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Tian Y, Wu X, Luo S, Xiong D, Liu R, Hu L, Yuan Y, Shi G, Yao J, Huang Z, Fu F, Yang X, Tang Z, Zhang J, Hu K. A multi-omic single-cell landscape of cellular diversification in the developing human cerebral cortex. Comput Struct Biotechnol J 2024; 23:2173-2189. [PMID: 38827229 PMCID: PMC11141146 DOI: 10.1016/j.csbj.2024.05.019] [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: 02/20/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 06/04/2024] Open
Abstract
The vast neuronal diversity in the human neocortex is vital for high-order brain functions, necessitating elucidation of the regulatory mechanisms underlying such unparalleled diversity. However, recent studies have yet to comprehensively reveal the diversity of neurons and the molecular logic of neocortical origin in humans at single-cell resolution through profiling transcriptomic or epigenomic landscapes, owing to the application of unimodal data alone to depict exceedingly heterogeneous populations of neurons. In this study, we generated a comprehensive compendium of the developing human neocortex by simultaneously profiling gene expression and open chromatin from the same cell. We computationally reconstructed the differentiation trajectories of excitatory projection neurons of cortical origin and inferred the regulatory logic governing lineage bifurcation decisions for neuronal diversification. We demonstrated that neuronal diversity arises from progenitor cell lineage specificity and postmitotic differentiation at distinct stages. Our data paves the way for understanding the primarily coordinated regulatory logic for neuronal diversification in the neocortex.
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Affiliation(s)
- Yuhan Tian
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Xia Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Songhao Luo
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Dan Xiong
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Rong Liu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Lanqi Hu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuchen Yuan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Guowei Shi
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Junjie Yao
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhiwei Huang
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Fang Fu
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 511436, China
| | - Xin Yang
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 511436, China
| | - Zhonghui Tang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Jiajun Zhang
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Kunhua Hu
- Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
- Public Platform Laboratory, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
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2
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Wang S, Tong S, Jin X, Li N, Dang P, Sui Y, Liu Y, Wang D. Single-cell RNA sequencing analysis of the retina under acute high intraocular pressure. Neural Regen Res 2024; 19:2522-2531. [PMID: 38526288 PMCID: PMC11090430 DOI: 10.4103/1673-5374.389363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/27/2023] [Accepted: 09/13/2023] [Indexed: 03/26/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202419110-00032/figure1/v/2024-03-08T184507Z/r/image-tiff High intraocular pressure causes retinal ganglion cell injury in primary and secondary glaucoma diseases, yet the molecular landscape characteristics of retinal cells under high intraocular pressure remain unknown. Rat models of acute hypertension ocular pressure were established by injection of cross-linked hyaluronic acid hydrogel (Healaflow®). Single-cell RNA sequencing was then used to describe the cellular composition and molecular profile of the retina following high intraocular pressure. Our results identified a total of 12 cell types, namely retinal pigment epithelial cells, rod-photoreceptor cells, bipolar cells, Müller cells, microglia, cone-photoreceptor cells, retinal ganglion cells, endothelial cells, retinal progenitor cells, oligodendrocytes, pericytes, and fibroblasts. The single-cell RNA sequencing analysis of the retina under acute high intraocular pressure revealed obvious changes in the proportions of various retinal cells, with ganglion cells decreased by 23%. Hematoxylin and eosin staining and TUNEL staining confirmed the damage to retinal ganglion cells under high intraocular pressure. We extracted data from retinal ganglion cells and analyzed the retinal ganglion cell cluster with the most distinct expression. We found upregulation of the B3gat2 gene, which is associated with neuronal migration and adhesion, and downregulation of the Tsc22d gene, which participates in inhibition of inflammation. This study is the first to reveal molecular changes and intercellular interactions in the retina under high intraocular pressure. These data contribute to understanding of the molecular mechanism of retinal injury induced by high intraocular pressure and will benefit the development of novel therapies.
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Affiliation(s)
- Shaojun Wang
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Siti Tong
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Xin Jin
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Na Li
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Pingxiu Dang
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Yang Sui
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Ying Liu
- Department of Ophthalmology, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China
| | - Dajiang Wang
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
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Ding LY, Chang CJ, Chen SY, Chen KL, Li YS, Wu YC, Hsu TY, Ying HY, Wu HY, Hughes MW, Wang CY, Chang CH, Tang MJ, Chuang WJ, Shan YS, Chang CJ, Huang PH. Stromal Rigidity Stress Accelerates Pancreatic Intraepithelial Neoplasia Progression and Chromosomal Instability via Nuclear Protein Tyrosine Kinase 2 Localization. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:1346-1373. [PMID: 38631549 DOI: 10.1016/j.ajpath.2024.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/11/2024] [Accepted: 02/21/2024] [Indexed: 04/19/2024]
Abstract
Because the mechanotransduction by stromal stiffness stimulates the rupture and repair of the nuclear envelope in pancreatic progenitor cells, accumulated genomic aberrations are under selection in the tumor microenvironment. Analysis of cell growth, micronuclei, and phosphorylated Ser-139 residue of the histone variant H2AX (γH2AX) foci linked to mechanotransduction pressure in vivo during serial orthotopic passages of mouse KrasLSL-G12D/+;Trp53flox/flox;Pdx1-Cre (KPC) cancer cells in the tumor and in migrating through the size-restricted 3-μm micropores. To search for pancreatic cancer cell-of-origin, analysis of single-cell data sets revealed that the extracellular matrix shaped an alternate route of acinar-ductal transdifferentiation of acinar cells into topoisomerase II α (TOP2A)-overexpressing cancer cells and derived subclusters with copy number amplifications in MYC-PTK2 (protein tyrosine kinase 2) locus and PIK3CA. High-PTK2 expression is associated with 171 differentially methylated CpG loci, 319 differentially expressed genes, and poor overall survival in The Cancer Genome Atlas-Pancreatic Adenocarcinoma cohort. Abolished RGD-integrin signaling by disintegrin KG blocked the PTK2 phosphorylation, increased cancer apoptosis, decreased vav guanine nucleotide exchange factor 1 (VAV1) expression, and prolonged overall survival in the KPC mice. Reduction of α-smooth muscle actin deposition in the CD248 knockout KPC mice remodeled the tissue stroma and down-regulated TOP2A expression in the epithelium. In summary, stromal stiffness induced the onset of cancer cells-of-origin by ectopic TOP2A expression, and the genomic amplification of MYC-PTK2 locus via alternative transdifferentiation of pancreatic progenitor cells is the vulnerability useful for disintegrin KG treatment.
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Affiliation(s)
- Li-Yun Ding
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Jung Chang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Szu-Ying Chen
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Kuan-Lin Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yueh-Shan Li
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yun-Chieh Wu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ting-Yi Hsu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hsin-Yu Ying
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hsin-Yi Wu
- Instrumentation Center, College of Science, National Taiwan University, Taipei, Taiwan
| | - Michael W Hughes
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Life Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan; International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Yih Wang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chih-Han Chang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan; Medical Device Innovation Center, National Cheng Kung University, Tainan, Taiwan
| | - Ming-Jer Tang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan; Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Woei-Jer Chuang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Center of Cell Therapy, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yan-Shen Shan
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Center of Cell Therapy, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Division of General Surgery, Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Jung Chang
- Department of Internal Medicine, Ditmanson Medical Foundation, Chia-Yi Christian Hospital, Chia-Yi, Taiwan.
| | - Po-Hsien Huang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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Schonfeld M, O’Neil M, Weinman SA, Tikhanovich I. Alcohol-induced epigenetic changes prevent fibrosis resolution after alcohol cessation in miceresolution. Hepatology 2024; 80:119-135. [PMID: 37943941 PMCID: PMC11078890 DOI: 10.1097/hep.0000000000000675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND AND AIMS Alcohol-associated liver disease is a major cause of alcohol-associated mortality. Recently, we identified hepatic demethylases lysine demethylase (KDM)5B and KDM5C as important epigenetic regulators of alcohol response in the liver. In this study, we aimed to investigate the role of KDM5 demethylases in alcohol-associated liver disease resolution. APPROACH AND RESULTS We showed that alcohol-induced liver steatosis rapidly resolved after alcohol cessation. In contrast, fibrosis persisted in the liver for up to 8 weeks after the end of alcohol exposure. Defects in fibrosis resolution were in part due to alcohol-induced KDM5B and KDM5C-dependent epigenetic changes in hepatocytes. Using cell-type-specific knockout mice, we found that adeno-associated virus-mediated knockout of KDM5B and KDM5C demethylases in hepatocytes at the time of alcohol withdrawal promoted fibrosis resolution. Single-cell ATAC sequencing analysis showed that during alcohol-associated liver disease resolution epigenetic cell states largely reverted to control conditions. In addition, we found unique epigenetic cell states distinct from both control and alcohol states and identified associated transcriptional regulators, including liver X receptor (LXR) alpha (α). In vitro and in vivo analysis confirmed that knockout of KDM5B and KDM5C demethylases promoted LXRα activity, likely through regulation of oxysterol biosynthesis, and this activity was critical for the fibrosis resolution process. Reduced LXR activity by small molecule inhibitors prevented fibrosis resolution in KDM5-deficient mice. CONCLUSIONS In summary, KDM5B and KDM5C demethylases prevent liver fibrosis resolution after alcohol cessation in part through suppression of LXR activity.
