201
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Liu S, Ezran C, Wang MFZ, Li Z, Awayan K, Long JZ, De Vlaminck I, Wang S, Epelbaum J, Kuo CS, Terrien J, Krasnow MA, Ferrell JE. An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome. Nat Commun 2024; 15:2188. [PMID: 38467625 PMCID: PMC10928088 DOI: 10.1038/s41467-024-46070-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 02/07/2024] [Indexed: 03/13/2024] Open
Abstract
Hormones mediate long-range cell communication and play vital roles in physiology, metabolism, and health. Traditionally, endocrinologists have focused on one hormone or organ system at a time. Yet, hormone signaling by its very nature connects cells of different organs and involves crosstalk of different hormones. Here, we leverage the organism-wide single cell transcriptional atlas of a non-human primate, the mouse lemur (Microcebus murinus), to systematically map source and target cells for 84 classes of hormones. This work uncovers previously-uncharacterized sites of hormone regulation, and shows that the hormonal signaling network is densely connected, decentralized, and rich in feedback loops. Evolutionary comparisons of hormonal genes and their expression patterns show that mouse lemur better models human hormonal signaling than mouse, at both the genomic and transcriptomic levels, and reveal primate-specific rewiring of hormone-producing/target cells. This work complements the scale and resolution of classical endocrine studies and sheds light on primate hormone regulation.
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Affiliation(s)
- Shixuan Liu
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
| | - Camille Ezran
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
| | - Michael F Z Wang
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Zhengda Li
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kyle Awayan
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jonathan Z Long
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford, CA, USA
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Sheng Wang
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Jacques Epelbaum
- Adaptive Mechanisms and Evolution (MECADEV), UMR 7179, National Center for Scientific Research, National Museum of Natural History, Brunoy, France
| | - Christin S Kuo
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jérémy Terrien
- Adaptive Mechanisms and Evolution (MECADEV), UMR 7179, National Center for Scientific Research, National Museum of Natural History, Brunoy, France
| | - Mark A Krasnow
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford, CA, USA.
| | - James E Ferrell
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
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202
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Zorc M, Dolinar M, Dovč P. A Single-Cell Transcriptome of Bovine Milk Somatic Cells. Genes (Basel) 2024; 15:349. [PMID: 38540408 PMCID: PMC10970057 DOI: 10.3390/genes15030349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 06/14/2024] Open
Abstract
The production of milk by dairy cows far exceeds the nutritional needs of the calf and is vital for the economical use of dairy cattle. High milk yield is a unique production trait that can be effectively enhanced through traditional selection methods. The process of lactation in cows serves as an excellent model for studying the biological aspects of lactation with the aim of exploring the mechanistic base of this complex trait at the cellular level. In this study, we analyzed the milk transcriptome at the single-cell level by conducting scRNA-seq analysis on milk samples from two Holstein Friesian cows at mid-lactation (75 and 93 days) using the 10× Chromium platform. Cells were pelleted and fat was removed from milk by centrifugation. The cell suspension from each cow was loaded on separate channels, resulting in the recovery of 9313 and 14,544 cells. Library samples were loaded onto two lanes of the NovaSeq 6000 (Illumina) instrument. After filtering at the cell and gene levels, a total of 7988 and 13,973 cells remained, respectively. We were able to reconstruct different cell types (milk-producing cells, progenitor cells, macrophages, monocytes, dendritic cells, T cells, B cells, mast cells, and neutrophils) in bovine milk. Our findings provide a valuable resource for identifying regulatory elements associated with various functions of the mammary gland such as lactation, tissue renewal, native immunity, protein and fat synthesis, and hormonal response.
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Affiliation(s)
| | | | - Peter Dovč
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; (M.Z.); (M.D.)
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203
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Zhang Z, Leng XK, Zhai YY, Zhang X, Sun ZW, Xiao JY, Lu JF, Liu K, Xia B, Gao Q, Jia M, Xu CQ, Jiang YN, Zhang XG, Tao KS, Wu JW. Deficiency of ASGR1 promotes liver injury by increasing GP73-mediated hepatic endoplasmic reticulum stress. Nat Commun 2024; 15:1908. [PMID: 38459023 PMCID: PMC10924105 DOI: 10.1038/s41467-024-46135-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 02/13/2024] [Indexed: 03/10/2024] Open
Abstract
Liver injury is a core pathological process in the majority of liver diseases, yet the genetic factors predisposing individuals to its initiation and progression remain poorly understood. Here we show that asialoglycoprotein receptor 1 (ASGR1), a lectin specifically expressed in the liver, is downregulated in patients with liver fibrosis or cirrhosis and male mice with liver injury. ASGR1 deficiency exacerbates while its overexpression mitigates acetaminophen-induced acute and CCl4-induced chronic liver injuries in male mice. Mechanistically, ASGR1 binds to an endoplasmic reticulum stress mediator GP73 and facilitates its lysosomal degradation. ASGR1 depletion increases circulating GP73 levels and promotes the interaction between GP73 and BIP to activate endoplasmic reticulum stress, leading to liver injury. Neutralization of GP73 not only attenuates ASGR1 deficiency-induced liver injuries but also improves survival in mice received a lethal dose of acetaminophen. Collectively, these findings identify ASGR1 as a potential genetic determinant of susceptibility to liver injury and propose it as a therapeutic target for the treatment of liver injury.
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Affiliation(s)
- Zhe Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiang Kai Leng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yuan Yuan Zhai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiao Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhi Wei Sun
- Beijing Sungen Biomedical Technology Co. Ltd, Beijing, China
| | - Jun Ying Xiao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jun Feng Lu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Kun Liu
- Department of Hepatobiliary Surgery, Xi-Jing Hospital, Air Force Medical University, Xi'an, China
| | - Bo Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qi Gao
- Beijing Sungen Biomedical Technology Co. Ltd, Beijing, China
| | - Miao Jia
- Beijing Sungen Biomedical Technology Co. Ltd, Beijing, China
| | - Cheng Qi Xu
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Na Jiang
- Department of Pathology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiao Gang Zhang
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
| | - Kai Shan Tao
- Department of Hepatobiliary Surgery, Xi-Jing Hospital, Air Force Medical University, Xi'an, China.
| | - Jiang Wei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.
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204
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Kao YR, Chen J, Kumari R, Ng A, Zintiridou A, Tatiparthy M, Ma Y, Aivalioti MM, Moulik D, Sundaravel S, Sun D, Reisz JA, Grimm J, Martinez-Lopez N, Stransky S, Sidoli S, Steidl U, Singh R, D'Alessandro A, Will B. An iron rheostat controls hematopoietic stem cell fate. Cell Stem Cell 2024; 31:378-397.e12. [PMID: 38402617 PMCID: PMC10939794 DOI: 10.1016/j.stem.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 12/20/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
Mechanisms governing the maintenance of blood-producing hematopoietic stem and multipotent progenitor cells (HSPCs) are incompletely understood, particularly those regulating fate, ensuring long-term maintenance, and preventing aging-associated stem cell dysfunction. We uncovered a role for transitory free cytoplasmic iron as a rheostat for adult stem cell fate control. We found that HSPCs harbor comparatively small amounts of free iron and show the activation of a conserved molecular response to limited iron-particularly during mitosis. To study the functional and molecular consequences of iron restriction, we developed models allowing for transient iron bioavailability limitation and combined single-molecule RNA quantification, metabolomics, and single-cell transcriptomic analyses with functional studies. Our data reveal that the activation of the limited iron response triggers coordinated metabolic and epigenetic events, establishing stemness-conferring gene regulation. Notably, we find that aging-associated cytoplasmic iron loading reversibly attenuates iron-dependent cell fate control, explicating intervention strategies for dysfunctional aged stem cells.
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Affiliation(s)
- Yun-Ruei Kao
- Department of Oncology, Albert Einstein College of Medicine, New York, NY, USA.
| | - Jiahao Chen
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Rajni Kumari
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Anita Ng
- Karches Center for Oncology Research, the Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Aliona Zintiridou
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Madhuri Tatiparthy
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Yuhong Ma
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Maria M Aivalioti
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Deeposree Moulik
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Sriram Sundaravel
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Daqian Sun
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Julie A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Juliane Grimm
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Nuria Martinez-Lopez
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, Los Angeles, CA, USA; Comprehensive Liver Research Center at University of California Los Angeles, CA, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Ulrich Steidl
- Department of Oncology, Albert Einstein College of Medicine, New York, NY, USA; Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA; Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, New York, NY, USA; Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA; Cancer Dormancy and Tumor Microenvironment Institute, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rajat Singh
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, Los Angeles, CA, USA; Comprehensive Liver Research Center at University of California Los Angeles, CA, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Britta Will
- Department of Oncology, Albert Einstein College of Medicine, New York, NY, USA; Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA; Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, New York, NY, USA; Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA; Cancer Dormancy and Tumor Microenvironment Institute, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA; Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY, USA.
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205
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Zhang Z, Schaefer C, Jiang W, Lu Z, Lee J, Sziraki A, Abdulraouf A, Wick B, Haeussler M, Li Z, Molla G, Satija R, Zhou W, Cao J. A Panoramic View of Cell Population Dynamics in Mammalian Aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.583001. [PMID: 38496474 PMCID: PMC10942312 DOI: 10.1101/2024.03.01.583001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
To elucidate the aging-associated cellular population dynamics throughout the body, here we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissue samples, encompassing a range of organs across different life stages, sexes, and genotypes. This comprehensive dataset allowed us to identify more than 3,000 unique cellular states and catalog over 200 distinct aging-associated cell populations experiencing significant depletion or expansion. Our panoramic analysis uncovered temporally structured, organ- and lineage-specific shifts of cellular dynamics during lifespan progression. Moreover, we investigated aging-associated alterations in immune cell populations, revealing both widespread shifts and organ-specific changes. We further explored the regulatory roles of the immune system on aging and pinpointed specific age-related cell population expansions that are lymphocyte-dependent. The breadth and depth of our 'cell-omics' methodology not only enhance our comprehension of cellular aging but also lay the groundwork for exploring the complex regulatory networks among varied cell types in the context of aging and aging-associated diseases.
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Affiliation(s)
- Zehao Zhang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Chloe Schaefer
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Weirong Jiang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Ziyu Lu
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Jasper Lee
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Andras Sziraki
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Abdulraouf Abdulraouf
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The Tri-Institutional M.D-Ph.D Program, New York, NY, USA
| | - Brittney Wick
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | - Zhuoyan Li
- New York Genome Center, New York, NY, USA
| | | | - Rahul Satija
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Wei Zhou
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Junyue Cao
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
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206
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Hanhart D, Gossi F, Rapsomaniki MA, Kruithof-de Julio M, Chouvardas P. ScLinear predicts protein abundance at single-cell resolution. Commun Biol 2024; 7:267. [PMID: 38438709 PMCID: PMC10912329 DOI: 10.1038/s42003-024-05958-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/22/2024] [Indexed: 03/06/2024] Open
Abstract
Single-cell multi-omics have transformed biomedical research and present exciting machine learning opportunities. We present scLinear, a linear regression-based approach that predicts single-cell protein abundance based on RNA expression. ScLinear is vastly more efficient than state-of-the-art methodologies, without compromising its accuracy. ScLinear is interpretable and accurately generalizes in unseen single-cell and spatial transcriptomics data. Importantly, we offer a critical view in using complex algorithms ignoring simpler, faster, and more efficient approaches.
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Affiliation(s)
- Daniel Hanhart
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Federico Gossi
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | | | - Marianna Kruithof-de Julio
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Department of Urology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
| | - Panagiotis Chouvardas
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland.
- Department of Urology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland.
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207
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Michielsen L, Reinders MJT, Mahfouz A. Predicting cell population-specific gene expression from genomic sequence. FRONTIERS IN BIOINFORMATICS 2024; 4:1347276. [PMID: 38501113 PMCID: PMC10944912 DOI: 10.3389/fbinf.2024.1347276] [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: 11/30/2023] [Accepted: 01/23/2024] [Indexed: 03/20/2024] Open
Abstract
Most regulatory elements, especially enhancer sequences, are cell population-specific. One could even argue that a distinct set of regulatory elements is what defines a cell population. However, discovering which non-coding regions of the DNA are essential in which context, and as a result, which genes are expressed, is a difficult task. Some computational models tackle this problem by predicting gene expression directly from the genomic sequence. These models are currently limited to predicting bulk measurements and mainly make tissue-specific predictions. Here, we present a model that leverages single-cell RNA-sequencing data to predict gene expression. We show that cell population-specific models outperform tissue-specific models, especially when the expression profile of a cell population and the corresponding tissue are dissimilar. Further, we show that our model can prioritize GWAS variants and learn motifs of transcription factor binding sites. We envision that our model can be useful for delineating cell population-specific regulatory elements.
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Affiliation(s)
- Lieke Michielsen
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
| | - Marcel J. T. Reinders
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
| | - Ahmed Mahfouz
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
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208
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Furtado J, Eichmann A. Vascular development, remodeling and maturation. Curr Top Dev Biol 2024; 159:344-370. [PMID: 38729681 DOI: 10.1016/bs.ctdb.2024.02.001] [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] [Indexed: 05/12/2024]
Abstract
The development of the vascular system is crucial in supporting the growth and health of all other organs in the body, and vascular system dysfunction is the major cause of human morbidity and mortality. This chapter discusses three successive processes that govern vascular system development, starting with the differentiation of the primitive vascular system in early embryonic development, followed by its remodeling into a functional circulatory system composed of arteries and veins, and its final maturation and acquisition of an organ specific semi-permeable barrier that controls nutrient uptake into tissues and hence controls organ physiology. Along these steps, endothelial cells forming the inner lining of all blood vessels acquire extensive heterogeneity in terms of gene expression patterns and function, that we are only beginning to understand. These advances contribute to overall knowledge of vascular biology and are predicted to unlock the unprecedented therapeutic potential of the endothelium as an avenue for treatment of diseases associated with dysfunctional vasculature.
