDLSCs through the inactivation of PI3K/Akt signaling pathway. Concomitant findings might shed novel light on the roles and potential mechanisms of METTL3 in the LPS-stimulated inflammatory microenvironments of PDLSCs.
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Affiliation(s)
- Hang Chen
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
| | - Limin Peng
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
| | - Zhenxiang Wang
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
| | - Yujuan He
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing, China
| | - Xiaonan Zhang
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
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199
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Skinnider MA, Gautier M, Teo AYY, Kathe C, Hutson TH, Laskaratos A, de Coucy A, Regazzi N, Aureli V, James ND, Schneider B, Sofroniew MV, Barraud Q, Bloch J, Anderson MA, Squair JW, Courtine G. Single-cell and spatial atlases of spinal cord injury in the Tabulae Paralytica. Nature 2024; 631:150-163. [PMID: 38898272 DOI: 10.1038/s41586-024-07504-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 05/01/2024] [Indexed: 06/21/2024]
Abstract
Here, we introduce the Tabulae Paralytica-a compilation of four atlases of spinal cord injury (SCI) comprising a single-nucleus transcriptome atlas of half a million cells, a multiome atlas pairing transcriptomic and epigenomic measurements within the same nuclei, and two spatial transcriptomic atlases of the injured spinal cord spanning four spatial and temporal dimensions. We integrated these atlases into a common framework to dissect the molecular logic that governs the responses to injury within the spinal cord1. The Tabulae Paralytica uncovered new biological principles that dictate the consequences of SCI, including conserved and divergent neuronal responses to injury; the priming of specific neuronal subpopulations to upregulate circuit-reorganizing programs after injury; an inverse relationship between neuronal stress responses and the activation of circuit reorganization programs; the necessity of re-establishing a tripartite neuroprotective barrier between immune-privileged and extra-neural environments after SCI and a failure to form this barrier in old mice. We leveraged the Tabulae Paralytica to develop a rejuvenative gene therapy that re-established this tripartite barrier, and restored the natural recovery of walking after paralysis in old mice. The Tabulae Paralytica provides a window into the pathobiology of SCI, while establishing a framework for integrating multimodal, genome-scale measurements in four dimensions to study biology and medicine.
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Affiliation(s)
- Michael A Skinnider
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Ludwig Institute for Cancer Research, Princeton University, Princeton, NJ, USA
| | - Matthieu Gautier
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Alan Yue Yang Teo
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Claudia Kathe
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Thomas H Hutson
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
- Wyss Center for Bio and Neuroengineering, Geneva, Switzerland
| | - Achilleas Laskaratos
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Alexandra de Coucy
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Nicola Regazzi
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Viviana Aureli
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
- Department of Neurosurgery, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Nicholas D James
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Bernard Schneider
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Bertarelli Platform for Gene Therapy, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Michael V Sofroniew
- Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Quentin Barraud
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Jocelyne Bloch
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
- Department of Neurosurgery, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Mark A Anderson
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland.
- Wyss Center for Bio and Neuroengineering, Geneva, Switzerland.
- Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
| | - Jordan W Squair
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland.
- Department of Neurosurgery, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
| | - Grégoire Courtine
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland.
- Department of Neurosurgery, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
- Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
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Derisoud E, Jiang H, Zhao A, Chavatte-Palmer P, Deng Q. Revealing the molecular landscape of human placenta: a systematic review and meta-analysis of single-cell RNA sequencing studies. Hum Reprod Update 2024; 30:410-441. [PMID: 38478759 PMCID: PMC11215163 DOI: 10.1093/humupd/dmae006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 02/12/2024] [Indexed: 07/02/2024] Open
Abstract
BACKGROUND With increasing significance of developmental programming effects associated with placental dysfunction, more investigations are devoted to improving the characterization and understanding of placental signatures in health and disease. The placenta is a transitory but dynamic organ adapting to the shifting demands of fetal development and available resources of the maternal supply throughout pregnancy. Trophoblasts (cytotrophoblasts, syncytiotrophoblasts, and extravillous trophoblasts) are placental-specific cell types responsible for the main placental exchanges and adaptations. Transcriptomic studies with single-cell resolution have led to advances in understanding the placenta's role in health and disease. These studies, however, often show discrepancies in characterization of the different placental cell types. OBJECTIVE AND RATIONALE We aim to review the knowledge regarding placental structure and function gained from the use of single-cell RNA sequencing (scRNAseq), followed by comparing cell-type-specific genes, highlighting their similarities and differences. Moreover, we intend to identify consensus marker genes for the various trophoblast cell types across studies. Finally, we will discuss the contributions and potential applications of scRNAseq in studying pregnancy-related diseases. SEARCH METHODS We conducted a comprehensive systematic literature review to identify different cell types and their functions at the human maternal-fetal interface, focusing on all original scRNAseq studies on placentas published before March 2023 and published reviews (total of 28 studies identified) using PubMed search. Our approach involved curating cell types and subtypes that had previously been defined using scRNAseq and comparing the genes used as markers or identified as potential new markers. Next, we reanalyzed expression matrices from the six available scRNAseq raw datasets with cell annotations (four from first trimester and two at term), using Wilcoxon rank-sum tests to compare gene expression among studies and annotate trophoblast cell markers in both first trimester and term placentas. Furthermore, we integrated scRNAseq raw data available from 18 healthy first trimester and nine term placentas, and performed clustering and differential gene expression analysis. We further compared markers obtained with the analysis of annotated and raw datasets with the literature to obtain a common signature gene list for major placental cell types. OUTCOMES Variations in the sampling site, gestational age, fetal sex, and subsequent sequencing and analysis methods were observed between the studies. Although their proportions varied, the three trophoblast types were consistently identified across all scRNAseq studies, unlike other non-trophoblast cell types. Notably, no marker genes were shared by all studies for any of the investigated cell types. Moreover, most of the newly defined markers in one study were not observed in other studies. These discrepancies were confirmed by our analysis on trophoblast cell types, where hundreds of potential marker genes were identified in each study but with little overlap across studies. From 35 461 and 23 378 cells of high quality in the first trimester and term placentas, respectively, we obtained major placental cell types, including perivascular cells that previously had not been identified in the first trimester. Importantly, our meta-analysis provides marker genes for major placental cell types based on our extensive curation. WIDER IMPLICATIONS This review and meta-analysis emphasizes the need for establishing a consensus for annotating placental cell types from scRNAseq data. The marker genes identified here can be deployed for defining human placental cell types, thereby facilitating and improving the reproducibility of trophoblast cell annotation.
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Affiliation(s)
- Emilie Derisoud
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Hong Jiang
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Allan Zhao
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Pascale Chavatte-Palmer
- INRAE, BREED, Université Paris-Saclay, UVSQ, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
| | - Qiaolin Deng
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska University Hospital, Solna, Stockholm, Sweden
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