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Affiliation(s)
- Michael Schonfeld
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS 66160, U.S.A
| | - Maura O’Neil
- Department of Pathology, University of Kansas Medical Center, Kansas City, KS 66160, U.S.A
| | - Steven A Weinman
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS 66160, U.S.A
- Kansas City VA Medical Center, Kansas City, MO, USA
| | - Irina Tikhanovich
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS 66160, U.S.A
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Liu C, Li K, Sui X, Zhao T, Zhang T, Chen Z, Wu H, Li C, Li H, Yang F, Liu Z, Lu YY, Wang J, Chen X, Liu P. Patient-Derived Tumor Organoids Combined with Function-Associated ScRNA-Seq for Dissecting the Local Immune Response of Lung Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400185. [PMID: 38896792 DOI: 10.1002/advs.202400185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 06/03/2024] [Indexed: 06/21/2024]
Abstract
In vitro models coupled with multimodal approaches are needed to dissect the dynamic response of local tumor immune microenvironment (TIME) to immunotherapy. Here the patient-derived primary lung cancer organoids (pLCOs) are generated by isolating tumor cell clusters, including the infiltrated immune cells. A function-associated single-cell RNA sequencing (FascRNA-seq) platform allowing both phenotypic evaluation and scRNA-seq at single-organoid level is developed to dissect the TIME of individual pLCOs. The analysis of 171 individual pLCOs derived from seven patients reveals that pLCOs retain the TIME heterogeneity in the parenchyma of parental tumor tissues, providing models with identical genetic background but various TIME. Linking the scRNA-seq data of individual pLCOs with their responses to anti-PD-1 (αPD-1) immune checkpoint blockade (ICB) allows to confirm the central role of CD8+ T cells in anti-tumor immunity, to identify potential tumor-reactive T cells with a set of 10 genes, and to unravel the factors regulating T cell activity, including CD99 gene. In summary, the study constructs a joint phenotypic and transcriptomic FascRNA-seq platform to dissect the dynamic response of local TIME under ICB treatment, providing a promising approach to evaluate novel immunotherapies and to understand the underlying molecular mechanisms.
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Affiliation(s)
- Chang Liu
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Kaiyi Li
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xizhao Sui
- Department of Thoracic Surgery, People's Hospital, Peking University, Beijing, 100034, China
| | - Tian Zhao
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Ting Zhang
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Zhongyao Chen
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Hainan Wu
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Chao Li
- Department of Thoracic Surgery, People's Hospital, Peking University, Beijing, 100034, China
| | - Hao Li
- Department of Thoracic Surgery, People's Hospital, Peking University, Beijing, 100034, China
| | - Fan Yang
- Department of Thoracic Surgery, People's Hospital, Peking University, Beijing, 100034, China
| | - Zhidong Liu
- Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101125, China
| | - You-Yong Lu
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Oncology, Beijing Cancer Hospital and Institute, Peking University, Beijing, 100142, China
| | - Jun Wang
- Department of Thoracic Surgery, People's Hospital, Peking University, Beijing, 100034, China
| | - Xiaofang Chen
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Peng Liu
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
- Changping Laboratory, Beijing, 102299, China
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6
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Zhang Y, Zhang C, He J, Lai G, Li W, Zeng H, Zhong X, Xie B. Comprehensive analysis of single cell and bulk RNA sequencing reveals the heterogeneity of melanoma tumor microenvironment and predicts the response of immunotherapy. Inflamm Res 2024:10.1007/s00011-024-01905-5. [PMID: 38896289 DOI: 10.1007/s00011-024-01905-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/07/2024] [Accepted: 06/09/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Tumor microenvironment (TME) heterogeneity is an important factor affecting the treatment response of immune checkpoint inhibitors (ICI). However, the TME heterogeneity of melanoma is still widely characterized. METHODS We downloaded the single-cell sequencing data sets of two melanoma patients from the GEO database, and used the "Scissor" algorithm and the "BayesPrism" algorithm to comprehensively analyze the characteristics of microenvironment cells based on single-cell and bulk RNA-seq data. The prediction model of immunotherapy response was constructed by machine learning and verified in three cohorts of GEO database. RESULTS We identified seven cell types. In the Scissor+ subtype cell population, the top three were T cells, B cells and melanoma cells. In the Scissor- subtype, there are more macrophages. By quantifying the characteristics of TME, significant differences in B cells between responders and non-responders were observed. The higher the proportion of B cells, the better the prognosis. At the same time, macrophages in the non-responsive group increased significantly. Finally, nine gene features for predicting ICI response were constructed, and their predictive performance was superior in three external validation groups. CONCLUSION Our study revealed the heterogeneity of melanoma TME and found a new predictive biomarker, which provided theoretical support and new insights for precise immunotherapy of melanoma patients.
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Affiliation(s)
- Yuan Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China
- Research Center for Medicine and Social Development, Chongqing Medical University, Chongqing, China
| | - Cong Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China
- Research Center for Medicine and Social Development, Chongqing Medical University, Chongqing, China
| | - Jing He
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China
- Research Center for Medicine and Social Development, Chongqing Medical University, Chongqing, China
| | - Guichuan Lai
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China
- Research Center for Medicine and Social Development, Chongqing Medical University, Chongqing, China
| | - Wenlong Li
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China
- Research Center for Medicine and Social Development, Chongqing Medical University, Chongqing, China
| | - Haijiao Zeng
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China
- Research Center for Medicine and Social Development, Chongqing Medical University, Chongqing, China
| | - Xiaoni Zhong
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China.
- Research Center for Medicine and Social Development, Chongqing Medical University, Chongqing, China.
| | - Biao Xie
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China.
- Research Center for Medicine and Social Development, Chongqing Medical University, Chongqing, China.
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Kobayashi T, Yamashita A, Tsumaki N, Watanabe H. Subpopulations of fibroblasts derived from human iPS cells. Commun Biol 2024; 7:736. [PMID: 38890483 DOI: 10.1038/s42003-024-06419-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
Organ fibrosis causes collagen fiber overgrowth and impairs organ function. Cardiac fibrosis after myocardial infarction impairs cardiac function significantly, pulmonary fibrosis reduces gas exchange efficiency, and liver fibrosis disturbs the natural function of the liver. Its development is associated with the differentiation of fibroblasts into myofibroblasts and increased collagen synthesis. Fibrosis has organ specificity, defined by the heterogeneity of fibroblasts. Although this heterogeneity is established during embryonic development, it has not been defined yet. Fibroblastic differentiation of induced pluripotent stem cells (iPSCs) recapitulates the process by which fibroblasts acquire diversity. Here, we differentiated iPSCs into cardiac, hepatic, and dermal fibroblasts and analyzed their properties using single-cell RNA sequencing. We observed characteristic subpopulations with different ratios in each organ-type fibroblast group, which contained both resting and distinct ACTA2+ myofibroblasts. These findings provide crucial information on the ontogeny-based heterogeneity of fibroblasts, leading to the development of therapeutic strategies to control fibrosis.