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Affiliation(s)
- Jessica Furtado
- Department of Molecular and Cellular Physiology, Yale University School of Medicine, New Haven, CT, United States; Cardiovascular Research Center, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Anne Eichmann
- Department of Molecular and Cellular Physiology, Yale University School of Medicine, New Haven, CT, United States; Cardiovascular Research Center, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, United States; Paris Cardiovascular Research Center, Inserm U970, Université Paris, Paris, France.
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209
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Alcober-Boquet L, Kraus N, Huber LS, Vutukuri R, Fuhrmann DC, Stross C, Schaefer L, Scholich K, Zeuzem S, Piiper A, Schulz MH, Trebicka J, Welsch C, Ortiz C. BI-3231, an enzymatic inhibitor of HSD17B13, reduces lipotoxic effects induced by palmitic acid in murine and human hepatocytes. Am J Physiol Cell Physiol 2024; 326:C880-C892. [PMID: 38223924 DOI: 10.1152/ajpcell.00413.2023] [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: 08/29/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/16/2024]
Abstract
17-β-hydroxysteroid dehydrogenase 13 (HSD17B13), a lipid droplet-associated enzyme, is primarily expressed in the liver and plays an important role in lipid metabolism. Targeted inhibition of enzymatic function is a potential therapeutic strategy for treating steatotic liver disease (SLD). The present study is aimed at investigating the effects of the first selective HSD17B13 inhibitor, BI-3231, in a model of hepatocellular lipotoxicity using human cell lines and primary mouse hepatocytes in vitro. Lipotoxicity was induced with palmitic acid in HepG2 cells and freshly isolated mouse hepatocytes and the cells were coincubated with BI-3231 to assess the protective effects. Under lipotoxic stress, triglyceride (TG) accumulation was significantly decreased in the BI-3231-treated cells compared with that of the control untreated human and mouse hepatocytes. In addition, treatment with BI-3231 led to considerable improvement in hepatocyte proliferation, cell differentiation, and lipid homeostasis. Mechanistically, BI-3231 increased the mitochondrial respiratory function without affecting β-oxidation. BI-3231 inhibited the lipotoxic effects of palmitic acid in hepatocytes, highlighting the potential of targeting HSD17B13 as a specific therapeutic approach in steatotic liver disease.NEW & NOTEWORTHY 17-β-Hydroxysteroid dehydrogenase 13 (HSD17B13) is a lipid droplet protein primarily expressed in the liver hepatocytes. HSD17B13 is associated with the clinical outcome of chronic liver diseases and is therefore a target for the development of drugs. Here, we demonstrate the promising therapeutic effect of BI-3231 as a potent inhibitor of HSD17B13 based on its ability to inhibit triglyceride accumulation in lipid droplets (LDs), restore lipid metabolism and homeostasis, and increase mitochondrial activity in vitro.
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Affiliation(s)
- Lucia Alcober-Boquet
- Medical Clinic 1, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - Nico Kraus
- Medical Clinic 1, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - Lisa Sophie Huber
- Faculty of Medicine, Institute of Pharmacology and Toxicology, Goethe University Frankfurt, Frankfurt, Germany
| | - Rajkumar Vutukuri
- Faculty of Medicine, Institute of Pharmacology and Toxicology, Goethe University Frankfurt, Frankfurt, Germany
| | - Dominik C Fuhrmann
- Faculty of Medicine, Institute of Biochemistry I, Goethe University Frankfurt, Frankfurt, Germany
| | - Claudia Stross
- Medical Clinic 1, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - Liliana Schaefer
- Faculty of Medicine, Institute of Pharmacology and Toxicology, Goethe University Frankfurt, Frankfurt, Germany
| | - Klaus Scholich
- Faculty of Medicine, Institute of Clinical Pharmacology, Goethe University Frankfurt, Frankfurt, Germany
| | - Stefan Zeuzem
- Medical Clinic 1, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - Albrecht Piiper
- Medical Clinic 1, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - Marcel H Schulz
- Faculty of Medicine, Institute of Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt, Germany
| | - Jonel Trebicka
- Department of Internal Medicine B, University Hospital Münster, Münster, Germany
| | - Christoph Welsch
- Medical Clinic 1, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - Cristina Ortiz
- Medical Clinic 1, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
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210
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Elliott A, Walters RK, Pirinen M, Kurki M, Junna N, Goldstein JI, Reeve MP, Siirtola H, Lemmelä SM, Turley P, Lahtela E, Mehtonen J, Reis K, Elnahas AG, Reigo A, Palta P, Esko T, Mägi R, Palotie A, Daly MJ, Widén E. Distinct and shared genetic architectures of gestational diabetes mellitus and type 2 diabetes. Nat Genet 2024; 56:377-382. [PMID: 38182742 PMCID: PMC10937370 DOI: 10.1038/s41588-023-01607-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 11/07/2023] [Indexed: 01/07/2024]
Abstract
Gestational diabetes mellitus (GDM) is a common metabolic disorder affecting more than 16 million pregnancies annually worldwide1,2. GDM is related to an increased lifetime risk of type 2 diabetes (T2D)1-3, with over a third of women developing T2D within 15 years of their GDM diagnosis. The diseases are hypothesized to share a genetic predisposition1-7, but few studies have sought to uncover the genetic underpinnings of GDM. Most studies have evaluated the impact of T2D loci only8-10, and the three prior genome-wide association studies of GDM11-13 have identified only five loci, limiting the power to assess to what extent variants or biological pathways are specific to GDM. We conducted the largest genome-wide association study of GDM to date in 12,332 cases and 131,109 parous female controls in the FinnGen study and identified 13 GDM-associated loci, including nine new loci. Genetic features distinct from T2D were identified both at the locus and genomic scale. Our results suggest that the genetics of GDM risk falls into the following two distinct categories: one part conventional T2D polygenic risk and one part predominantly influencing mechanisms disrupted in pregnancy. Loci with GDM-predominant effects map to genes related to islet cells, central glucose homeostasis, steroidogenesis and placental expression.
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Grants
- R00 AG062787 NIA NIH HHS
- R01 MH101244 NIMH NIH HHS
- A.E. was a research Scholar supported by Sarnoff Cardiovascular Research Foundation
- U.S. Department of Health & Human Services | National Institutes of Health (NIH)
- Academy of Finland (Suomen Akatemia)
- U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)
- The FinnGen project is funded by two grants from Business Finland (HUS 4685/31/2016 and UH 4386/31/2016) and by eleven industry partners (AbbVie Inc, AstraZeneca UK Ltd, Biogen MA Inc, Celgene Corporation, Celgene International II Sàrl, Genentech Inc, Merck Sharp & Dohme Corp, Pfizer Inc., GlaxoSmithKline, Sanofi, Maze Therapeutics Inc., Janssen Biotech Inc).
- EstBB GWAS analysis is supported by research funding from the Estonian Research Council: Team grant PRG1291 and PRG1911.
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Affiliation(s)
- Amanda Elliott
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Raymond K Walters
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Matti Pirinen
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Mitja Kurki
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Nella Junna
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Jacqueline I Goldstein
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mary Pat Reeve
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Harri Siirtola
- TAUCHI Research Center, Faculty of Information Technology and Communication Sciences (ITC), Tampere University, Tampere, Finland
| | - Susanna M Lemmelä
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Patrick Turley
- Center for Economic and Social Research, University of Southern California, Los Angeles, CA, USA
- Department of Economics, University of Southern California, Los Angeles, CA, USA
| | - Elisa Lahtela
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Juha Mehtonen
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Kadri Reis
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Anu Reigo
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Priit Palta
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tõnu Esko
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Aarno Palotie
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland.
| | - Elisabeth Widén
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland.
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211
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Li T, Qian K, Wang X, Li WV, Li H. scBiG for representation learning of single-cell gene expression data based on bipartite graph embedding. NAR Genom Bioinform 2024; 6:lqae004. [PMID: 38288376 PMCID: PMC10823585 DOI: 10.1093/nargab/lqae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/19/2023] [Accepted: 01/09/2024] [Indexed: 01/31/2024] Open
Abstract
Analyzing single-cell RNA sequencing (scRNA-seq) data remains a challenge due to its high dimensionality, sparsity and technical noise. Recognizing the benefits of dimensionality reduction in simplifying complexity and enhancing the signal-to-noise ratio, we introduce scBiG, a novel graph node embedding method designed for representation learning in scRNA-seq data. scBiG establishes a bipartite graph connecting cells and expressed genes, and then constructs a multilayer graph convolutional network to learn cell and gene embeddings. Through a series of extensive experiments, we demonstrate that scBiG surpasses commonly used dimensionality reduction techniques in various analytical tasks. Downstream tasks encompass unsupervised cell clustering, cell trajectory inference, gene expression reconstruction and gene co-expression analysis. Additionally, scBiG exhibits notable computational efficiency and scalability. In summary, scBiG offers a useful graph neural network framework for representation learning in scRNA-seq data, empowering a diverse array of downstream analyses.
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Affiliation(s)
- Ting Li
- School of Mathematics and Physics, China University of Geosciences, Wuhan 430074, China
| | - Kun Qian
- School of Mathematics and Physics, China University of Geosciences, Wuhan 430074, China
| | - Xiang Wang
- School of Mathematics and Physics, China University of Geosciences, Wuhan 430074, China
| | - Wei Vivian Li
- Department of Statistics, University of California, Riverside, Riverside, CA 92507, USA
| | - Hongwei Li
- School of Mathematics and Physics, China University of Geosciences, Wuhan 430074, China
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212
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Lin A, Ramaswamy Y, Misra A. Developmental heterogeneity of vascular cells: Insights into cellular plasticity in atherosclerosis? Semin Cell Dev Biol 2024; 155:3-15. [PMID: 37316416 DOI: 10.1016/j.semcdb.2023.06.002] [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: 05/03/2023] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 06/16/2023]
Abstract
Smooth muscle cells, endothelial cells and macrophages display remarkable heterogeneity within the healthy vasculature and under pathological conditions. During development, these cells arise from numerous embryological origins, which confound with different microenvironments to generate postnatal vascular cell diversity. In the atherosclerotic plaque milieu, all these cell types exhibit astonishing plasticity, generating a variety of plaque burdening or plaque stabilizing phenotypes. And yet how developmental origin influences intraplaque cell plasticity remains largely unexplored despite evidence suggesting this may be the case. Uncovering the diversity and plasticity of vascular cells is being revolutionized by unbiased single cell whole transcriptome analysis techniques that will likely continue to pave the way for therapeutic research. Cellular plasticity is only just emerging as a target for future therapeutics, and uncovering how intraplaque plasticity differs across vascular beds may provide key insights into why different plaques behave differently and may confer different risks of subsequent cardiovascular events.
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Affiliation(s)
- Alexander Lin
- Atherosclerosis and Vascular Remodeling Group, Heart Research Institute, Sydney, NSW, Australia; School of Biomedical Engineering, Faculty of Engineering, The University of Sydney, Sydney, NSW, Australia
| | - Yogambha Ramaswamy
- School of Biomedical Engineering, Faculty of Engineering, The University of Sydney, Sydney, NSW, Australia
| | - Ashish Misra
- Atherosclerosis and Vascular Remodeling Group, Heart Research Institute, Sydney, NSW, Australia; Heart Research Institute, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
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213
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Lin QY, Yu WJ, Bai J, Jiang WX, Li HH. Mac-1 deficiency ameliorates pressure overloaded heart failure through inhibiting macrophage polarization and activation. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167048. [PMID: 38296117 DOI: 10.1016/j.bbadis.2024.167048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/03/2024]
Abstract
Persistent pressure overload commonly leads to pathological cardiac hypertrophy and remodeling, ultimately leading to heart failure (HF). Cardiac remodeling is associated with the involvement of immune cells and the inflammatory response in pathogenesis. The macrophage-1 antigen (Mac-1) is specifically expressed on leukocytes and regulates their migration and polarization. Nonetheless, the involvement of Mac-1 in cardiac remodeling and HF caused by pressure overload has not been determined. The Mac-1-knockout (KO) and wild-type (WT) mice were subjected to transverse aortic constriction (TAC) for 6 weeks. Echocardiography and pressure-volume loop assessments were used to evaluate cardiac function, and cardiac remodeling and macrophage infiltration and polarization were estimated by histopathology and molecular techniques. The findings of our study demonstrated that Mac-1 expression was markedly increased in hearts subjected to TAC treatment. Moreover, compared with WT mice, Mac-1-KO mice exhibited dramatically ameliorated TAC-induced cardiac dysfunction, hypertrophy, fibrosis, oxidative stress and apoptosis. The potential positive impacts may be linked to the inhibition of macrophage infiltration and M1 polarization via reductions in NF-kB and STAT1 expression and upregulation of STAT6. In conclusion, this research reveals a new function of Mac-1 deficiency in reducing pathological cardiac remodeling and HF caused by pressure overload. Additionally, inhibiting Mac-1 could be a potential treatment option for patients with HF in a clinical setting.
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Affiliation(s)
- Qiu-Yue Lin
- Institute of Cardiovascular Diseases, First Affiliated Hospital of Dalian Medical University, Dalian, China.
| | - Wei-Jia Yu
- Institute of Cardiovascular Diseases, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jie Bai
- School of Public Health, Dalian Medical University, Dalian, China
| | - Wen-Xi Jiang
- Department of Emergency Medicine, Beijing Key Laboratory of Cardiopulmonary Cerebral Resuscitation, Beijing Chao-Yang Hospital, Capital Medical University, China
| | - Hui-Hua Li
- Institute of Cardiovascular Diseases, First Affiliated Hospital of Dalian Medical University, Dalian, China; Department of Emergency Medicine, Beijing Key Laboratory of Cardiopulmonary Cerebral Resuscitation, Beijing Chao-Yang Hospital, Capital Medical University, China.
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214
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Teichmann T, Malacarne P, Zehr S, Günther S, Pflüger-Müller B, Warwick T, Brandes RP. NCoR1 limits angiogenic capacity by altering Notch signaling. J Mol Cell Cardiol 2024; 188:65-78. [PMID: 38359551 DOI: 10.1016/j.yjmcc.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/15/2024] [Accepted: 02/06/2024] [Indexed: 02/17/2024]
Abstract
Corepressors negatively regulate gene expression by chromatin compaction. Targeted regulation of gene expression could provide a means to control endothelial cell phenotype. We hypothesize that by targeting corepressor proteins, endothelial angiogenic function can be improved. To study this, the expression and function of nuclear corepressors in human umbilical vein endothelial cells (HUVEC) and in murine organ culture was studied. RNA-seq revealed that nuclear receptor corepressor 1 (NCoR1), silencing mediator of retinoid and thyroid hormone receptors (SMRT) and repressor element-1 silencing transcription factor (REST) are the highest expressed corepressors in HUVECs. Knockout and knockdown strategies demonstrated that the depletion of NCoR1 increased the angiogenic capacity of endothelial cells, whereas depletion of SMRT or REST did not. Interestingly, the effect was VEGF signaling independent. NCoR1 depletion significantly upregulated angiogenesis-associated genes, especially tip cell genes, including ESM1, DLL4 and NOTCH4, as observed by RNA- and ATAC-seq. Confrontation assays comparing cells with and without NCoR1-deficiency revealed that loss of NCoR1 promotes a tip-cell position during spheroid sprouting. Moreover, a proximity ligation assay identified NCoR1 as a direct binding partner of the Notch-signaling-related transcription factor RBPJk. Luciferase assays showed that siRNA-mediated knockdown of NCOR1 promotes RBPJk activity. Furthermore, NCoR1 depletion prompts upregulation of several elements in the Notch signaling cascade. Downregulation of NOTCH4, but not NOTCH1, prevented the positive effect of NCOR1 knockdown on spheroid outgrowth. Collectively, these data indicate that decreasing NCOR1 expression is an attractive approach to promote angiogenic function.
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Affiliation(s)
- Tom Teichmann
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main 60590, Germany; German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt am Main, Germany
| | - Pedro Malacarne
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main 60590, Germany; German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt am Main, Germany
| | - Simonida Zehr
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main 60590, Germany; German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt am Main, Germany
| | - Stefan Günther
- Max-Planck-Institute for Heart- and Lung Research (MPI-HLR), Bad Nauheim 61231, Germany
| | - Beatrice Pflüger-Müller
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main 60590, Germany; German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt am Main, Germany
| | - Timothy Warwick
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main 60590, Germany; German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt am Main, Germany.
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main 60590, Germany; German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt am Main, Germany.
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215
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Moos P, Cheminant J, Adhikari U, Venosa A. Transcriptomic-based roadmap to the healthy and ozone-exposed lung. CURRENT OPINION IN TOXICOLOGY 2024; 37:100445. [PMID: 38187954 PMCID: PMC10769160 DOI: 10.1016/j.cotox.2023.100445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The lung is constantly exposed to a myriad of exogenous stressors. Ground-level ozone represents a ubiquitous and extremely reactive anthropogenic toxicant, impacting the health of millions across the globe. While abundant, epidemiological, in vivo, and in vitro data focuses the ozone toxicity in individual cell types (e.g. epithelial type II, alveolar macrophages) or signaling pathways involved in the injury (e.g., akt, glutathione). When appropriately used, bulk and single cell RNA sequencing techniques have the potential to provide complete, and in certain cases unbiased, information of the molecular events taking place in the steady state and injured lung, and even capture the phenotypic diversity of neighboring cells. To this end, this review compiles information pertaining to the latest understanding of lung cell identity and activation in the steady state and ozone exposed lung. In addition, it discusses the value and benefits of multi-omics approaches and other tools developed to predict cell-cell communication and dissect spatial heterogeneity.
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Affiliation(s)
- Philip Moos
- Department of Pharmacology and Toxicology, University of Utah College of Pharmacy, Salt Lake City, Utah
| | - Jenna Cheminant
- Department of Pharmacology and Toxicology, University of Utah College of Pharmacy, Salt Lake City, Utah
| | - Ujjwal Adhikari
- Department of Pharmacology and Toxicology, University of Utah College of Pharmacy, Salt Lake City, Utah
| | - Alessandro Venosa
- Department of Pharmacology and Toxicology, University of Utah College of Pharmacy, Salt Lake City, Utah
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216
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Xu Y, Zhang W, Zheng X, Cai X. Combining Global-Constrained Concept Factorization and a Regularized Gaussian Graphical Model for Clustering Single-Cell RNA-seq Data. Interdiscip Sci 2024; 16:1-15. [PMID: 37815679 DOI: 10.1007/s12539-023-00587-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 10/11/2023]
Abstract
Single-cell RNA sequencing technology is one of the most cost-effective ways to uncover transcriptomic heterogeneity. With the rapid rise of this technology, enormous amounts of scRNA-seq data have been produced. Due to the high dimensionality, noise, sparsity and missing features of the available scRNA-seq data, accurately clustering the scRNA-seq data for downstream analysis is a significant challenge. Many computational methods have been designed to address this issue; nevertheless, the efficacy of the available methods is still inadequate. In addition, most similarity-based methods require a number of clusters as input, which is difficult to achieve in real applications. In this study, we developed a novel computational method for clustering scRNA-seq data by considering both global and local information, named GCFG. This method characterizes the global properties of data by applying concept factorization, and the regularized Gaussian graphical model is utilized to evaluate the local embedding relationship of data. To learn the cell-cell similarity matrix, we integrated the two components, and an iterative optimization algorithm was developed. The categorization of single cells is obtained by applying Louvain, a modularity-based community discovery algorithm, to the similarity matrix. The behavior of the GCFG approach is assessed on 14 real scRNA-seq datasets in terms of ACC and ARI, and comparison results with 17 other competitive methods suggest that GCFG is effective and robust.
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Affiliation(s)
- Yaxin Xu
- School of Sciences, East China Jiaotong University, Nanchang, 330013, China
| | - Wei Zhang
- School of Sciences, East China Jiaotong University, Nanchang, 330013, China.
| | - Xiaoying Zheng
- Operations Research and Planning Department, Naval University of Engineering, Wuhan, 430033, China
| | - Xianxian Cai
- School of Sciences, East China Jiaotong University, Nanchang, 330013, China
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217
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Mao A, Zhang K, Kan H, Gao M, Wang Z, Zhou T, Shao J, He D. Single-Cell RNA-Seq Reveals Coronary Heterogeneity and Identifies CD133 +TRPV4 high Endothelial Subpopulation in Regulating Flow-Induced Vascular Tone in Mice. Arterioscler Thromb Vasc Biol 2024; 44:653-665. [PMID: 38269590 PMCID: PMC10880935 DOI: 10.1161/atvbaha.123.319516] [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: 04/27/2023] [Accepted: 01/10/2024] [Indexed: 01/26/2024]
Abstract
BACKGROUND Single-cell RNA-Seq analysis can determine the heterogeneity of cells between different tissues at a single-cell level. Coronary artery endothelial cells (ECs) are important to coronary blood flow. However, little is known about the heterogeneity of coronary artery ECs, and cellular identity responses to flow. Identifying endothelial subpopulations will contribute to the precise localization of vascular endothelial subpopulations, thus enabling the precision of vascular injury treatment. METHODS Here, we performed a single-cell RNA sequencing of 31 962 cells and functional assays of 3 branches of the coronary arteries (right coronary artery/circumflex left coronary artery/anterior descending left coronary artery) in wild-type mice. RESULTS We found a compendium of 7 distinct cell types in mouse coronary arteries, mainly ECs, granulocytes, cardiac myocytes, smooth muscle cells, lymphocytes, myeloid cells, and fibroblast cells, and showed spatial heterogeneity between arterial branches. Furthermore, we revealed a subpopulation of coronary artery ECs, CD133+TRPV4high ECs. TRPV4 (transient receptor potential vanilloid 4) in CD133+TRPV4high ECs is important for regulating vasodilation and coronary blood flow. CONCLUSIONS Our study elucidates the nature and range of coronary arterial cell diversity and highlights the importance of coronary CD133+TRPV4high ECs in regulating coronary vascular tone.
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Affiliation(s)
- Aiqin Mao
- Wuxi School of Medicine (A.M., K.Z., H.K., M.G., Z.W., T.Z., J.S.), Jiangnan University, China
- School of Food Science and Technology (A.M., D.H.), Jiangnan University, China
| | - Ka Zhang
- Wuxi School of Medicine (A.M., K.Z., H.K., M.G., Z.W., T.Z., J.S.), Jiangnan University, China
| | - Hao Kan
- Wuxi School of Medicine (A.M., K.Z., H.K., M.G., Z.W., T.Z., J.S.), Jiangnan University, China
| | - Mengru Gao
- Wuxi School of Medicine (A.M., K.Z., H.K., M.G., Z.W., T.Z., J.S.), Jiangnan University, China
| | - Zhiwei Wang
- Wuxi School of Medicine (A.M., K.Z., H.K., M.G., Z.W., T.Z., J.S.), Jiangnan University, China
| | - Tingting Zhou
- Wuxi School of Medicine (A.M., K.Z., H.K., M.G., Z.W., T.Z., J.S.), Jiangnan University, China
| | - Jing Shao
- Wuxi School of Medicine (A.M., K.Z., H.K., M.G., Z.W., T.Z., J.S.), Jiangnan University, China
| | - Dongxu He
- School of Food Science and Technology (A.M., D.H.), Jiangnan University, China
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218
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Radványi Á, Röszer T. Interleukin-6: An Under-Appreciated Inducer of Thermogenic Adipocyte Differentiation. Int J Mol Sci 2024; 25:2810. [PMID: 38474057 DOI: 10.3390/ijms25052810] [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: 01/27/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Adipose tissue inflammation is a key factor leading to obesity-associated immune disorders, such as insulin resistance, beta cell loss in the pancreatic islets, meta-inflammation, and autoimmunity. Inhibiting adipose tissue inflammation is considered a straightforward approach to abrogate these diseases. However, recent findings show that certain pro-inflammatory cytokines are essential for the proper differentiation and functioning of adipocytes. Lipolysis is stimulated, and the thermogenic competence of adipocytes is unlocked by interleukin-6 (IL-6), a cytokine that was initially recognized as a key trigger of adipose tissue inflammation. Coherently, signal transducer and activator of transcription 3 (STAT3), which is a signal transducer for IL-6, is necessary for thermogenic adipocyte development. Given the impact of thermogenic adipocytes in increasing energy expenditure and reducing body adiposity, functions of IL-6 in the adipose tissue have gained attention recently. In this review, we show that IL-6 signaling may protect from excess fat accumulation by stimulating thermogenesis in adipocytes.
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Affiliation(s)
- Ádám Radványi
- Department of Pediatrics, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Tamás Röszer
- Department of Pediatrics, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
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219
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Merotto L, Sturm G, Dietrich A, List M, Finotello F. Making mouse transcriptomics deconvolution accessible with immunedeconv. BIOINFORMATICS ADVANCES 2024; 4:vbae032. [PMID: 38464974 PMCID: PMC10924280 DOI: 10.1093/bioadv/vbae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/01/2024] [Accepted: 02/26/2024] [Indexed: 03/12/2024]
Abstract
Summary Transcriptome deconvolution has emerged as a reliable technique to estimate cell-type abundances from bulk RNA sequencing data. Unlike their human equivalents, methods to quantify the cellular composition of complex tissues from murine transcriptomics are sparse and sometimes not easy to use. We extended the immunedeconv R package to facilitate the deconvolution of mouse transcriptomics, enabling the quantification of murine immune-cell types using 13 different methods. Through immunedeconv, we further offer the possibility of tweaking cell signatures used by deconvolution methods, providing custom annotations tailored for specific cell types and tissues. These developments strongly facilitate the study of the immune-cell composition of mouse models and further open new avenues in the investigation of the cellular composition of other tissues and organisms. Availability and implementation The R package and the documentation are available at https://github.com/omnideconv/immunedeconv.
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Affiliation(s)
- Lorenzo Merotto
- Department of Molecular Biology, Digital Science Center (DiSC), University of Innsbruck, Innsbruck 6020, Austria
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck 6020, Austria
- Boehringer Ingelheim International Pharma GmbH & Co KG, Biberach 88400, Germany
| | - Alexander Dietrich
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Markus List
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Francesca Finotello
- Department of Molecular Biology, Digital Science Center (DiSC), University of Innsbruck, Innsbruck 6020, Austria
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220
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Shin YJ, Lee JH. Exploring the Molecular and Developmental Dynamics of Endothelial Cell Differentiation. Int J Stem Cells 2024; 17:15-29. [PMID: 37879853 PMCID: PMC10899884 DOI: 10.15283/ijsc23086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/06/2023] [Accepted: 09/05/2023] [Indexed: 10/27/2023] Open
Abstract
The development and differentiation of endothelial cells (ECs) are fundamental processes with significant implications for both health and disease. ECs, which are found in all organs and blood vessels, play a crucial role in facilitating nutrient and waste exchange and maintaining proper vessel function. Understanding the intricate signaling pathways involved in EC development holds great promise for enhancing vascularization, tissue engineering, and vascular regeneration. Hematopoietic stem cells originating from hemogenic ECs, give rise to diverse immune cell populations, and the interaction between ECs and immune cells is vital for maintaining vascular integrity and regulating immune responses. Dysregulation of vascular development pathways can lead to various diseases, including cancer, where tumor-specific ECs promote tumor growth through angiogenesis. Recent advancements in single-cell genomics and in vivo genetic labeling have shed light on EC development, plasticity, and heterogeneity, uncovering tissue-specific gene expression and crucial signaling pathways. This review explores the potential of ECs in various applications, presenting novel opportunities for advancing vascular medicine and treatment strategies.