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Affiliation(s)
- Takashi Kobayashi
- Institute for Molecular Science of Medicine, Aichi Medical University, Aichi, Japan
| | - Akihiro Yamashita
- Department of Tissue Biochemistry, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
| | - Noriyuki Tsumaki
- Department of Tissue Biochemistry, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
| | - Hideto Watanabe
- Institute for Molecular Science of Medicine, Aichi Medical University, Aichi, Japan.
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Lee DH, Yoo JK, Um KH, Ha W, Lee SM, Park J, Kye MJ, Suh J, Choi JW. Intravesical instillation-based mTOR-STAT3 dual targeting for bladder cancer treatment. J Exp Clin Cancer Res 2024; 43:170. [PMID: 38886756 PMCID: PMC11184849 DOI: 10.1186/s13046-024-03088-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Recent intravesical administration of adenoviral vectors, either as a single injection or in combination with immune checkpoint inhibitors, exemplified by cretostimogene grenadenorepvec and nadofaragene firadenovec, has demonstrated remarkable efficacy in clinical trials for non-muscle invasive bladder cancer. Despite their ability to induce an enhanced immune reaction within the lesion, the intracellular survival signaling of cancer cells has not been thoroughly addressed. METHODS An analysis of the prognostic data revealed a high probability of therapeutic efficacy with simultaneous inhibition of mTOR and STAT3. Considering the challenges of limited pharmaco-accessibility to the bladder due to its pathophysiological structure and the partially undruggable nature of target molecules, we designed a dual siRNA system targeting both mRNAs. Subsequently, this dual siRNA system was encoded into the adenovirus 5/3 (Ad 5/3) to enhance in vivo delivery efficiency. RESULTS Gene-targeting efficacy was assessed using cells isolated from xenografted tumors using a single-cell analysis system. Our strategy demonstrated a balanced downregulation of mTOR and STAT3 at the single-cell resolution, both in vitro and in vivo. This approach reduced tumor growth in bladder cancer xenograft and orthotopic animal experiments. In addition, increased infiltration of CD8+ T cells was observed in a humanized mouse model. We provided helpful and safe tissue distribution data for intravesical therapy of siRNAs coding adenoviruses. CONCLUSIONS The bi-specific siRNA strategy, encapsulated in an adenovirus, could be a promising tool to augment cancer treatment efficacy and overcome conventional therapy limitations associated with "undruggability." Hence, we propose that dual targeting of mTOR and STAT3 is an advantageous strategy for intravesical therapy using adenoviruses.
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Affiliation(s)
- Dae Hoon Lee
- Department of Pharmacology, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
- R&D Center of Curigin Ltd., Curigin, Seoul, 04778, Republic of Korea
| | - Jung Ki Yoo
- Department of Pharmacology, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
- R&D Center of Curigin Ltd., Curigin, Seoul, 04778, Republic of Korea
| | - Ki Hwan Um
- Department of Pharmacology, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
- R&D Center of Curigin Ltd., Curigin, Seoul, 04778, Republic of Korea
- Department of Regulatory Science, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Wootae Ha
- R&D Center of Curigin Ltd., Curigin, Seoul, 04778, Republic of Korea
| | - Soo Min Lee
- Department of Pharmacology, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
- Department of Regulatory Science, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Junseong Park
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Min Jeong Kye
- R&D Center of Curigin Ltd., Curigin, Seoul, 04778, Republic of Korea
| | - Jungyo Suh
- Department of Urology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Jin Woo Choi
- Department of Pharmacology, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea.
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea.
- R&D Center of Curigin Ltd., Curigin, Seoul, 04778, Republic of Korea.
- Department of Regulatory Science, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea.
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9
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Gioacchino E, Zhang W, Koyunlar C, Zink J, de Looper H, Gussinklo KJ, Hoogenboezem R, Bosch D, Bindels E, Touw IP, de Pater E. GATA2 heterozygosity causes an epigenetic feedback mechanism resulting in myeloid and erythroid dysplasia. Br J Haematol 2024. [PMID: 38887897 DOI: 10.1111/bjh.19585] [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: 04/03/2024] [Accepted: 05/27/2024] [Indexed: 06/20/2024]
Abstract
The transcription factor GATA2 has a pivotal role in haematopoiesis. Heterozygous germline GATA2 mutations result in a syndrome characterized by immunodeficiency, bone marrow failure and predispositions to myelodysplastic syndrome (MDS) and acute myeloid leukaemia. Clinical symptoms in these patients are diverse and mechanisms driving GATA2-related phenotypes are largely unknown. To explore the impact of GATA2 haploinsufficiency on haematopoiesis, we generated a zebrafish model carrying a heterozygous mutation of gata2b (gata2b+/-), an orthologue of GATA2. Morphological analysis revealed myeloid and erythroid dysplasia in gata2b+/- kidney marrow. Because Gata2b could affect both transcription and chromatin accessibility during lineage differentiation, this was assessed by single-cell (sc) RNA-seq and single-nucleus (sn) ATAC-seq. Sn-ATAC-seq showed that the co-accessibility between the transcription start site (TSS) and a -3.5-4.1 kb putative enhancer was more robust in gata2b+/- zebrafish HSPCs compared to wild type, increasing gata2b expression and resulting in higher genome-wide Gata2b motif use in HSPCs. As a result of increased accessibility of the gata2b locus, gata2b+/- chromatin was also more accessible during lineage differentiation. scRNA-seq data revealed myeloid differentiation defects, that is, impaired cell cycle progression, reduced expression of cebpa and cebpb and increased signatures of ribosome biogenesis. These data also revealed a differentiation delay in erythroid progenitors, aberrant proliferative signatures and down-regulation of Gata1a, a master regulator of erythropoiesis, which worsened with age. These findings suggest that cell-intrinsic compensatory mechanisms, needed to obtain normal levels of Gata2b in heterozygous HSPCs to maintain their integrity, result in aberrant lineage differentiation, thereby representing a critical step in the predisposition to MDS.
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Affiliation(s)
- Emanuele Gioacchino
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Wei Zhang
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Cansu Koyunlar
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Joke Zink
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Hans de Looper
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
- Cancer Genome Editing Center, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Kirsten J Gussinklo
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Remco Hoogenboezem
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Dennis Bosch
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Eric Bindels
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Ivo P Touw
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Emma de Pater
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
- Cancer Genome Editing Center, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
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10
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Li H, Humphreys BD. Protocol for multimodal profiling of human kidneys with simultaneous high-throughput ATAC and RNA expression with sequencing. STAR Protoc 2024; 5:103049. [PMID: 38900631 DOI: 10.1016/j.xpro.2024.103049] [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: 03/05/2024] [Revised: 03/31/2024] [Accepted: 04/15/2024] [Indexed: 06/22/2024] Open
Abstract
Simultaneous high-throughput ATAC and RNA expression with sequencing (SHARE-seq) profiles transcriptomics and chromatin accessibility in the same cells at high throughput. Here, we present a protocol for multimodal profiling of human kidneys with SHARE-seq. We describe steps for processing fixed nuclei for SHARE-seq split-pool barcoding and library preparation. We also detail how to determine the optimal working concentration of Tn5 transposase for transposition and tagmentation. This protocol allows researchers to generate large-scale single-cell multiomics data at low reagent cost. For complete details on the use and execution of this protocol, please refer to Li et al.1.
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Affiliation(s)
- Haikuo Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63105, USA.
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63105, USA; Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO 63105, USA.