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Affiliation(s)
- Yu Jung Shin
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Jung Hyun Lee
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Dermatology, School of Medicine, University of Washington, Seattle, WA, USA
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221
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Xia L, Lee C, Li JJ. Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters. Nat Commun 2024; 15:1753. [PMID: 38409103 PMCID: PMC10897166 DOI: 10.1038/s41467-024-45891-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 02/06/2024] [Indexed: 02/28/2024] Open
Abstract
Two-dimensional (2D) embedding methods are crucial for single-cell data visualization. Popular methods such as t-distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP) are commonly used for visualizing cell clusters; however, it is well known that t-SNE and UMAP's 2D embeddings might not reliably inform the similarities among cell clusters. Motivated by this challenge, we present a statistical method, scDEED, for detecting dubious cell embeddings output by a 2D-embedding method. By calculating a reliability score for every cell embedding based on the similarity between the cell's 2D-embedding neighbors and pre-embedding neighbors, scDEED identifies the cell embeddings with low reliability scores as dubious and those with high reliability scores as trustworthy. Moreover, by minimizing the number of dubious cell embeddings, scDEED provides intuitive guidance for optimizing the hyperparameters of an embedding method. We show the effectiveness of scDEED on multiple datasets for detecting dubious cell embeddings and optimizing the hyperparameters of t-SNE and UMAP.
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Affiliation(s)
- Lucy Xia
- Department of ISOM, School of Business and Management, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Christy Lee
- Department of Statistics and Data Science, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jingyi Jessica Li
- Department of Statistics and Data Science, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
- Radcliffe Institute of Advanced Study, Harvard University, Cambridge, MA, USA.
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222
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Dorando HK, Mutic EC, Li JY, Perrin EP, Wurtz MK, Quinn CC, Payton JE. LPS and type I and II interferons have opposing effects on epigenetic regulation of LAIR1 expression in mouse and human macrophages. J Leukoc Biol 2024; 115:547-564. [PMID: 38011310 DOI: 10.1093/jleuko/qiad148] [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: 07/31/2023] [Revised: 10/26/2023] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
Inhibitory immune receptors are important for maintaining immune homeostasis. We identified epigenetic alterations in 2 members of this group, LAIR1 and LAIR2, in lymphoma patients with inflammatory tissue damage and susceptibility to infection. We predicted that the expression of LAIR genes is controlled by immune mediators acting on transcriptional regulatory elements. Using flow cytometry, quantitative reverse-transcription polymerase chain reaction, and RNA sequencing, we measured LAIR1 and LAIR2 in human and murine immune cell subsets at baseline and posttreatment with immune mediators, including type I and II interferons, tumor necrosis factor α, and lipopolysaccharide (LPS). We identified candidate regulatory elements using epigenome profiling and measured their regulatory activity using luciferase reporters. LAIR1 expression substantially increases during monocyte differentiation to macrophages in both species. In contrast, murine and human macrophages exhibited opposite changes in LAIR1 in response to immune stimuli: human LAIR1 increased with LPS while mouse LAIR1 increased with interferon γ. LAIR genes had distinct patterns of enhancer activity with variable responses to immune stimuli. To identify relevant transcription factors (TFs), we developed integrative bioinformatic techniques applied to TF chromatin immunoprecipitation sequencing, RNA sequencing, and luciferase activity, revealing distinct sets of TFs for each LAIR gene. Most strikingly, LAIR1 TFs include nuclear factor kappa B factors RELA and RELB, while Lair1 and LAIR2 instead include STAT3 and/or STAT5. Regulation by nuclear factor kappa B factors may therefore explain the LPS-induced increase in LAIR1 expression, in contrast to Lair1 decrease. Our findings reveal new insights into transcriptional mechanisms that control distinct expression patterns of LAIR genes in response to inflammatory stimuli in human and murine myeloid and lymphoid cells.
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Affiliation(s)
- Hannah K Dorando
- Department of Pathology and Immunology, Washington University School of Medicine in St.Louis, 660 S. Euclid Avenue, Box 8118, St. Louis, MO 63110, United States
| | - Evan C Mutic
- Department of Pathology and Immunology, Washington University School of Medicine in St.Louis, 660 S. Euclid Avenue, Box 8118, St. Louis, MO 63110, United States
| | - Joanna Y Li
- Department of Pathology and Immunology, Washington University School of Medicine in St.Louis, 660 S. Euclid Avenue, Box 8118, St. Louis, MO 63110, United States
| | - Ezri P Perrin
- Department of Pathology and Immunology, Washington University School of Medicine in St.Louis, 660 S. Euclid Avenue, Box 8118, St. Louis, MO 63110, United States
| | - Mellisa K Wurtz
- Department of Pathology and Immunology, Washington University School of Medicine in St.Louis, 660 S. Euclid Avenue, Box 8118, St. Louis, MO 63110, United States
| | - Chaz C Quinn
- Department of Pathology and Immunology, Washington University School of Medicine in St.Louis, 660 S. Euclid Avenue, Box 8118, St. Louis, MO 63110, United States
| | - Jacqueline E Payton
- Department of Pathology and Immunology, Washington University School of Medicine in St.Louis, 660 S. Euclid Avenue, Box 8118, St. Louis, MO 63110, United States
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Talvi S, Jokinen J, Sipilä K, Rappu P, Zhang FP, Poutanen M, Rantakari P, Heino J. Embigin deficiency leads to delayed embryonic lung development and high neonatal mortality in mice. iScience 2024; 27:108914. [PMID: 38318368 PMCID: PMC10839689 DOI: 10.1016/j.isci.2024.108914] [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: 06/13/2023] [Revised: 10/20/2023] [Accepted: 01/11/2024] [Indexed: 02/07/2024] Open
Abstract
Embigin (Gp70), a receptor for fibronectin and an ancillary protein for monocarboxylate transporters, is known to regulate stem cell niches in sebaceous gland and bone marrow. Here, we show that embigin expression is at high level during early mouse embryogenesis and that embigin is essential for lung development. Markedly increased neonatal mortality of Emb-/- mice can be explained by the compromised lung maturation: in Emb-/- mice (E17.5) the number and the size of the small airways and distal airspace are significantly smaller, there are fewer ATI and ATII cells, and the alkaline phosphatase activity in amniotic fluid is lower. Emb-/- lungs show less peripheral branching already at E12.5, and embigin is highly expressed in lung primordium. Thus, embigin function is essential at early pseudoglandular stage or even earlier. Furthermore, our RNA-seq analysis and Ki67 staining results support the idea that the development of Emb-/- lungs is rather delayed than defected.
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Affiliation(s)
- Salli Talvi
- Department of Life Technologies, University of Turku, 20014 Turku, Finland
- Medicity Research Laboratory, University of Turku, 20014 Turku, Finland
- InFLAMES Research Flagship, University of Turku, 20014 Turku, Finland
| | - Johanna Jokinen
- Department of Life Technologies, University of Turku, 20014 Turku, Finland
- Medicity Research Laboratory, University of Turku, 20014 Turku, Finland
- InFLAMES Research Flagship, University of Turku, 20014 Turku, Finland
| | - Kalle Sipilä
- Department of Life Technologies, University of Turku, 20014 Turku, Finland
- Centre for Stem Cells and Regenerative Medicine, King’s College London, London WC2R2LS, UK
| | - Pekka Rappu
- Department of Life Technologies, University of Turku, 20014 Turku, Finland
- InFLAMES Research Flagship, University of Turku, 20014 Turku, Finland
| | - Fu-Ping Zhang
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, 20014 Turku, Finland
- Turku Center for Disease Modeling, University of Turku, 20014 Turku, Finland
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Matti Poutanen
- InFLAMES Research Flagship, University of Turku, 20014 Turku, Finland
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, 20014 Turku, Finland
- Turku Center for Disease Modeling, University of Turku, 20014 Turku, Finland
| | - Pia Rantakari
- InFLAMES Research Flagship, University of Turku, 20014 Turku, Finland
- Institute of Biomedicine, University of Turku, 20014 Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20014 Turku, Finland
| | - Jyrki Heino
- Department of Life Technologies, University of Turku, 20014 Turku, Finland
- Medicity Research Laboratory, University of Turku, 20014 Turku, Finland
- InFLAMES Research Flagship, University of Turku, 20014 Turku, Finland
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224
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Braithwaite AT, Akbar N, Pezzolla D, Paget D, Krausgruber T, Bock C, Carnicer R, Choudhury RP. Multi-organ single-cell RNA sequencing in mice reveals early hyperglycemia responses that converge on fibroblast dysregulation. FASEB J 2024; 38:e23448. [PMID: 38305779 DOI: 10.1096/fj.202302003r] [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: 09/30/2023] [Revised: 12/19/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024]
Abstract
Diabetes causes a range of complications that can affect multiple organs. Hyperglycemia is an important driver of diabetes-associated complications, mediated by biological processes such as dysfunction of endothelial cells, fibrosis, and alterations in leukocyte number and function. Here, we dissected the transcriptional response of key cell types to hyperglycemia across multiple tissues using single-cell RNA sequencing (scRNA-seq) and identified conserved, as well as organ-specific, changes associated with diabetes complications. By studying an early time point of diabetes, we focus on biological processes involved in the initiation of the disease, before the later organ-specific manifestations had supervened. We used a mouse model of type 1 diabetes and performed scRNA-seq on cells isolated from the heart, kidney, liver, and spleen of streptozotocin-treated and control male mice after 8 weeks and assessed differences in cell abundance, gene expression, pathway activation, and cell signaling across organs and within organs. In response to hyperglycemia, endothelial cells, macrophages, and monocytes displayed organ-specific transcriptional responses, whereas fibroblasts showed similar responses across organs, exhibiting altered metabolic gene expression and increased myeloid-like fibroblasts. Furthermore, we found evidence of endothelial dysfunction in the kidney, and of endothelial-to-mesenchymal transition in streptozotocin-treated mouse organs. In summary, our study represents the first single-cell and multi-organ analysis of early dysfunction in type 1 diabetes-associated hyperglycemia, and our large-scale dataset (comprising 67 611 cells) will serve as a starting point, reference atlas, and resource for further investigating the events leading to early diabetic disease.
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Affiliation(s)
- Adam T Braithwaite
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Naveed Akbar
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Daniela Pezzolla
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Daan Paget
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas Krausgruber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Vienna, Austria
| | - Ricardo Carnicer
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Robin P Choudhury
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
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225
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Vogt CC, Zipple MN, Sprockett DD, Miller CH, Hardy SX, Arthur MK, Greenstein AM, Colvin MS, Michel LM, Moeller AH, Sheehan MJ. Female behavior drives the formation of distinct social structures in C57BL/6J versus wild-derived outbred mice in field enclosures. BMC Biol 2024; 22:35. [PMID: 38355587 PMCID: PMC10865716 DOI: 10.1186/s12915-024-01809-0] [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: 11/09/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Social behavior and social organization have major influences on individual health and fitness. Yet, biomedical research focuses on studying a few genotypes under impoverished social conditions. Understanding how lab conditions have modified social organizations of model organisms, such as lab mice, relative to natural populations is a missing link between socioecology and biomedical science. RESULTS Using a common garden design, we describe the formation of social structure in the well-studied laboratory mouse strain, C57BL/6J, in replicated mixed-sex populations over 10-day trials compared to control trials with wild-derived outbred house mice in outdoor field enclosures. We focus on three key features of mouse social systems: (i) territory establishment in males, (ii) female social relationships, and (iii) the social networks formed by the populations. Male territorial behaviors were similar but muted in C57 compared to wild-derived mice. Female C57 sharply differed from wild-derived females, showing little social bias toward cage mates and exploring substantially more of the enclosures compared to all other groups. Female behavior consistently generated denser social networks in C57 than in wild-derived mice. CONCLUSIONS C57 and wild-derived mice individually vary in their social and spatial behaviors which scale to shape overall social organization. The repeatable societies formed under field conditions highlights opportunities to experimentally study the interplay between society and individual biology using model organisms.
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Affiliation(s)
- Caleb C Vogt
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA.
| | - Matthew N Zipple
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Daniel D Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Caitlin H Miller
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Summer X Hardy
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew K Arthur
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Adam M Greenstein
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Melanie S Colvin
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Lucie M Michel
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Michael J Sheehan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA.
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226
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Sun H, Qu H, Duan K, Du W. scMGCN: A Multi-View Graph Convolutional Network for Cell Type Identification in scRNA-seq Data. Int J Mol Sci 2024; 25:2234. [PMID: 38396909 PMCID: PMC10889820 DOI: 10.3390/ijms25042234] [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: 12/06/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) data reveal the complexity and diversity of cellular ecosystems and molecular interactions in various biomedical research. Hence, identifying cell types from large-scale scRNA-seq data using existing annotations is challenging and requires stable and interpretable methods. However, the current cell type identification methods have limited performance, mainly due to the intrinsic heterogeneity among cell populations and extrinsic differences between datasets. Here, we present a robust graph artificial intelligence model, a multi-view graph convolutional network model (scMGCN) that integrates multiple graph structures from raw scRNA-seq data and applies graph convolutional networks with attention mechanisms to learn cell embeddings and predict cell labels. We evaluate our model on single-dataset, cross-species, and cross-platform experiments and compare it with other state-of-the-art methods. Our results show that scMGCN outperforms the other methods regarding stability, accuracy, and robustness to batch effects. Our main contributions are as follows: Firstly, we introduce multi-view learning and multiple graph construction methods to capture comprehensive cellular information from scRNA-seq data. Secondly, we construct a scMGCN that combines graph convolutional networks with attention mechanisms to extract shared, high-order information from cells. Finally, we demonstrate the effectiveness and superiority of the scMGCN on various datasets.
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Affiliation(s)
| | | | | | - Wei Du
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China; (H.S.); (H.Q.); (K.D.)