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11
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Bielefeld P, Martirosyan A, Martín-Suárez S, Apresyan A, Meerhoff GF, Pestana F, Poovathingal S, Reijner N, Koning W, Clement RA, Van der Veen I, Toledo EM, Polzer O, Durá I, Hovhannisyan S, Nilges BS, Bogdoll A, Kashikar ND, Lucassen PJ, Belgard TG, Encinas JM, Holt MG, Fitzsimons CP. Traumatic brain injury promotes neurogenesis at the cost of astrogliogenesis in the adult hippocampus of male mice. Nat Commun 2024; 15:5222. [PMID: 38890340 DOI: 10.1038/s41467-024-49299-6] [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: 04/21/2023] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
Traumatic brain injury (TBI) can result in long-lasting changes in hippocampal function. The changes induced by TBI on the hippocampus contribute to cognitive deficits. The adult hippocampus harbors neural stem cells (NSCs) that generate neurons (neurogenesis), and astrocytes (astrogliogenesis). While deregulation of hippocampal NSCs and neurogenesis have been observed after TBI, it is not known how TBI may affect hippocampal astrogliogenesis. Using a controlled cortical impact model of TBI in male mice, single cell RNA sequencing and spatial transcriptomics, we assessed how TBI affected hippocampal NSCs and the neuronal and astroglial lineages derived from them. We observe an increase in NSC-derived neuronal cells and a concomitant decrease in NSC-derived astrocytic cells, together with changes in gene expression and cell dysplasia within the dentate gyrus. Here, we show that TBI modifies NSC fate to promote neurogenesis at the cost of astrogliogenesis and identify specific cell populations as possible targets to counteract TBI-induced cellular changes in the adult hippocampus.
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Affiliation(s)
- P Bielefeld
- Brain Plasticity Department, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - A Martirosyan
- VIB Center for Brain and Disease Research, Leuven, Belgium
- KU Leuven-Department of Neurosciences, Leuven, Belgium
| | - S Martín-Suárez
- Achucarro Basque Center for Neuroscience, Sede Bldg, Campus, UPV/EHU, Barrio Sarriena S/N, Leioa, Spain
| | - A Apresyan
- Armenian Bioinformatics Institute, Yerevan, Armenia
| | - G F Meerhoff
- Brain Plasticity Department, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - F Pestana
- VIB Center for Brain and Disease Research, Leuven, Belgium
- KU Leuven-Department of Neurosciences, Leuven, Belgium
| | - S Poovathingal
- VIB Center for Brain and Disease Research, Leuven, Belgium
- KU Leuven-Department of Neurosciences, Leuven, Belgium
| | - N Reijner
- Brain Plasticity Department, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - W Koning
- Brain Plasticity Department, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - R A Clement
- Brain Plasticity Department, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - I Van der Veen
- Brain Plasticity Department, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - E M Toledo
- Brain Plasticity Department, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - O Polzer
- Brain Plasticity Department, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - I Durá
- Achucarro Basque Center for Neuroscience, Sede Bldg, Campus, UPV/EHU, Barrio Sarriena S/N, Leioa, Spain
| | - S Hovhannisyan
- Department of Mathematics and Mechanics, Yerevan State University, Yerevan, Armenia
| | - B S Nilges
- Resolve Biosciences GmbH, Monheim am Rhein, Germany
- OMAPiX GmbH, Langenfeld (Rheinland), Langenfeld, Germany
| | - A Bogdoll
- Resolve Biosciences GmbH, Monheim am Rhein, Germany
| | - N D Kashikar
- Resolve Biosciences GmbH, Monheim am Rhein, Germany
- OMAPiX GmbH, Langenfeld (Rheinland), Langenfeld, Germany
| | - P J Lucassen
- Brain Plasticity Department, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | | | - J M Encinas
- Achucarro Basque Center for Neuroscience, Sede Bldg, Campus, UPV/EHU, Barrio Sarriena S/N, Leioa, Spain
- Department of Neuroscience, University of the Basque Country (UPV/EHU), Campus, UPV/EHU, Barrio Sarriena S/N, Leioa, Spain
- IKERBASQUE, The Basque Foundation for Science, Plaza Euskadi 5, Bilbao, Spain
| | - M G Holt
- VIB Center for Brain and Disease Research, Leuven, Belgium.
- KU Leuven-Department of Neurosciences, Leuven, Belgium.
- Instituto de Investigaçāo e Inovaçāo em Saúde (i3S), University of Porto, Porto, Portugal.
| | - C P Fitzsimons
- Brain Plasticity Department, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands.
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12
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Simpson L, Strange A, Klisch D, Kraunsoe S, Azami T, Goszczynski D, Le Minh T, Planells B, Holmes N, Sang F, Henson S, Loose M, Nichols J, Alberio R. A single-cell atlas of pig gastrulation as a resource for comparative embryology. Nat Commun 2024; 15:5210. [PMID: 38890321 DOI: 10.1038/s41467-024-49407-6] [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: 08/21/2023] [Accepted: 06/04/2024] [Indexed: 06/20/2024] Open
Abstract
Cell-fate decisions during mammalian gastrulation are poorly understood outside of rodent embryos. The embryonic disc of pig embryos mirrors humans, making them a useful proxy for studying gastrulation. Here we present a single-cell transcriptomic atlas of pig gastrulation, revealing cell-fate emergence dynamics, as well as conserved and divergent gene programs governing early porcine, primate, and murine development. We highlight heterochronicity in extraembryonic cell-types, despite the broad conservation of cell-type-specific transcriptional programs. We apply these findings in combination with functional investigations, to outline conserved spatial, molecular, and temporal events during definitive endoderm specification. We find early FOXA2 + /TBXT- embryonic disc cells directly form definitive endoderm, contrasting later-emerging FOXA2/TBXT+ node/notochord progenitors. Unlike mesoderm, none of these progenitors undergo epithelial-to-mesenchymal transition. Endoderm/Node fate hinges on balanced WNT and hypoblast-derived NODAL, which is extinguished upon endodermal differentiation. These findings emphasise the interplay between temporal and topological signalling in fate determination during gastrulation.
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Affiliation(s)
- Luke Simpson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Andrew Strange
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Doris Klisch
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Sophie Kraunsoe
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Takuya Azami
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Daniel Goszczynski
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Triet Le Minh
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Benjamin Planells
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Nadine Holmes
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Fei Sang
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Sonal Henson
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Matthew Loose
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Jennifer Nichols
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Ramiro Alberio
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK.
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13
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Liu J, Ma J, Wen J, Zhou X. A Cell Cycle-Aware Network for Data Integration and Label Transferring of Single-Cell RNA-Seq and ATAC-Seq. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401815. [PMID: 38887194 DOI: 10.1002/advs.202401815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/22/2024] [Indexed: 06/20/2024]
Abstract
In recent years, the integration of single-cell multi-omics data has provided a more comprehensive understanding of cell functions and internal regulatory mechanisms from a non-single omics perspective, but it still suffers many challenges, such as omics-variance, sparsity, cell heterogeneity, and confounding factors. As it is known, the cell cycle is regarded as a confounder when analyzing other factors in single-cell RNA-seq data, but it is not clear how it will work on the integrated single-cell multi-omics data. Here, a cell cycle-aware network (CCAN) is developed to remove cell cycle effects from the integrated single-cell multi-omics data while keeping the cell type-specific variations. This is the first computational model to study the cell-cycle effects in the integration of single-cell multi-omics data. Validations on several benchmark datasets show the outstanding performance of CCAN in a variety of downstream analyses and applications, including removing cell cycle effects and batch effects of scRNA-seq datasets from different protocols, integrating paired and unpaired scRNA-seq and scATAC-seq data, accurately transferring cell type labels from scRNA-seq to scATAC-seq data, and characterizing the differentiation process from hematopoietic stem cells to different lineages in the integration of differentiation data.
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Affiliation(s)
- Jiajia Liu
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Jian Ma
- Department of Electronic Information and Computer Engineering, The Engineering & Technical College of Chengdu University of Technology, Leshan, Sichuan, 614000, China
| | - Jianguo Wen
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
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14
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Xue Y, Friedl V, Ding H, Wong CK, Stuart JM. Single-cell signatures identify microenvironment factors in tumors associated with patient outcomes. CELL REPORTS METHODS 2024; 4:100799. [PMID: 38889686 DOI: 10.1016/j.crmeth.2024.100799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 04/30/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024]
Abstract
The cellular components of tumors and their microenvironment play pivotal roles in tumor progression, patient survival, and the response to cancer treatments. Unveiling a comprehensive cellular profile within bulk tumors via single-cell RNA sequencing (scRNA-seq) data is crucial, as it unveils intrinsic tumor cellular traits that elude identification through conventional cancer subtyping methods. Our contribution, scBeacon, is a tool that derives cell-type signatures by integrating and clustering multiple scRNA-seq datasets to extract signatures for deconvolving unrelated tumor datasets on bulk samples. Through the employment of scBeacon on the The Cancer Genome Atlas (TCGA) cohort, we find cellular and molecular attributes within specific tumor categories, many with patient outcome relevance. We developed a tumor cell-type map to visually depict the relationships among TCGA samples based on the cell-type inferences.