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227
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Zhao S, Wang L, Liang Y, Zheng J, Umpierre AD, Wu LJ. Chemogenetic activation of microglial Gi signaling decreases microglial surveillance and impairs neuronal synchronization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.579861. [PMID: 38405754 PMCID: PMC10888941 DOI: 10.1101/2024.02.12.579861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Microglia actively survey the brain and dynamically interact with neurons to maintain brain homeostasis. Microglial Gi-protein coupled receptors (Gi-GPCRs) play a critical role in microglia-neuron communications. However, the impact of temporally activating microglial Gi signaling on microglial dynamics and neuronal activity in the homeostatic brain remains largely unknown. In this study, we employed Gi-based Designer Receptors Exclusively Activated by Designer Drugs (Gi-DREADD) to selectively and temporally modulate microglial Gi signaling pathway. By integrating this chemogenetic approach with in vivo two-photon imaging, we observed that exogenous activation of microglial Gi signaling transiently inhibited microglial process dynamics, reduced neuronal activity, and impaired neuronal synchronization. These altered neuronal functions were associated with a decrease in interactions between microglia and neuron somata. Altogether, this study demonstrates that acute, exogenous activation of microglial Gi signaling can regulate neuronal circuit function, offering a potential pharmacological target for neuromodulation through microglia.
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228
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Carlantoni C, Liekfeld LMH, Hemkemeyer SA, Schreier D, Saygi C, Kurelic R, Cardarelli S, Kalucka J, Schulte C, Beerens M, Mailer RK, Schäffer TE, Naro F, Pellegrini M, Nikolaev VO, Renné T, Frye M. The phosphodiesterase 2A controls lymphatic junctional maturation via cGMP-dependent notch signaling. Dev Cell 2024; 59:308-325.e11. [PMID: 38159569 DOI: 10.1016/j.devcel.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 11/01/2023] [Accepted: 12/07/2023] [Indexed: 01/03/2024]
Abstract
The molecular mechanisms by which lymphatic vessels induce cell contact inhibition are not understood. Here, we identify the cGMP-dependent phosphodiesterase 2A (PDE2A) as a selective regulator of lymphatic but not of blood endothelial contact inhibition. Conditional deletion of Pde2a in mouse embryos reveals severe lymphatic dysplasia, whereas blood vessel architecture remains unaltered. In the absence of PDE2A, human lymphatic endothelial cells fail to induce mature junctions and cell cycle arrest, whereas cGMP levels, but not cAMP levels, are increased. Loss of PDE2A-mediated cGMP hydrolysis leads to the activation of p38 signaling and downregulation of NOTCH signaling. However, DLL4-induced NOTCH activation restores junctional maturation and contact inhibition in PDE2A-deficient human lymphatic endothelial cells. In postnatal mouse mesenteries, PDE2A is specifically enriched in collecting lymphatic valves, and loss of Pde2a results in the formation of abnormal valves. Our data demonstrate that PDE2A selectively finetunes a crosstalk of cGMP, p38, and NOTCH signaling during lymphatic vessel maturation.
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Affiliation(s)
- Claudia Carlantoni
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany; German Centre of Cardiovascular Research (DZHK), Partner Site Hamburg/Luebeck/Kiel, Hamburg, Germany
| | - Leon M H Liekfeld
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Sandra A Hemkemeyer
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany; German Centre of Cardiovascular Research (DZHK), Partner Site Hamburg/Luebeck/Kiel, Hamburg, Germany
| | - Danny Schreier
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Ceren Saygi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Roberta Kurelic
- Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Silvia Cardarelli
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of Rome, 00161 Rome, Italy
| | - Joanna Kalucka
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Christian Schulte
- German Centre of Cardiovascular Research (DZHK), Partner Site Hamburg/Luebeck/Kiel, Hamburg, Germany; Department of Cardiology, University Heart & Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manu Beerens
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany; German Centre of Cardiovascular Research (DZHK), Partner Site Hamburg/Luebeck/Kiel, Hamburg, Germany
| | - Reiner K Mailer
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Tilman E Schäffer
- Institute of Applied Physics, University of Tuebingen, 72076 Tuebingen, Germany
| | - Fabio Naro
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of Rome, 00161 Rome, Italy
| | - Manuela Pellegrini
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of Rome, 00161 Rome, Italy; Institute of Biochemistry and Cell Biology, IBBC-CNR, Campus A. Buzzati Traverso, Monterotondo Scalo, Rome 00015, Italy
| | - Viacheslav O Nikolaev
- German Centre of Cardiovascular Research (DZHK), Partner Site Hamburg/Luebeck/Kiel, Hamburg, Germany; Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Thomas Renné
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany; Center for Thrombosis and Hemostasis (CTH), Johannes Gutenberg University Medical Center, Mainz, Germany; Irish Centre for Vascular Biology, School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Maike Frye
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany; German Centre of Cardiovascular Research (DZHK), Partner Site Hamburg/Luebeck/Kiel, Hamburg, Germany.
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229
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Company C, Schmitt MJ, Dramaretska Y, Serresi M, Kertalli S, Jiang B, Yin JA, Aguzzi A, Barozzi I, Gargiulo G. Logical design of synthetic cis-regulatory DNA for genetic tracing of cell identities and state changes. Nat Commun 2024; 15:897. [PMID: 38316783 PMCID: PMC10844330 DOI: 10.1038/s41467-024-45069-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/12/2024] [Indexed: 02/07/2024] Open
Abstract
Descriptive data are rapidly expanding in biomedical research. Instead, functional validation methods with sufficient complexity remain underdeveloped. Transcriptional reporters allow experimental characterization and manipulation of developmental and disease cell states, but their design lacks flexibility. Here, we report logical design of synthetic cis-regulatory DNA (LSD), a computational framework leveraging phenotypic biomarkers and trans-regulatory networks as input to design reporters marking the activity of selected cellular states and pathways. LSD uses bulk or single-cell biomarkers and a reference genome or custom cis-regulatory DNA datasets with user-defined boundary regions. By benchmarking validated reporters, we integrate LSD with a computational ranking of phenotypic specificity of putative cis-regulatory DNA. Experimentally, LSD-designed reporters targeting a wide range of cell states are functional without minimal promoters. Applied to broadly expressed genes from human and mouse tissues, LSD generates functional housekeeper-like sLCRs compatible with size constraints of AAV vectors for gene therapy applications. A mesenchymal glioblastoma reporter designed by LSD outperforms previously validated ones and canonical cell surface markers. In genome-scale CRISPRa screens, LSD facilitates the discovery of known and novel bona fide cell-state drivers. Thus, LSD captures core principles of cis-regulation and is broadly applicable to studying complex cell states and mechanisms of transcriptional regulation.
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Affiliation(s)
- Carlos Company
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Matthias Jürgen Schmitt
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Yuliia Dramaretska
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Michela Serresi
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Sonia Kertalli
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Ben Jiang
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Jiang-An Yin
- Institute of Neuropathology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
| | - Adriano Aguzzi
- Institute of Neuropathology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
| | - Iros Barozzi
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090, Vienna, Austria
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Gaetano Gargiulo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany.
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230
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Lim HS, Qiu P. Quantifying the clusterness and trajectoriness of single-cell RNA-seq data. PLoS Comput Biol 2024; 20:e1011866. [PMID: 38416795 PMCID: PMC10927072 DOI: 10.1371/journal.pcbi.1011866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 03/11/2024] [Accepted: 01/28/2024] [Indexed: 03/01/2024] Open
Abstract
Among existing computational algorithms for single-cell RNA-seq analysis, clustering and trajectory inference are two major types of analysis that are routinely applied. For a given dataset, clustering and trajectory inference can generate vastly different visualizations that lead to very different interpretations of the data. To address this issue, we propose multiple scores to quantify the "clusterness" and "trajectoriness" of single-cell RNA-seq data, in other words, whether the data looks like a collection of distinct clusters or a continuum of progression trajectory. The scores we introduce are based on pairwise distance distribution, persistent homology, vector magnitude, Ripley's K, and degrees of connectivity. Using simulated datasets, we demonstrate that the proposed scores are able to effectively differentiate between cluster-like data and trajectory-like data. Using real single-cell RNA-seq datasets, we demonstrate the scores can serve as indicators of whether clustering analysis or trajectory inference is a more appropriate choice for biological interpretation of the data.
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Affiliation(s)
- Hong Seo Lim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
| | - Peng Qiu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
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Ren W, Hua M, Cao F, Zeng W. The Sympathetic-Immune Milieu in Metabolic Health and Diseases: Insights from Pancreas, Liver, Intestine, and Adipose Tissues. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306128. [PMID: 38039489 PMCID: PMC10885671 DOI: 10.1002/advs.202306128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/28/2023] [Indexed: 12/03/2023]
Abstract
Sympathetic innervation plays a crucial role in maintaining energy balance and contributes to metabolic pathophysiology. Recent evidence has begun to uncover the innervation landscape of sympathetic projections and sheds light on their important functions in metabolic activities. Additionally, the immune system has long been studied for its essential roles in metabolic health and diseases. In this review, the aim is to provide an overview of the current research progress on the sympathetic regulation of key metabolic organs, including the pancreas, liver, intestine, and adipose tissues. In particular, efforts are made to highlight the critical roles of the peripheral nervous system and its potential interplay with immune components. Overall, it is hoped to underscore the importance of studying metabolic organs from a comprehensive and interconnected perspective, which will provide valuable insights into the complex mechanisms underlying metabolic regulation and may lead to novel therapeutic strategies for metabolic diseases.
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Affiliation(s)
- Wenran Ren
- Institute for Immunology and School of MedicineTsinghua Universityand Tsinghua‐Peking Center for Life SciencesBeijing100084China
| | - Meng Hua
- Institute for Immunology and School of MedicineTsinghua Universityand Tsinghua‐Peking Center for Life SciencesBeijing100084China
| | - Fang Cao
- Department of NeurosurgeryAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhou563000China
| | - Wenwen Zeng
- Institute for Immunology and School of MedicineTsinghua Universityand Tsinghua‐Peking Center for Life SciencesBeijing100084China
- SXMU‐Tsinghua Collaborative Innovation Center for Frontier MedicineTaiyuan030001China
- Beijing Key Laboratory for Immunological Research on Chronic DiseasesBeijing100084China
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232
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Ke D, Ni J, Yuan Y, Cao M, Chen S, Zhou H. Identification and Validation of Hub Genes Related to Neutrophil Extracellular Traps-Mediated Cell Damage During Myocardial Infarction. J Inflamm Res 2024; 17:617-637. [PMID: 38323113 PMCID: PMC10844013 DOI: 10.2147/jir.s444975] [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: 11/06/2023] [Accepted: 01/23/2024] [Indexed: 02/08/2024] Open
Abstract
Purpose Studies have shown that neutrophil-mediated formation of neutrophil extracellular traps (NETs) leads to increased inflammatory response and cellular tissue damage during myocardial infarction (MI). We aimed to identify and validate possible hub genes in the process of NETs-mediated cell damage. Methods We performed an immune cell infiltration analysis of the MI transcriptome dataset based on CIBERSORT and ssGSEA algorithms. Gene expression profiles of NETs formation (GSE178883) were used to analyze the physiological processes of peripheral blood neutrophils after phorbol myristate acetate (PMA) stimulation. Bioinformatics and machine learning algorithms were utilized to find candidate hub genes based on NETs-related genes and transcriptome datasets (GSE66360 and GSE179828). We generated the receiver operating curve (ROC) to evaluate the diagnostic value of hub genes. Next, the correlation between hub genes and immune cells was analyzed using CIBERSORT, ssGSEA and xCell algorithms. Finally, we used quantitative real-time PCR (qRT-PCR) and immunohistochemistry to verify gene expression. Results Immune cell infiltration analysis revealed that inflammatory cells such as neutrophils were highly expressed in the peripheral blood of patients with MI. Functional analysis of differentially expressed genes (DEGs) in GSE178883 indicated that the potential pathogenesis lies in immune terms. Using weighted gene co-expression network analysis (WGCNA) and machine learning algorithms, we finally identified the seven hub genes (FCAR, IL1B, MMP9, NFIL3, CXCL2, ICAM1, and ZFP36). The qRT-PCR results showed that IL-1B, MMP9, and NFIL3 mRNA expression was up-regulated in the MI group compared to the control. Immunohistochemical results showed high MMP9, IL-1B, and NFIL3 expression in the infarcted area compared to the non-infarcted area and sham-operated groups. Conclusion We identified seven hub genes associated with NETs-mediated cellular damage during MI. Our results may provide insights into the mechanisms of neutrophil-mediated cell injury during MI.
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Affiliation(s)
- Da Ke
- Department of Cardiology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, 430060, People’s Republic of China
| | - Jian Ni
- Department of Cardiology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, 430060, People’s Republic of China
| | - Yuan Yuan
- Department of Cardiology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, 430060, People’s Republic of China
| | - Mingzhen Cao
- Department of Cardiology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, 430060, People’s Republic of China
| | - Si Chen
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, 430060, People’s Republic of China
| | - Heng Zhou
- Department of Cardiology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, 430060, People’s Republic of China
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233
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Ye F, Wang J, Li J, Mei Y, Guo G. Mapping Cell Atlases at the Single-Cell Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305449. [PMID: 38145338 PMCID: PMC10885669 DOI: 10.1002/advs.202305449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/01/2023] [Indexed: 12/26/2023]
Abstract
Recent advancements in single-cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characterization of cellular diversity at the single-cell level. Global efforts in developing comprehensive cell atlases have profound implications for both basic research and clinical applications. This review provides a broad overview of the cellular diversity and dynamics across various biological systems. In addition, the incorporation of machine learning techniques into cell atlas analyses opens up exciting prospects for the field of integrative biology.
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Affiliation(s)
- Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jiaqi Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative MedicineDr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative MedicineHangzhouZhejiang310058China
- Institute of HematologyZhejiang UniversityHangzhouZhejiang310000China
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234
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Hao Y, Stuart T, Kowalski MH, Choudhary S, Hoffman P, Hartman A, Srivastava A, Molla G, Madad S, Fernandez-Granda C, Satija R. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nat Biotechnol 2024; 42:293-304. [PMID: 37231261 PMCID: PMC10928517 DOI: 10.1038/s41587-023-01767-y] [Citation(s) in RCA: 316] [Impact Index Per Article: 316.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/28/2023] [Indexed: 05/27/2023]
Abstract
Mapping single-cell sequencing profiles to comprehensive reference datasets provides a powerful alternative to unsupervised analysis. However, most reference datasets are constructed from single-cell RNA-sequencing data and cannot be used to annotate datasets that do not measure gene expression. Here we introduce 'bridge integration', a method to integrate single-cell datasets across modalities using a multiomic dataset as a molecular bridge. Each cell in the multiomic dataset constitutes an element in a 'dictionary', which is used to reconstruct unimodal datasets and transform them into a shared space. Our procedure accurately integrates transcriptomic data with independent single-cell measurements of chromatin accessibility, histone modifications, DNA methylation and protein levels. Moreover, we demonstrate how dictionary learning can be combined with sketching techniques to improve computational scalability and harmonize 8.6 million human immune cell profiles from sequencing and mass cytometry experiments. Our approach, implemented in version 5 of our Seurat toolkit ( http://www.satijalab.org/seurat ), broadens the utility of single-cell reference datasets and facilitates comparisons across diverse molecular modalities.
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Affiliation(s)
- Yuhan Hao
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Tim Stuart
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Madeline H Kowalski
- New York Genome Center, New York, NY, USA
- Institute for System Genetics, NYU Langone Medical Center, New York, NY, USA
| | - Saket Choudhary
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Paul Hoffman
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Austin Hartman
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Avi Srivastava
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | | | - Shaista Madad
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Carlos Fernandez-Granda
- Center for Data Science, New York University, New York, NY, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Rahul Satija
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
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235
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Garcia-Bonilla L, Shahanoor Z, Sciortino R, Nazarzoda O, Racchumi G, Iadecola C, Anrather J. Analysis of brain and blood single-cell transcriptomics in acute and subacute phases after experimental stroke. Nat Immunol 2024; 25:357-370. [PMID: 38177281 DOI: 10.1038/s41590-023-01711-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 11/13/2023] [Indexed: 01/06/2024]
Abstract
Cerebral ischemia triggers a powerful inflammatory reaction involving peripheral leukocytes and brain resident cells that contribute to both tissue injury and repair. However, their dynamics and diversity remain poorly understood. To address these limitations, we performed a single-cell transcriptomic study of brain and blood cells 2 or 14 days after ischemic stroke in mice. We observed a strong divergence of post-ischemic microglia, monocyte-derived macrophages and neutrophils over time, while endothelial cells and brain-associated macrophages showed altered transcriptomic signatures at 2 days poststroke. Trajectory inference predicted the in situ trans-differentiation of macrophages from blood monocytes into day 2 and day 14 phenotypes, while neutrophils were projected to be continuously de novo recruited from the blood. Brain single-cell transcriptomes from both female and male aged mice were similar to that of young male mice, but aged and young brains differed in their immune cell composition. Although blood leukocyte analysis also revealed altered transcriptomes after stroke, brain-infiltrating leukocytes displayed higher transcriptomic divergence than their circulating counterparts, indicating that phenotypic diversification occurs within the brain in the early and recovery phases of ischemic stroke. A portal ( https://anratherlab.shinyapps.io/strokevis/ ) is provided to allow user-friendly access to our data.
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Affiliation(s)
- Lidia Garcia-Bonilla
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
| | - Ziasmin Shahanoor
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Rose Sciortino
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Omina Nazarzoda
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Gianfranco Racchumi
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Costantino Iadecola
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Josef Anrather
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
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236
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Bauzá-Thorbrügge M, Vujičić M, Chanclón B, Palsdottir V, Pillon NJ, Benrick A, Wernstedt Asterholm I. Adiponectin stimulates Sca1 +CD34 --adipocyte precursor cells associated with hyperplastic expansion and beiging of brown and white adipose tissue. Metabolism 2024; 151:155716. [PMID: 37918793 DOI: 10.1016/j.metabol.2023.155716] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND The adipocyte hormone adiponectin improves insulin sensitivity and there is an inverse correlation between adiponectin levels and type-2 diabetes risk. Previous research shows that adiponectin remodels the adipose tissue into a more efficient metabolic sink. For instance, mice that overexpress adiponectin show increased capacity for hyperplastic adipose tissue expansion as evident from smaller and metabolically more active white adipocytes. In contrast, the brown adipose tissue (BAT) of these mice looks "whiter" possibly indicating reduced metabolic activity. Here, we aimed to further establish the effect of adiponectin on adipose tissue expansion and adipocyte mitochondrial function as well as to unravel mechanistic aspects in this area. METHODS Brown and white adipose tissues from adiponectin overexpressing (APN tg) mice and littermate wildtype controls, housed at room and cold temperature, were studied by histological, gene/protein expression and flow cytometry analyses. Metabolic and mitochondrial functions were studied by radiotracers and Seahorse-based technology. In addition, mitochondrial function was assessed in cultured adiponectin deficient adipocytes from APN knockout and heterozygote mice. RESULTS APN tg BAT displayed increased proliferation prenatally leading to enlarged BAT. Postnatally, APN tg BAT turned whiter than control BAT, confirming previous reports. Furthermore, elevated adiponectin augmented the sympathetic innervation/activation within adipose tissue. APN tg BAT displayed reduced metabolic activity and reduced mitochondrial oxygen consumption rate (OCR). In contrast, APN tg inguinal white adipose tissue (IWAT) displayed enhanced metabolic activity. These metabolic differences between genotypes were apparent also in cultured adipocytes differentiated from BAT and IWAT stroma vascular fraction, and the OCR was reduced in both brown and white APN heterozygote adipocytes. In both APN tg BAT and IWAT, the mesenchymal stem cell-related genes were upregulated along with an increased abundance of Lineage-Sca1+CD34- "beige-like" adipocyte precursor cells. In vitro, the adiponectin receptor agonist Adiporon increased the expression of the proliferation marker Pcna and decreased the expression of Cd34 in Sca1+ mesenchymal stem cells. CONCLUSIONS We propose that the seemingly opposite effect of adiponectin on BAT and IWAT is mediated by a common mechanism; while reduced adiponectin levels are linked to lower adipocyte OCR, elevated adiponectin levels stimulate expansion of adipocyte precursor cells that produce adipocytes with intrinsically higher metabolic rate than classical white but lower metabolic rate than classical brown adipocytes. Moreover, adiponectin can modify the adipocytes' metabolic activity directly and by enhancing the sympathetic innervation within a fat depot.
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Affiliation(s)
- Marco Bauzá-Thorbrügge
- Unit for Metabolic Physiology, Department of Physiology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Milica Vujičić
- Unit for Metabolic Physiology, Department of Physiology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Belén Chanclón
- Unit for Metabolic Physiology, Department of Physiology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Vilborg Palsdottir
- Unit for Endocrine Physiology, Department of Physiology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Nicolas J Pillon
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Anna Benrick
- Unit for Metabolic Physiology, Department of Physiology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden; School of Health Sciences, University of Skövde, Skövde, Sweden
| | - Ingrid Wernstedt Asterholm
- Unit for Metabolic Physiology, Department of Physiology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.
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237
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Sassu E, Tumlinson G, Stefanovska D, Fernández MC, Iaconianni P, Madl J, Brennan TA, Koch M, Cameron BA, Preissl S, Ravens U, Schneider-Warme F, Kohl P, Zgierski-Johnston CM, Hortells L. Age-related structural and functional changes of the intracardiac nervous system. J Mol Cell Cardiol 2024; 187:1-14. [PMID: 38103633 DOI: 10.1016/j.yjmcc.2023.12.002] [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: 08/14/2023] [Revised: 11/14/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Although aging is known to be associated with an increased incidence of both atrial and ventricular arrhythmias, there is limited knowledge about how Schwann cells (SC) and the intracardiac nervous system (iCNS) remodel with age. Here we investigate the differences in cardiac SC, parasympathetic nerve fibers, and muscarinic acetylcholine receptor M2 (M2R) expression in young and old mice. Additionally, we examine age-related changes in cardiac responses to sympathomimetic and parasympathomimetic drugs. METHODS AND RESULTS Lower SC density, lower SC proliferation and fewer parasympathetic nerve fibers were observed in cardiac and, as a control sciatic nerves from old (20-24 months) compared to young mice (2-3 months). In old mice, chondroitin sulfate proteoglycan 4 (CSPG4) was increased in sciatic but not cardiac nerves. Expression of M2R was lower in ventricular myocardium and ventricular conduction system from old mice compared to young mice, while no significant difference was seen in M2R expression in sino-atrial or atrio-ventricular node pacemaker tissue. Heart rate was slower and PQ intervals were longer in Langendorff-perfused hearts from old mice. Ventricular tachycardia and fibrillation were more frequently observed in response to carbachol administration in hearts from old mice versus those from young mice. CONCLUSIONS On the background of reduced presence of SC and parasympathetic nerve fibers, and of lower M2R expression in ventricular cardiomyocytes and conduction system of aged hearts, the propensity of ventricular arrhythmogenesis upon parasympathomimetic drug application is increased. Whether this is caused by an increase in heterogeneity of iCNS structure and function remains to be elucidated.
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Affiliation(s)
- Eliza Sassu
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, 79110 Freiburg, Germany
| | - Gavin Tumlinson
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Dragana Stefanovska
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, 79110 Freiburg, Germany
| | - Marbely C Fernández
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Pia Iaconianni
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Josef Madl
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Tomás A Brennan
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Manuel Koch
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Breanne A Cameron
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Sebastian Preissl
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, 79110 Freiburg, Germany
| | - Ursula Ravens
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Franziska Schneider-Warme
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, and Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Peter Kohl
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, and Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Callum M Zgierski-Johnston
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany.
| | - Luis Hortells
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, 79110 Freiburg, Germany.
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238
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Camunas-Soler J. Integrating single-cell transcriptomics with cellular phenotypes: cell morphology, Ca 2+ imaging and electrophysiology. Biophys Rev 2024; 16:89-107. [PMID: 38495444 PMCID: PMC10937895 DOI: 10.1007/s12551-023-01174-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/29/2023] [Indexed: 03/19/2024] Open
Abstract
I review recent technological advancements in coupling single-cell transcriptomics with cellular phenotypes including morphology, calcium signaling, and electrophysiology. Single-cell RNA sequencing (scRNAseq) has revolutionized cell type classifications by capturing the transcriptional diversity of cells. A new wave of methods to integrate scRNAseq and biophysical measurements is facilitating the linkage of transcriptomic data to cellular function, which provides physiological insight into cellular states. I briefly discuss critical factors of these phenotypical characterizations such as timescales, information content, and analytical tools. Dedicated sections focus on the integration with cell morphology, calcium imaging, and electrophysiology (patch-seq), emphasizing their complementary roles. I discuss their application in elucidating cellular states, refining cell type classifications, and uncovering functional differences in cell subtypes. To illustrate the practical applications and benefits of these methods, I highlight their use in tissues with excitable cell-types such as the brain, pancreatic islets, and the retina. The potential of combining functional phenotyping with spatial transcriptomics for a detailed mapping of cell phenotypes in situ is explored. Finally, I discuss open questions and future perspectives, emphasizing the need for a shift towards broader accessibility through increased throughput.
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Affiliation(s)
- Joan Camunas-Soler
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, 405 30 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
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239
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Yang S, Zhou X. SRT-Server: powering the analysis of spatial transcriptomic data. Genome Med 2024; 16:18. [PMID: 38279156 PMCID: PMC10811909 DOI: 10.1186/s13073-024-01288-6] [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: 05/23/2023] [Accepted: 01/15/2024] [Indexed: 01/28/2024] Open
Abstract
BACKGROUND Spatial resolved transcriptomics (SRT) encompasses a rapidly developing set of technologies that enable the measurement of gene expression in tissue while retaining spatial localization information. SRT technologies and the enabled SRT studies have provided unprecedent insights into the structural and functional underpinnings of complex tissues. As SRT technologies have advanced and an increasing number of SRT studies have emerged, numerous sophisticated statistical and computational methods have been developed to facilitate the analysis and interpretation of SRT data. However, despite the growing popularity of SRT studies and the widespread availability of SRT analysis methods, analysis of large-scale and complex SRT datasets remains challenging and not easily accessible to researchers with limited statistical and computational backgrounds. RESULTS Here, we present SRT-Server, the first webserver designed to carry out comprehensive SRT analyses for a wide variety of SRT technologies while requiring minimal prior computational knowledge. Implemented with cutting-edge web development technologies, SRT-Server is user-friendly and features multiple analytic modules that can perform a range of SRT analyses. With a flowchart-style interface, these different analytic modules on the SRT-Server can be dragged into the main panel and connected to each other to create custom analytic pipelines. SRT-Server then automatically executes the desired analyses, generates corresponding figures, and outputs results-all without requiring prior programming knowledge. We demonstrate the advantages of SRT-Server through three case studies utilizing SRT data collected from two common platforms, highlighting its versatility and values to researchers with varying analytic expertise. CONCLUSIONS Overall, SRT-Server presents a user-friendly, efficient, effective, secure, and expandable solution for SRT data analysis, opening new doors for researchers in the field. SRT-Server is freely available at https://spatialtranscriptomicsanalysis.com/ .
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Affiliation(s)
- Sheng Yang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, China.
| | - Xiang Zhou
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA.