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Affiliation(s)
- Yuanqing Xue
- UC Santa Cruz Department, Biomolecular Engineering, Genomics Institute, Santa Cruz, CA, USA
| | - Verena Friedl
- UC Santa Cruz Department, Biomolecular Engineering, Genomics Institute, Santa Cruz, CA, USA
| | - Hongxu Ding
- UC Santa Cruz Department, Biomolecular Engineering, Genomics Institute, Santa Cruz, CA, USA
| | - Christopher K Wong
- UC Santa Cruz Department, Biomolecular Engineering, Genomics Institute, Santa Cruz, CA, USA
| | - Joshua M Stuart
- UC Santa Cruz Department, Biomolecular Engineering, Genomics Institute, Santa Cruz, CA, USA.
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15
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Bolondi A, Law BK, Kretzmer H, Gassaloglu SI, Buschow R, Riemenschneider C, Yang D, Walther M, Veenvliet JV, Meissner A, Smith ZD, Chan MM. Reconstructing axial progenitor field dynamics in mouse stem cell-derived embryoids. Dev Cell 2024; 59:1489-1505.e14. [PMID: 38579718 PMCID: PMC11187653 DOI: 10.1016/j.devcel.2024.03.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/13/2023] [Accepted: 03/12/2024] [Indexed: 04/07/2024]
Abstract
Embryogenesis requires substantial coordination to translate genetic programs to the collective behavior of differentiating cells, but understanding how cellular decisions control tissue morphology remains conceptually and technically challenging. Here, we combine continuous Cas9-based molecular recording with a mouse embryonic stem cell-based model of the embryonic trunk to build single-cell phylogenies that describe the behavior of transient, multipotent neuro-mesodermal progenitors (NMPs) as they commit into neural and somitic cell types. We find that NMPs show subtle transcriptional signatures related to their recent differentiation and contribute to downstream lineages through a surprisingly broad distribution of individual fate outcomes. Although decision-making can be heavily influenced by environmental cues to induce morphological phenotypes, axial progenitors intrinsically mature over developmental time to favor the neural lineage. Using these data, we present an experimental and analytical framework for exploring the non-homeostatic dynamics of transient progenitor populations as they shape complex tissues during critical developmental windows.
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Affiliation(s)
- Adriano Bolondi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Benjamin K Law
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Seher Ipek Gassaloglu
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - René Buschow
- Microscopy Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | | | - Dian Yang
- Department of Molecular Pharmacology and Therapeutics & Systems Biology, Columbia University, New York, NY 10032, USA
| | - Maria Walther
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Jesse V Veenvliet
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, Technische Universität Dresden, 01307 Dresden, Germany; Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany.
| | - Zachary D Smith
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06519, USA.
| | - Michelle M Chan
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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16
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Mandrycky C, Ishida T, Rayner SG, Heck AM, Hadland B, Zheng Y. Under pressure: integrated endothelial cell response to hydrostatic and shear stresses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596749. [PMID: 38854073 PMCID: PMC11160699 DOI: 10.1101/2024.05.30.596749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Blood flow within the vasculature is a critical determinant of endothelial cell (EC) identity and functionality, yet the intricate interplay of various hemodynamic forces and their collective impact on endothelial and vascular responses are not fully understood. Specifically, the role of hydrostatic pressure in the EC flow response is understudied, despite its known significance in vascular development and disease. To address this gap, we developed in vitro models to investigate how pressure influences EC responses to flow. Our study demonstrates that elevated pressure conditions significantly modify shear-induced flow alignment and increase endothelial cell density. Bulk and single-cell RNA sequencing analyses revealed that, while shear stress remains the primary driver of flow-induced transcriptional changes, pressure modulates shear-induced signaling in a dose-dependent manner. These pressure-responsive transcriptional signatures identified in human ECs were conserved during the onset of circulation in early mouse embryonic vascular development, where pressure was notably associated with transcriptional programs essential to arterial and hemogenic EC fates. Our findings suggest that pressure plays a synergistic role with shear stress on ECs and emphasizes the need for an integrative approach to endothelial cell mechanotransduction, one that encompasses the effects induced by pressure alongside other hemodynamic forces.
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17
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Cameron D, Vinh NN, Prapaiwongs P, Perry EA, Walters JTR, Li M, O'Donovan MC, Bray NJ. Genetic Implication of Prenatal GABAergic and Cholinergic Neuron Development in Susceptibility to Schizophrenia. Schizophr Bull 2024:sbae083. [PMID: 38869145 DOI: 10.1093/schbul/sbae083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
BACKGROUND The ganglionic eminences (GE) are fetal-specific structures that give rise to gamma-aminobutyric acid (GABA)- and acetylcholine-releasing neurons of the forebrain. Given the evidence for GABAergic, cholinergic, and neurodevelopmental disturbances in schizophrenia, we tested the potential involvement of GE neuron development in mediating genetic risk for the condition. STUDY DESIGN We combined data from a recent large-scale genome-wide association study of schizophrenia with single-cell RNA sequencing data from the human GE to test the enrichment of schizophrenia risk variation in genes with high expression specificity for developing GE cell populations. We additionally performed the single nuclei Assay for Transposase-Accessible Chromatin with Sequencing (snATAC-Seq) to map potential regulatory genomic regions operating in individual cell populations of the human GE, using these to test for enrichment of schizophrenia common genetic variant liability and to functionally annotate non-coding variants-associated with the disorder. STUDY RESULTS Schizophrenia common variant liability was enriched in genes with high expression specificity for developing neuron populations that are predicted to form dopamine D1 and D2 receptor-expressing GABAergic medium spiny neurons of the striatum, cortical somatostatin-positive GABAergic interneurons, calretinin-positive GABAergic neurons, and cholinergic neurons. Consistent with these findings, schizophrenia genetic risk was concentrated in predicted regulatory genomic sequence mapped in developing neuronal populations of the GE. CONCLUSIONS Our study implicates prenatal development of specific populations of GABAergic and cholinergic neurons in later susceptibility to schizophrenia, and provides a map of predicted regulatory genomic elements operating in cells of the GE.