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
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Zanini F, Che X, Suresh NE, Knutsen C, Klavina P, Xie Y, Domingo-Gonzalez R, Liu M, Kum A, Jones RC, Quake SR, Alvira CM, Cornfield DN. Hyperoxia prevents the dynamic neonatal increases in lung mesenchymal cell diversity. Sci Rep 2024; 14:2033. [PMID: 38263350 PMCID: PMC10805790 DOI: 10.1038/s41598-023-50717-w] [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: 05/05/2023] [Accepted: 12/23/2023] [Indexed: 01/25/2024] Open
Abstract
Rapid expansion of the pulmonary microvasculature through angiogenesis drives alveolarization, the final stage of lung development that occurs postnatally and dramatically increases lung gas-exchange surface area. Disruption of pulmonary angiogenesis induces long-term structural and physiologic lung abnormalities, including bronchopulmonary dysplasia, a disease characterized by compromised alveolarization. Although endothelial cells are primary determinants of pulmonary angiogenesis, mesenchymal cells (MC) play a critical and dual role in angiogenesis and alveolarization. Therefore, we performed single cell transcriptomics and in-situ imaging of the developing lung to profile mesenchymal cells during alveolarization and in the context of lung injury. Specific mesenchymal cell subtypes were present at birth with increasing diversity during alveolarization even while expressing a distinct transcriptomic profile from more mature correlates. Hyperoxia arrested the transcriptomic progression of the MC, revealed differential cell subtype vulnerability with pericytes and myofibroblasts most affected, altered cell to cell communication, and led to the emergence of Acta1 expressing cells. These insights hold the promise of targeted treatment for neonatal lung disease, which remains a major cause of infant morbidity and mortality across the world.
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Affiliation(s)
- Fabio Zanini
- School of Clinical Medicine, University of New South Wales, Sydney, Australia.
- Cellular Genomics Futures Institute, University of New South Wales, Sydney, NSW, Australia.
- Evolution & Ecology Research Centre, University of New South Wales, Sydney, NSW, Australia.
| | - Xibing Che
- Center for Excellence in Pulmonary Biology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Pulmonary, Asthma and Sleep Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Nina E Suresh
- Center for Excellence in Pulmonary Biology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Pulmonary, Asthma and Sleep Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Carsten Knutsen
- Center for Excellence in Pulmonary Biology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Critical Care Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Paula Klavina
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Yike Xie
- School of Clinical Medicine, University of New South Wales, Sydney, Australia
| | - Racquel Domingo-Gonzalez
- Center for Excellence in Pulmonary Biology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Critical Care Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Min Liu
- Center for Excellence in Pulmonary Biology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Critical Care Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexander Kum
- Center for Excellence in Pulmonary Biology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Critical Care Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert C Jones
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
| | - Cristina M Alvira
- Center for Excellence in Pulmonary Biology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Critical Care Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - David N Cornfield
- Center for Excellence in Pulmonary Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Division of Pulmonary, Asthma and Sleep Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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241
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Wan H, Yuan M, Fu Y, Deng M. Continually adapting pre-trained language model to universal annotation of single-cell RNA-seq data. Brief Bioinform 2024; 25:bbae047. [PMID: 38388681 PMCID: PMC10883808 DOI: 10.1093/bib/bbae047] [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: 10/04/2023] [Revised: 12/29/2023] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
MOTIVATION Cell-type annotation of single-cell RNA-sequencing (scRNA-seq) data is a hallmark of biomedical research and clinical application. Current annotation tools usually assume the simultaneous acquisition of well-annotated data, but without the ability to expand knowledge from new data. Yet, such tools are inconsistent with the continuous emergence of scRNA-seq data, calling for a continuous cell-type annotation model. In addition, by their powerful ability of information integration and model interpretability, transformer-based pre-trained language models have led to breakthroughs in single-cell biology research. Therefore, the systematic combining of continual learning and pre-trained language models for cell-type annotation tasks is inevitable. RESULTS We herein propose a universal cell-type annotation tool, called CANAL, that continuously fine-tunes a pre-trained language model trained on a large amount of unlabeled scRNA-seq data, as new well-labeled data emerges. CANAL essentially alleviates the dilemma of catastrophic forgetting, both in terms of model inputs and outputs. For model inputs, we introduce an experience replay schema that repeatedly reviews previous vital examples in current training stages. This is achieved through a dynamic example bank with a fixed buffer size. The example bank is class-balanced and proficient in retaining cell-type-specific information, particularly facilitating the consolidation of patterns associated with rare cell types. For model outputs, we utilize representation knowledge distillation to regularize the divergence between previous and current models, resulting in the preservation of knowledge learned from past training stages. Moreover, our universal annotation framework considers the inclusion of new cell types throughout the fine-tuning and testing stages. We can continuously expand the cell-type annotation library by absorbing new cell types from newly arrived, well-annotated training datasets, as well as automatically identify novel cells in unlabeled datasets. Comprehensive experiments with data streams under various biological scenarios demonstrate the versatility and high model interpretability of CANAL. AVAILABILITY An implementation of CANAL is available from https://github.com/aster-ww/CANAL-torch. CONTACT dengmh@pku.edu.cn. SUPPLEMENTARY INFORMATION Supplementary data are available at Journal Name online.
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Affiliation(s)
- Hui Wan
- School of Mathematical Sciences, Peking University, Beijing, China, 100871
| | - Musu Yuan
- Center for Quantitative Biology, Peking University, Beijing, China, 100871
| | - Yiwei Fu
- School of Mathematical Sciences, Peking University, Beijing, China, 100871
| | - Minghua Deng
- School of Mathematical Sciences, Peking University, Beijing, China, 100871
- Center for Quantitative Biology, Peking University, Beijing, China, 100871
- Center for Statistical Science, Peking university, Beijing, China, 100871
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242
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Zhai Y, Chen L, Deng M. scEVOLVE: cell-type incremental annotation without forgetting for single-cell RNA-seq data. Brief Bioinform 2024; 25:bbae039. [PMID: 38366803 PMCID: PMC10939389 DOI: 10.1093/bib/bbae039] [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: 10/24/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 02/18/2024] Open
Abstract
The evolution in single-cell RNA sequencing (scRNA-seq) technology has opened a new avenue for researchers to inspect cellular heterogeneity with single-cell precision. One crucial aspect of this technology is cell-type annotation, which is fundamental for any subsequent analysis in single-cell data mining. Recently, the scientific community has seen a surge in the development of automatic annotation methods aimed at this task. However, these methods generally operate at a steady-state total cell-type capacity, significantly restricting the cell annotation systems'capacity for continuous knowledge acquisition. Furthermore, creating a unified scRNA-seq annotation system remains challenged by the need to progressively expand its understanding of ever-increasing cell-type concepts derived from a continuous data stream. In response to these challenges, this paper presents a novel and challenging setting for annotation, namely cell-type incremental annotation. This concept is designed to perpetually enhance cell-type knowledge, gleaned from continuously incoming data. This task encounters difficulty with data stream samples that can only be observed once, leading to catastrophic forgetting. To address this problem, we introduce our breakthrough methodology termed scEVOLVE, an incremental annotation method. This innovative approach is built upon the methodology of contrastive sample replay combined with the fundamental principle of partition confidence maximization. Specifically, we initially retain and replay sections of the old data in each subsequent training phase, then establish a unique prototypical learning objective to mitigate the cell-type imbalance problem, as an alternative to using cross-entropy. To effectively emulate a model that trains concurrently with complete data, we introduce a cell-type decorrelation strategy that efficiently scatters feature representations of each cell type uniformly. We constructed the scEVOLVE framework with simplicity and ease of integration into most deep softmax-based single-cell annotation methods. Thorough experiments conducted on a range of meticulously constructed benchmarks consistently prove that our methodology can incrementally learn numerous cell types over an extended period, outperforming other strategies that fail quickly. As far as our knowledge extends, this is the first attempt to propose and formulate an end-to-end algorithm framework to address this new, practical task. Additionally, scEVOLVE, coded in Python using the Pytorch machine-learning library, is freely accessible at https://github.com/aimeeyaoyao/scEVOLVE.
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Affiliation(s)
- Yuyao Zhai
- School of Mathematical Sciences, Peking University, Beijing, China
| | - Liang Chen
- Huawei Technologies Co., Ltd., Beijing, China
| | - Minghua Deng
- School of Mathematical Sciences, Peking University, Beijing, China
- Center for Statistical Science, Peking University, Beijing, China
- Center for Quantitative Biology, Peking University, Beijing, China
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243
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Fan Q, Yan R, Li Y, Lu L, Liu J, Li S, Fu T, Xue Y, Liu J, Li Z. Exploring Immune Cell Diversity in the Lacrimal Glands of Healthy Mice: A Single-Cell RNA-Sequencing Atlas. Int J Mol Sci 2024; 25:1208. [PMID: 38279208 PMCID: PMC10816500 DOI: 10.3390/ijms25021208] [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: 11/26/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 01/28/2024] Open
Abstract
The lacrimal gland is responsible for maintaining the health of the ocular surface through the production of tears. However, our understanding of the immune system within the lacrimal gland is currently limited. Therefore, in this study, we utilized single-cell RNA sequencing and bioinformatic analysis to identify and analyze immune cells and molecules present in the lacrimal glands of normal mice. A total of 34,891 cells were obtained from the lacrimal glands of mice and classified into 18 distinct cell clusters using Seurat clustering. Within these cell populations, 26 different immune cell subpopulations were identified, including T cells, innate lymphocytes, macrophages, mast cells, dendritic cells, and B cells. Network analysis revealed complex cell-cell interactions between these immune cells, with particularly significant interactions observed among T cells, macrophages, plasma cells, and dendritic cells. Interestingly, T cells were found to be the main source of ligands for the Thy1 signaling pathway, while M2 macrophages were identified as the primary target of this pathway. Moreover, some of these immune cells were validated using immunohistological techniques. Collectively, these findings highlight the abundance and interactions of immune cells and provide valuable insights into the complexity of the lacrimal gland immune system and its relevance to associated diseases.
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Affiliation(s)
- Qiwei Fan
- Department of Pathology, School of Medicine, Jinan University, Guangzhou 510632, China; (Q.F.); (J.L.)
- International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; (R.Y.); (Y.L.); (L.L.); (S.L.); (T.F.); (Y.X.); (J.L.)
| | - Ruyu Yan
- International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; (R.Y.); (Y.L.); (L.L.); (S.L.); (T.F.); (Y.X.); (J.L.)
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China
| | - Yan Li
- International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; (R.Y.); (Y.L.); (L.L.); (S.L.); (T.F.); (Y.X.); (J.L.)
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China
| | - Liyuan Lu
- International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; (R.Y.); (Y.L.); (L.L.); (S.L.); (T.F.); (Y.X.); (J.L.)
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China
| | - Jiangman Liu
- Department of Pathology, School of Medicine, Jinan University, Guangzhou 510632, China; (Q.F.); (J.L.)
- International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; (R.Y.); (Y.L.); (L.L.); (S.L.); (T.F.); (Y.X.); (J.L.)
| | - Senmao Li
- International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; (R.Y.); (Y.L.); (L.L.); (S.L.); (T.F.); (Y.X.); (J.L.)
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China
| | - Ting Fu
- International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; (R.Y.); (Y.L.); (L.L.); (S.L.); (T.F.); (Y.X.); (J.L.)
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China
| | - Yunxia Xue
- International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; (R.Y.); (Y.L.); (L.L.); (S.L.); (T.F.); (Y.X.); (J.L.)
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China
| | - Jun Liu
- International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; (R.Y.); (Y.L.); (L.L.); (S.L.); (T.F.); (Y.X.); (J.L.)
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China
| | - Zhijie Li
- International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; (R.Y.); (Y.L.); (L.L.); (S.L.); (T.F.); (Y.X.); (J.L.)
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China
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244
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Saxena P, Sinha A, Singh SK. Computer-assisted interpretation, in-depth exploration and single cell type annotation of RNA sequence data using k-means clustering algorithm. Comput Methods Biomech Biomed Engin 2024:1-11. [PMID: 38235728 DOI: 10.1080/10255842.2023.2300685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/24/2023] [Indexed: 01/19/2024]
Abstract
At now, the majority of approaches rely on manual techniques for annotating cell types subsequent to clustering the data obtained from single-cell RNA sequencing (scRNA-seq). These approaches require a significant amount of physical exertion and depend substantially on the user's skill, perhaps resulting in uneven outcomes and inconsistency in treatment. In this paper, we provide a computer-assisted interpretation of every single cell of a tissue sample, along with an in-depth exploration of an individual cell's molecular, phenotypic and functional attributes. The paper will also perform k-means clustering followed by silhouette validation based on similar phenotype and functional attributes, and also, cell type annotation is performed, where we match a cell's gene profile against some known database by applying certain statistical conditions. Finally, all the genes are mapped spatially on the tissue sample. This paper is an aid to medicine to know which cells are expressed/not expressed in a tissue sample and their spatial location on the tissue sample.