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Affiliation(s)
- Darren Cameron
- Division of Psychological Medicine and Clinical Neurosciences, Centre for Neuropsychiatric Genetics & Genomics, Cardiff University, Cardiff, UK
| | - Ngoc-Nga Vinh
- Division of Psychological Medicine and Clinical Neurosciences, Centre for Neuropsychiatric Genetics & Genomics, Cardiff University, Cardiff, UK
| | - Parinda Prapaiwongs
- Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, UK
| | - Elizabeth A Perry
- Division of Psychological Medicine and Clinical Neurosciences, Centre for Neuropsychiatric Genetics & Genomics, Cardiff University, Cardiff, UK
| | - James T R Walters
- Division of Psychological Medicine and Clinical Neurosciences, Centre for Neuropsychiatric Genetics & Genomics, Cardiff University, Cardiff, UK
| | - Meng Li
- Division of Psychological Medicine and Clinical Neurosciences, Centre for Neuropsychiatric Genetics & Genomics, Cardiff University, Cardiff, UK
- Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, UK
| | - Michael C O'Donovan
- Division of Psychological Medicine and Clinical Neurosciences, Centre for Neuropsychiatric Genetics & Genomics, Cardiff University, Cardiff, UK
| | - Nicholas J Bray
- Division of Psychological Medicine and Clinical Neurosciences, Centre for Neuropsychiatric Genetics & Genomics, Cardiff University, Cardiff, UK
- Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, UK
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18
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Cheng J, Xiao M, Meng Q, Zhang M, Zhang D, Liu L, Jin Q, Fu Z, Li Y, Chen X, Xie H. Decoding temporal heterogeneity in NSCLC through machine learning and prognostic model construction. World J Surg Oncol 2024; 22:156. [PMID: 38872167 PMCID: PMC11170806 DOI: 10.1186/s12957-024-03435-0] [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: 03/11/2024] [Accepted: 06/01/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) is a prevalent and heterogeneous disease with significant genomic variations between the early and advanced stages. The identification of key genes and pathways driving NSCLC tumor progression is critical for improving the diagnosis and treatment outcomes of this disease. METHODS In this study, we conducted single-cell transcriptome analysis on 93,406 cells from 22 NSCLC patients to characterize malignant NSCLC cancer cells. Utilizing cNMF, we classified these cells into distinct modules, thus identifying the diverse molecular profiles within NSCLC. Through pseudotime analysis, we delineated temporal gene expression changes during NSCLC evolution, thus demonstrating genes associated with disease progression. Using the XGBoost model, we assessed the significance of these genes in the pseudotime trajectory. Our findings were validated by using transcriptome sequencing data from The Cancer Genome Atlas (TCGA), supplemented via LASSO regression to refine the selection of characteristic genes. Subsequently, we established a risk score model based on these genes, thus providing a potential tool for cancer risk assessment and personalized treatment strategies. RESULTS We used cNMF to classify malignant NSCLC cells into three functional modules, including the metabolic reprogramming module, cell cycle module, and cell stemness module, which can be used for the functional classification of malignant tumor cells in NSCLC. These findings also indicate that metabolism, the cell cycle, and tumor stemness play important driving roles in the malignant evolution of NSCLC. We integrated cNMF and XGBoost to select marker genes that are indicative of both early and advanced NSCLC stages. The expression of genes such as CHCHD2, GAPDH, and CD24 was strongly correlated with the malignant evolution of NSCLC at the single-cell data level. These genes have been validated via histological data. The risk score model that we established (represented by eight genes) was ultimately validated with GEO data. CONCLUSION In summary, our study contributes to the identification of temporal heterogeneous biomarkers in NSCLC, thus offering insights into disease progression mechanisms and potential therapeutic targets. The developed workflow demonstrates promise for future applications in clinical practice.
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Affiliation(s)
- Junpeng Cheng
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China
| | - Meizhu Xiao
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China
| | - Qingkang Meng
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China
| | - Min Zhang
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China
| | - Denan Zhang
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China
| | - Lei Liu
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China
| | - Qing Jin
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China
| | - Zhijin Fu
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China
| | - Yanjiao Li
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China
| | - Xiujie Chen
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China.
| | - Hongbo Xie
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China.
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19
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Weiler P, Lange M, Klein M, Pe'er D, Theis F. CellRank 2: unified fate mapping in multiview single-cell data. Nat Methods 2024:10.1038/s41592-024-02303-9. [PMID: 38871986 DOI: 10.1038/s41592-024-02303-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 05/09/2024] [Indexed: 06/15/2024]
Abstract
Single-cell RNA sequencing allows us to model cellular state dynamics and fate decisions using expression similarity or RNA velocity to reconstruct state-change trajectories; however, trajectory inference does not incorporate valuable time point information or utilize additional modalities, whereas methods that address these different data views cannot be combined or do not scale. Here we present CellRank 2, a versatile and scalable framework to study cellular fate using multiview single-cell data of up to millions of cells in a unified fashion. CellRank 2 consistently recovers terminal states and fate probabilities across data modalities in human hematopoiesis and endodermal development. Our framework also allows combining transitions within and across experimental time points, a feature we use to recover genes promoting medullary thymic epithelial cell formation during pharyngeal endoderm development. Moreover, we enable estimating cell-specific transcription and degradation rates from metabolic-labeling data, which we apply to an intestinal organoid system to delineate differentiation trajectories and pinpoint regulatory strategies.
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Affiliation(s)
- Philipp Weiler
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
| | - Marius Lange
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Michal Klein
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Machine Learning Research, Apple, Paris, France
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Fabian Theis
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany.
- School of Computation, Information and Technology, Technical University of Munich, Munich, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
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20
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Wang HLV, Xiang JF, Yuan C, Veire AM, Gendron TF, Murray ME, Tansey MG, Hu J, Gearing M, Glass JD, Jin P, Corces VG, McEachin ZT. pTDP-43 levels correlate with cell type specific molecular alterations in the prefrontal cortex of C9orf72 ALS/FTD patients. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.12.523820. [PMID: 36711601 PMCID: PMC9882184 DOI: 10.1101/2023.01.12.523820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Repeat expansions in the C9orf72 gene are the most common genetic cause of amyotrophic lateral sclerosis and familial frontotemporal dementia (ALS/FTD). To identify molecular defects that take place in the dorsolateral frontal cortex of patients with C9orf72 ALS/FTD, we compared healthy controls with C9orf72 ALS/FTD donor samples staged based on the levels of cortical phosphorylated TAR DNA binding protein (pTDP-43), a neuropathological hallmark of disease progression. We identified distinct molecular changes in different cell types that take place during FTD development. Loss of neurosurveillance microglia and activation of the complement cascade take place early, when pTDP-43 aggregates are absent or very low, and become more pronounced in late stages, suggesting an initial involvement of microglia in disease progression. Reduction of layer 2-3 cortical projection neurons with high expression of CUX2/LAMP5 also occurs early, and the reduction becomes more pronounced as pTDP-43 accumulates. Several unique features were observed only in samples with high levels of pTDP-43, including global alteration of chromatin accessibility in oligodendrocytes, microglia, and astrocytes; higher ratios of premature oligodendrocytes; increased levels of the noncoding RNA NEAT1 in astrocytes and neurons, and higher amount of phosphorylated ribosomal protein S6. Our findings reveal previously unknown progressive functional changes in major cell types found in the frontal cortex of C9orf72 ALS/FTD patients that shed light on the mechanisms underlying the pathology of this disease.
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21
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Gonzalez-Ferrer J, Lehrer J, O'Farrell A, Paten B, Teodorescu M, Haussler D, Jonsson VD, Mostajo-Radji MA. SIMS: A deep-learning label transfer tool for single-cell RNA sequencing analysis. CELL GENOMICS 2024; 4:100581. [PMID: 38823397 DOI: 10.1016/j.xgen.2024.100581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 04/02/2024] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
Abstract
Cell atlases serve as vital references for automating cell labeling in new samples, yet existing classification algorithms struggle with accuracy. Here we introduce SIMS (scalable, interpretable machine learning for single cell), a low-code data-efficient pipeline for single-cell RNA classification. We benchmark SIMS against datasets from different tissues and species. We demonstrate SIMS's efficacy in classifying cells in the brain, achieving high accuracy even with small training sets (<3,500 cells) and across different samples. SIMS accurately predicts neuronal subtypes in the developing brain, shedding light on genetic changes during neuronal differentiation and postmitotic fate refinement. Finally, we apply SIMS to single-cell RNA datasets of cortical organoids to predict cell identities and uncover genetic variations between cell lines. SIMS identifies cell-line differences and misannotated cell lineages in human cortical organoids derived from different pluripotent stem cell lines. Altogether, we show that SIMS is a versatile and robust tool for cell-type classification from single-cell datasets.
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Affiliation(s)
- Jesus Gonzalez-Ferrer
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Live Cell Biotechnology Discovery Lab, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Julian Lehrer
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Live Cell Biotechnology Discovery Lab, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Applied Mathematics, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Ash O'Farrell
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Benedict Paten
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Mircea Teodorescu
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Electrical and Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - David Haussler
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Vanessa D Jonsson
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Applied Mathematics, University of California, Santa Cruz, Santa Cruz, CA 95060, USA.
| | - Mohammed A Mostajo-Radji
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Live Cell Biotechnology Discovery Lab, University of California, Santa Cruz, Santa Cruz, CA 95060, USA.
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22
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Ferreté-Bonastre AG, Martínez-Gallo M, Morante-Palacios O, Calvillo CL, Calafell-Segura J, Rodríguez-Ubreva J, Esteller M, Cortés-Hernández J, Ballestar E. Disease activity drives divergent epigenetic and transcriptomic reprogramming of monocyte subpopulations in systemic lupus erythematosus. Ann Rheum Dis 2024; 83:865-878. [PMID: 38413168 DOI: 10.1136/ard-2023-225433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024]
Abstract
OBJECTIVES Systemic lupus erythematosus (SLE) is characterised by systemic inflammation involving various immune cell types. Monocytes, pivotal in promoting and regulating inflammation in SLE, differentiate from classic monocytes into intermediate and non-classic monocytes, assuming diverse roles and changing their proportions in inflammation. In this study, we investigated the epigenetic and transcriptomic profiles of these and novel monocyte subsets in SLE in relation to activity and progression. METHODS We obtained the DNA methylomes and transcriptomes of classic, intermediate, non-classic monocytes in patients with SLE (at first and follow-up visits) and healthy donors. We integrated these data with single-cell transcriptomics of SLE and healthy donors and interrogated their relationships with activity and progression. RESULTS In addition to shared DNA methylation and transcriptomic alterations associated with a strong interferon signature, we identified monocyte subset-specific alterations, especially in DNA methylation, which reflect an impact of SLE on monocyte differentiation. SLE classic monocytes exhibited a proinflammatory profile and were primed for macrophage differentiation. SLE non-classic monocytes displayed a T cell differentiation-related phenotype, with Th17-regulating features. Changes in monocyte proportions, DNA methylation and expression occurred in relation to disease activity and involved the STAT pathway. Integration of bulk with single-cell RNA sequencing datasets revealed disease activity-dependent expansion of SLE-specific monocyte subsets, further supported the interferon signature for classic monocytes, and associated intermediate and non-classic populations with exacerbated complement activation. CONCLUSIONS Disease activity in SLE drives a subversion of the epigenome and transcriptome programme in monocyte differentiation, impacting the function of different subsets and allowing to generate predictive methods for activity and progression.
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Affiliation(s)
| | - Mónica Martínez-Gallo
- Immunology Division, Vall d'Hebron University Hospital and Diagnostic Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | | | - Celia Lourdes Calvillo
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Josep Calafell-Segura
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
- Centro de Investigación Biomédica en Red Cancer (CIBERONC), Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
| | - Josefina Cortés-Hernández
- Rheumatology Department, Hospital Vall d'Hebron and Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
- Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai, China
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23
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Shi Y, Yu Y, Li J, Sun S, Han L, Wang S, Guo K, Yang J, Qiu J, Wei W. Spatiotemporal cell landscape of human embryonic tooth development. Cell Prolif 2024:e13653. [PMID: 38867378 DOI: 10.1111/cpr.13653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 03/27/2024] [Accepted: 04/28/2024] [Indexed: 06/14/2024] Open
Abstract
Understanding the cellular composition and trajectory of human tooth development is valuable for dentistry and stem cell engineering research. Previous single-cell studies have focused on mature human teeth and developing mouse teeth, but the cell landscape of human embryonic dental development is still unknown. In this study, tooth germ tissues were collected from aborted foetus (17-24 weeks) for single-cell RNA sequence and spatial transcriptome analysis. The cells were classified into seven subclusters of epithelium, and seven clusters of mesenchyme, as well as other cell types such as Schwann cell precursor and pericyte. For epithelium, the stratum intermedium branch and the ameloblast branch diverged from the same set of outer enamel-inner enamel-ALCAM+ epithelial cell lineage, but their spatial distribution of two branches was not clearly distinct. This trajectory received spatially adjacent regulation signals from mesenchyme and pericyte, including JAG1 and APP. The differentiation of pulp cell and pre-odontoblast showed four waves of temporally distinct gene expression, which involved regulation networks of LHX9, DLX5 and SP7, and these genes were regulated by upstream ligands such as the BMP family. This provides a reference landscape for the research on early human tooth development, covering different spatial structures and developmental periods.
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Affiliation(s)
- Yueqi Shi
- Department of Stomatology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yejia Yu
- State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jutang Li
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shoufu Sun
- Department of Stomatology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Han
- Department of Obstetrics and Gynecology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shaoyi Wang
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ke Guo
- Department of Stomatology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingang Yang
- Department of Stomatology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jin Qiu
- Department of Obstetrics and Gynecology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenjia Wei
- Department of Stomatology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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24
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Barclay KM, Abduljawad N, Cheng Z, Kim MW, Zhou L, Yang J, Rustenhoven J, Mazzitelli JA, Smyth LCD, Kapadia D, Brioschi S, Beatty W, Hou J, Saligrama N, Colonna M, Yu G, Kipnis J, Li Q. An inducible genetic tool to track and manipulate specific microglial states reveals their plasticity and roles in remyelination. Immunity 2024; 57:1394-1412.e8. [PMID: 38821054 DOI: 10.1016/j.immuni.2024.05.005] [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: 08/18/2023] [Revised: 02/14/2024] [Accepted: 05/07/2024] [Indexed: 06/02/2024]
Abstract
Recent single-cell RNA sequencing studies have revealed distinct microglial states in development and disease. These include proliferative-region-associated microglia (PAMs) in developing white matter and disease-associated microglia (DAMs) prevalent in various neurodegenerative conditions. PAMs and DAMs share a similar core gene signature. However, the extent of the dynamism and plasticity of these microglial states, as well as their functional significance, remains elusive, partly due to the lack of specific tools. Here, we generated an inducible Cre driver line, Clec7a-CreERT2, that targets PAMs and DAMs in the brain parenchyma. Utilizing this tool, we profiled labeled cells during development and in several disease models, uncovering convergence and context-dependent differences in PAM and DAM gene expression. Through long-term tracking, we demonstrated microglial state plasticity. Lastly, we specifically depleted DAMs in demyelination, revealing their roles in disease recovery. Together, we provide a versatile genetic tool to characterize microglial states in CNS development and disease.
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Affiliation(s)
- Kia M Barclay
- Department of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Neuroscience Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nora Abduljawad
- Department of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Neuroscience Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Zuolin Cheng
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Min Woo Kim
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Immunology Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA; Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lu Zhou
- Department of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jin Yang
- Department of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Justin Rustenhoven
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Jose A Mazzitelli
- Neuroscience Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Leon C D Smyth
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Dvita Kapadia
- Department of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Simone Brioschi
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Wandy Beatty
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - JinChao Hou
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Naresha Saligrama
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Department of Neurology, Washington University School of Medicine in St. Louis, School of Medicine, St. Louis, MO 63110, USA; Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine in St. Louis, St. Louis, MO 63112, USA
| | - Marco Colonna
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Guoqiang Yu
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Jonathan Kipnis
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Qingyun Li
- Department of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, School of Medicine, St. Louis, MO 63110, USA.
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25
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Rahimi A, Vale-Silva LA, Fälth Savitski M, Tanevski J, Saez-Rodriguez J. DOT: a flexible multi-objective optimization framework for transferring features across single-cell and spatial omics. Nat Commun 2024; 15:4994. [PMID: 38862466 PMCID: PMC11167014 DOI: 10.1038/s41467-024-48868-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 05/14/2024] [Indexed: 06/13/2024] Open
Abstract
Single-cell transcriptomics and spatially-resolved imaging/sequencing technologies have revolutionized biomedical research. However, they suffer from lack of spatial information and a trade-off of resolution and gene coverage, respectively. We propose DOT, a multi-objective optimization framework for transferring cellular features across these data modalities, thus integrating their complementary information. DOT uses genes beyond those common to the data modalities, exploits the local spatial context, transfers spatial features beyond cell-type information, and infers absolute/relative abundance of cell populations at tissue locations. Thus, DOT bridges single-cell transcriptomics data with both high- and low-resolution spatially-resolved data. Moreover, DOT combines practical aspects related to cell composition, heterogeneity, technical effects, and integration of prior knowledge. Our fast implementation based on the Frank-Wolfe algorithm achieves state-of-the-art or improved performance in localizing cell features in high- and low-resolution spatial data and estimating the expression of unmeasured genes in low-coverage spatial data.
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Affiliation(s)
- Arezou Rahimi
- Institute for Computational Biomedicine, Heidelberg University & Heidelberg University Hospital, Heidelberg, Germany
- Cellzome GmbH, GlaxoSmithKline, Heidelberg, Germany
| | | | | | - Jovan Tanevski
- Institute for Computational Biomedicine, Heidelberg University & Heidelberg University Hospital, Heidelberg, Germany.