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Affiliation(s)
- Pranshu Saxena
- Department of Information Technology, ABES Engineering College, Ghaziabad, India
| | - Amit Sinha
- Department of Information Technology, ABES Engineering College, Ghaziabad, India
| | - Sanjay Kumar Singh
- University School of Automation and Robotics, Guru Gobind Singh Indraprastha University, Surajmal Vihar, Delhi, India
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245
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Siew JJ, Chen HM, Chiu FL, Lee CW, Chang YM, Chen HL, Nguyen TNA, Liao HT, Liu M, Hagar HT, Sun YC, Lai HL, Kuo MH, Blum D, Buée L, Jin LW, Chen SY, Ko TM, Huang JR, Kuo HC, Liu FT, Chern Y. Galectin-3 aggravates microglial activation and tau transmission in tauopathy. J Clin Invest 2024; 134:e165523. [PMID: 37988169 PMCID: PMC10786694 DOI: 10.1172/jci165523] [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: 09/19/2022] [Accepted: 11/16/2023] [Indexed: 11/23/2023] Open
Abstract
Alzheimer's disease is characterized by the accumulation of amyloid-β plaques, aggregation of hyperphosphorylated tau (pTau), and microglia activation. Galectin-3 (Gal3) is a β-galactoside-binding protein that has been implicated in amyloid pathology. Its role in tauopathy remains enigmatic. Here, we showed that Gal3 was upregulated in the microglia of humans and mice with tauopathy. pTau triggered the release of Gal3 from human induced pluripotent stem cell-derived microglia in both its free and extracellular vesicular-associated (EV-associated) forms. Both forms of Gal3 increased the accumulation of pathogenic tau in recipient cells. Binding of Gal3 to pTau greatly enhanced tau fibrillation. Besides Gal3, pTau was sorted into EVs for transmission. Moreover, pTau markedly enhanced the number of EVs released by iMGL in a Gal3-dependent manner, suggesting a role of Gal3 in biogenesis of EVs. Single-cell RNA-Seq analysis of the hippocampus of a mouse model of tauopathy (THY-Tau22) revealed a group of pathogenic tau-evoked, Gal3-associated microglia with altered cellular machineries implicated in neurodegeneration, including enhanced immune and inflammatory responses. Genetic removal of Gal3 in THY-Tau22 mice suppressed microglia activation, reduced the level of pTau and synaptic loss in neurons, and rescued memory impairment. Collectively, Gal3 is a potential therapeutic target for tauopathy.
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Affiliation(s)
| | | | - Feng-Lan Chiu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | | | | | | | | | | | - Mengyu Liu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Hsiao-Tien Hagar
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Yung-Chen Sun
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | | | - Min-Hao Kuo
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - David Blum
- Univ. Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
- Alzheimer & Tauopathies, LabEx DISTALZ, LiCEND, Lille, France
| | - Luc Buée
- Univ. Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
- Alzheimer & Tauopathies, LabEx DISTALZ, LiCEND, Lille, France
| | - Lee-Way Jin
- Department of Pathology and Laboratory Medicine, University of California Davis, Sacramento, California, USA
| | | | - Tai-Ming Ko
- Institute of Biomedical Sciences
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Jie-Rong Huang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Hung-Chih Kuo
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
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246
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Röthe J, Kraft R, Ricken A, Kaczmarek I, Matz-Soja M, Winter K, Dietzsch AN, Buchold J, Ludwig MG, Liebscher I, Schöneberg T, Thor D. The adhesion GPCR GPR116/ADGRF5 has a dual function in pancreatic islets regulating somatostatin release and islet development. Commun Biol 2024; 7:104. [PMID: 38228886 PMCID: PMC10791652 DOI: 10.1038/s42003-024-05783-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/05/2024] [Indexed: 01/18/2024] Open
Abstract
Glucose homeostasis is maintained by hormones secreted from different cell types of the pancreatic islets and controlled by manifold input including signals mediated through G protein-coupled receptors (GPCRs). RNA-seq analyses revealed expression of numerous GPCRs in mouse and human pancreatic islets, among them Gpr116/Adgrf5. GPR116 is an adhesion GPCR mainly found in lung and required for surfactant secretion. Here, we demonstrate that GPR116 is involved in the somatostatin release from pancreatic delta cells using a whole-body as well as a cell-specific knock-out mouse model. Interestingly, the whole-body GPR116 deficiency causes further changes such as decreased beta-cell mass, lower number of small islets, and reduced pancreatic insulin content. Glucose homeostasis in global GPR116-deficient mice is maintained by counter-acting mechanisms modulating insulin degradation. Our data highlight an important function of GPR116 in controlling glucose homeostasis.
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Affiliation(s)
- Juliane Röthe
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Robert Kraft
- Carl-Ludwig-Institute for Physiology, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Albert Ricken
- Institute of Anatomy, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Isabell Kaczmarek
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Madlen Matz-Soja
- Medical Department II - Gastroenterology, Hepatology, Infectious Diseases, Pneumology, University Medical Center, Leipzig, Germany
- Division of Hepatology, Clinic and Polyclinic for Oncology, Gastroenterology, Hepatology, Infectious Diseases, and Pneumology, University Hospital, Leipzig, Germany
| | - Karsten Winter
- Institute of Anatomy, Medical Faculty, Leipzig University, Leipzig, Germany
| | - André Nguyen Dietzsch
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Julia Buchold
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | | | - Ines Liebscher
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Doreen Thor
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany.
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247
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Dos Santos OAL, Carneiro RL, Requião RD, Ribeiro-Alves M, Domitrovic T, Palhano FL. Transcriptional profile of ribosome-associated quality control components and their associated phenotypes in mammalian cells. Sci Rep 2024; 14:1439. [PMID: 38228636 PMCID: PMC10792078 DOI: 10.1038/s41598-023-50811-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: 08/30/2023] [Accepted: 12/26/2023] [Indexed: 01/18/2024] Open
Abstract
During protein synthesis, organisms detect translation defects that induce ribosome stalling and result in protein aggregation. The Ribosome-associated Quality Control (RQC) complex, comprising TCF25, LTN1, and NEMF, is responsible for identifying incomplete protein products from unproductive translation events, targeting them for degradation. Although RQC disruption causes adverse effects on vertebrate neurons, data regarding mRNA/protein expression and regulation across tissues are lacking. Employing high-throughput methods, we analyzed public datasets to explore RQC gene expression and phenotypes. Our findings revealed widespread expression of RQC components in human tissues; however, silencing of RQC yielded only mild negative effects on cell growth. Notably, TCF25 exhibited elevated mRNA levels that were not reflected in the protein content. We experimentally demonstrated that this disparity arose from post-translational protein degradation by the proteasome. Additionally, we observed that cellular aging marginally influenced RQC expression, leading to reduced mRNA levels in specific tissues. Our results suggest the necessity of RQC expression in all mammalian tissues. Nevertheless, when RQC falters, alternative mechanisms seem to compensate, ensuring cell survival under nonstress conditions.
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Affiliation(s)
- Otávio Augusto Leitão Dos Santos
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Rodolfo L Carneiro
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Rodrigo D Requião
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marcelo Ribeiro-Alves
- Fundação Oswaldo Cruz, Instituto Nacional de Infectologia Evandro Chagas, Rio de Janeiro, 21040-900, Brazil
| | - Tatiana Domitrovic
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Fernando L Palhano
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil.
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248
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Casalino-Matsuda SM, Chen F, Gonzalez-Gonzalez FJ, Matsuda H, Nair A, Abdala-Valencia H, Budinger GS, Dong JT, Beitel GJ, Sporn PH. Myeloid Zfhx3 deficiency protects against hypercapnia-induced suppression of host defense against influenza A virus. JCI Insight 2024; 9:e170316. [PMID: 38227369 PMCID: PMC11143927 DOI: 10.1172/jci.insight.170316] [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: 03/10/2023] [Accepted: 01/10/2024] [Indexed: 01/17/2024] Open
Abstract
Hypercapnia, elevation of the partial pressure of CO2 in blood and tissues, is a risk factor for mortality in patients with severe acute and chronic lung diseases. We previously showed that hypercapnia inhibits multiple macrophage and neutrophil antimicrobial functions and that elevated CO2 increases the mortality of bacterial and viral pneumonia in mice. Here, we show that normoxic hypercapnia downregulates innate immune and antiviral gene programs in alveolar macrophages (AMØs). We also show that zinc finger homeobox 3 (Zfhx3) - a mammalian ortholog of zfh2, which mediates hypercapnic immune suppression in Drosophila - is expressed in mouse and human macrophages. Deletion of Zfhx3 in the myeloid lineage blocked the suppressive effect of hypercapnia on immune gene expression in AMØs and decreased viral replication, inflammatory lung injury, and mortality in hypercapnic mice infected with influenza A virus. To our knowledge, our results establish Zfhx3 as the first known mammalian mediator of CO2 effects on immune gene expression and lay the basis for future studies to identify therapeutic targets to interrupt hypercapnic immunosuppression in patients with advanced lung disease.
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Affiliation(s)
- S. Marina Casalino-Matsuda
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Fei Chen
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Francisco J. Gonzalez-Gonzalez
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Hiroaki Matsuda
- Department of Physical Sciences and Engineering, Wilbur Wright College, Chicago, Illinois, USA
| | - Aisha Nair
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - G.R. Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, USA
| | - Jin-Tang Dong
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Greg J. Beitel
- Department of Molecular Biosciences, Weinberg College of Arts and Sciences, Northwestern University, Evanston, Illinois, USA
| | - Peter H.S. Sporn
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, USA
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249
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Wang X, Kulik K, Wan TC, Lough JW, Auchampach JA. Evidence of Histone H2A.Z Deacetylation and Cardiomyocyte Dedifferentiation in Infarcted/Tip60-depleted Hearts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575312. [PMID: 38260622 PMCID: PMC10802610 DOI: 10.1101/2024.01.11.575312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Myocardial infarction (MI) in the human heart causes death of billions of cardiomyocytes (CMs), resulting in cardiac dysfunction that is incompatible with life or lifestyle. In order to re-muscularize injured myocardium, replacement CMs must be generated via renewed proliferation of surviving CMs. Approaches designed to induce proliferation of CMs after injury have been insufficient. Toward this end, we are targeting the Tip60 acetyltransferase, based on the rationale that its pleiotropic functions conspire to block the CM cell-cycle at several checkpoints. We previously reported that genetic depletion of Tip60 in a mouse model after MI reduces scarring, retains cardiac function, and activates the CM cell-cycle, although it is unclear whether this culminates in the generation of daughter CMs. For pre-existing CMs in the adult heart to resume proliferation, it is becoming widely accepted that they must first dedifferentiate, a process highlighted by loss of maturity, epithelial to mesenchymal transitioning (EMT), and reversion from fatty acid oxidation to glycolytic metabolism, accompanied by softening of the myocardial extracellular matrix. Findings in hematopoietic stem cells, and more recently in neural progenitor cells, have shown that Tip60 induces and maintains the differentiated state via site-specific acetylation of the histone variant H2A.Z. Here, we report that genetic depletion of Tip60 from naïve or infarcted hearts results in the near-complete absence of acetylated H2A.Z in CM nuclei, and that this is accordingly accompanied by altered gene expressions indicative of EMT induction, ECM softening, decreased fatty acid oxidation, and depressed expression of genes that regulate the TCA cycle. These findings, combined with our previous work, support the notion that because Tip60 has multiple targets that combinatorially maintain the differentiated state and inhibit proliferation, its transient therapeutic targeting to ameliorate the effects of cardiac injury should be considered.
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Affiliation(s)
- Xinrui Wang
- Department of Pharmacology and Toxicology, Medical College of Wisconsin Milwaukee, WI 53226
- Cardiovascular Center, Medical College of Wisconsin Milwaukee, WI 53226
| | - Katherine Kulik
- Department of Cell Biology Neurobiology and Anatomy, Medical College of Wisconsin Milwaukee, WI 53226
- Cardiovascular Center, Medical College of Wisconsin Milwaukee, WI 53226
| | - Tina C. Wan
- Department of Pharmacology and Toxicology, Medical College of Wisconsin Milwaukee, WI 53226
- Cardiovascular Center, Medical College of Wisconsin Milwaukee, WI 53226
| | - John W. Lough
- Department of Cell Biology Neurobiology and Anatomy, Medical College of Wisconsin Milwaukee, WI 53226
- Cardiovascular Center, Medical College of Wisconsin Milwaukee, WI 53226
| | - John A. Auchampach
- Department of Pharmacology and Toxicology, Medical College of Wisconsin Milwaukee, WI 53226
- Cardiovascular Center, Medical College of Wisconsin Milwaukee, WI 53226
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250
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Hekselman I, Vital A, Ziv-Agam M, Kerber L, Yairi I, Yeger-Lotem E. Affected cell types for hundreds of Mendelian diseases revealed by analysis of human and mouse single-cell data. eLife 2024; 13:e84613. [PMID: 38197427 PMCID: PMC10830129 DOI: 10.7554/elife.84613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/08/2023] [Indexed: 01/11/2024] Open
Abstract
Mendelian diseases tend to manifest clinically in certain tissues, yet their affected cell types typically remain elusive. Single-cell expression studies showed that overexpression of disease-associated genes may point to the affected cell types. Here, we developed a method that infers disease-affected cell types from the preferential expression of disease-associated genes in cell types (PrEDiCT). We applied PrEDiCT to single-cell expression data of six human tissues, to infer the cell types affected in Mendelian diseases. Overall, we inferred the likely affected cell types for 328 diseases. We corroborated our findings by literature text-mining, expert validation, and recapitulation in mouse corresponding tissues. Based on these findings, we explored characteristics of disease-affected cell types, showed that diseases manifesting in multiple tissues tend to affect similar cell types, and highlighted cases where gene functions could be used to refine inference. Together, these findings expand the molecular understanding of disease mechanisms and cellular vulnerability.
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Affiliation(s)
- Idan Hekselman
- Department of Clinical Biochemistry and Pharmacology, Ben-Gurion University of the NegevBe’er ShevaIsrael
| | - Assaf Vital
- Department of Clinical Biochemistry and Pharmacology, Ben-Gurion University of the NegevBe’er ShevaIsrael
| | - Maya Ziv-Agam
- Department of Clinical Biochemistry and Pharmacology, Ben-Gurion University of the NegevBe’er ShevaIsrael
| | - Lior Kerber
- Department of Clinical Biochemistry and Pharmacology, Ben-Gurion University of the NegevBe’er ShevaIsrael
| | - Ido Yairi
- Department of Clinical Biochemistry and Pharmacology, Ben-Gurion University of the NegevBe’er ShevaIsrael
| | - Esti Yeger-Lotem
- Department of Clinical Biochemistry and Pharmacology, Ben-Gurion University of the NegevBe’er ShevaIsrael
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the NegevBe’er ShevaIsrael
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