- Department of Knowledge Technologies, Jožef Stefan Institute, Ljubljana, Slovenia.
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Heidelberg University & Heidelberg University Hospital, Heidelberg, Germany.
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26
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Tan Z, Chen P, Dong X, Guo S, Leung VYL, Cheung JPY, Chan D, Richardson SM, Hoyland JA, To MKT, Cheah KSE. Progenitor-like cells contributing to cellular heterogeneity in the nucleus pulposus are lost in intervertebral disc degeneration. Cell Rep 2024; 43:114342. [PMID: 38865240 DOI: 10.1016/j.celrep.2024.114342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/14/2024] [Accepted: 05/23/2024] [Indexed: 06/14/2024] Open
Abstract
The nucleus pulposus (NP) in the intervertebral disc (IVD) arises from embryonic notochord. Loss of notochordal-like cells in humans correlates with onset of IVD degeneration, suggesting that they are critical for healthy NP homeostasis and function. Comparative transcriptomic analyses identified expression of progenitor-associated genes (GREM1, KRT18, and TAGLN) in the young mouse and non-degenerated human NP, with TAGLN expression reducing with aging. Lineage tracing using Tagln-CreERt2 mice identified peripherally located proliferative NP (PeriNP) cells in developing and postnatal NP that provide a continuous supply of cells to the entire NP. PeriNP cells were diminished in aged mice and absent in puncture-induced degenerated discs. Single-cell transcriptomes of postnatal Tagln-CreERt2 IVD cells indicate enrichment for TGF-β signaling in Tagln descendant NP sub-populations. Notochord-specific removal of TGF-β/BMP mediator Smad4 results in loss of Tagln+ cells and abnormal NP morphologies. We propose Tagln+ PeriNP cells are potential progenitors crucial for NP homeostasis.
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Affiliation(s)
- Zhijia Tan
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Department of Orthopaedics and Traumatology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China; Shenzhen Clinical Research Center for Rare Diseases, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China; Department of Orthopaedics and Traumatology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Peikai Chen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Department of Orthopaedics and Traumatology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China; Shenzhen Clinical Research Center for Rare Diseases, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China; Artificial Intelligence and Big Data Lab, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Xiaonan Dong
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Shuang Guo
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Victor Y L Leung
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jason P Y Cheung
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Danny Chan
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Stephen M Richardson
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Judith A Hoyland
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Michael K T To
- Department of Orthopaedics and Traumatology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China; Shenzhen Clinical Research Center for Rare Diseases, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China; Department of Orthopaedics and Traumatology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kathryn S E Cheah
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
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27
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Canzar S, Do VH, Jelić S, Laue S, Matijević D, Prusina T. Metric multidimensional scaling for large single-cell datasets using neural networks. Algorithms Mol Biol 2024; 19:21. [PMID: 38863064 PMCID: PMC11165904 DOI: 10.1186/s13015-024-00265-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 05/22/2024] [Indexed: 06/13/2024] Open
Abstract
Metric multidimensional scaling is one of the classical methods for embedding data into low-dimensional Euclidean space. It creates the low-dimensional embedding by approximately preserving the pairwise distances between the input points. However, current state-of-the-art approaches only scale to a few thousand data points. For larger data sets such as those occurring in single-cell RNA sequencing experiments, the running time becomes prohibitively large and thus alternative methods such as PCA are widely used instead. Here, we propose a simple neural network-based approach for solving the metric multidimensional scaling problem that is orders of magnitude faster than previous state-of-the-art approaches, and hence scales to data sets with up to a few million cells. At the same time, it provides a non-linear mapping between high- and low-dimensional space that can place previously unseen cells in the same embedding.
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Affiliation(s)
- Stefan Canzar
- Faculty of Informatics and Data Science, University of Regensburg, Regensburg, Germany.
| | - Van Hoan Do
- Center for Applied Mathematics and Informatics, Le Quy Don Technical University, Hanoi, Vietnam
| | - Slobodan Jelić
- School of Applied Mathematics and Informatics, University of Osijek, Osijek, Croatia
| | - Sören Laue
- Department of Informatics, Universität Hamburg, Hamburg, Germany
| | - Domagoj Matijević
- School of Applied Mathematics and Informatics, University of Osijek, Osijek, Croatia
| | - Tomislav Prusina
- Department of Informatics, Universität Hamburg, Hamburg, Germany
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28
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Hoedjes KM, Grath S, Posnien N, Ritchie MG, Schlötterer C, Abbott JK, Almudi I, Coronado-Zamora M, Durmaz Mitchell E, Flatt T, Fricke C, Glaser-Schmitt A, González J, Holman L, Kankare M, Lenhart B, Orengo DJ, Snook RR, Yılmaz VM, Yusuf L. From whole bodies to single cells: A guide to transcriptomic approaches for ecology and evolutionary biology. Mol Ecol 2024:e17382. [PMID: 38856653 DOI: 10.1111/mec.17382] [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: 12/07/2023] [Revised: 04/09/2024] [Accepted: 04/29/2024] [Indexed: 06/11/2024]
Abstract
RNA sequencing (RNAseq) methodology has experienced a burst of technological developments in the last decade, which has opened up opportunities for studying the mechanisms of adaptation to environmental factors at both the organismal and cellular level. Selecting the most suitable experimental approach for specific research questions and model systems can, however, be a challenge and researchers in ecology and evolution are commonly faced with the choice of whether to study gene expression variation in whole bodies, specific tissues, and/or single cells. A wide range of sometimes polarised opinions exists over which approach is best. Here, we highlight the advantages and disadvantages of each of these approaches to provide a guide to help researchers make informed decisions and maximise the power of their study. Using illustrative examples of various ecological and evolutionary research questions, we guide the readers through the different RNAseq approaches and help them identify the most suitable design for their own projects.
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Affiliation(s)
- Katja M Hoedjes
- Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sonja Grath
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Nico Posnien
- Department of Developmental Biology, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | - Michael G Ritchie
- Centre for Biological Diversity, University of St Andrews, St Andrews, UK
| | | | | | - Isabel Almudi
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | | | - Esra Durmaz Mitchell
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Claudia Fricke
- Institute for Zoology/Animal Ecology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | | | - Josefa González
- Institute of Evolutionary Biology, CSIC, UPF, Barcelona, Spain
| | - Luke Holman
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, UK
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Benedict Lenhart
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Dorcas J Orengo
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Rhonda R Snook
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Vera M Yılmaz
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Leeban Yusuf
- Centre for Biological Diversity, University of St Andrews, St Andrews, UK
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29
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Lee CY, Clatworthy MR, Withers DR. Decoding changes in tumor-infiltrating leukocytes through dynamic experimental models and single-cell technologies. Immunol Cell Biol 2024. [PMID: 38853634 DOI: 10.1111/imcb.12787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 06/11/2024]
Abstract
The ability to characterize immune cells and explore the molecular interactions that govern their functions has never been greater, fueled in recent years by the revolutionary advance of single-cell analysis platforms. However, precisely how immune cells respond to different stimuli and where differentiation processes and effector functions operate remain incompletely understood. Inferring cellular fate within single-cell transcriptomic analyses is now omnipresent, despite the assumptions typically required in such analyses. Recently developed experimental models support dynamic analyses of the immune response, providing insights into the temporal changes that occur within cells and the tissues in which such transitions occur. Here we will review these approaches and discuss how these can be combined with single-cell technologies to develop a deeper understanding of the immune responses that should support the development of better therapeutic options for patients.
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Affiliation(s)
- Colin Yc Lee
- Cambridge Institute of Therapeutic Immunology and Infection Disease, University of Cambridge, Cambridge, UK
| | - Menna R Clatworthy
- Cambridge Institute of Therapeutic Immunology and Infection Disease, University of Cambridge, Cambridge, UK
| | - David R Withers
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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30
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Zhao Y, Kohl C, Rosebrock D, Hu Q, Hu Y, Vingron M. CAbiNet: joint clustering and visualization of cells and genes for single-cell transcriptomics. Nucleic Acids Res 2024:gkae480. [PMID: 38850160 DOI: 10.1093/nar/gkae480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 04/10/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024] Open
Abstract
A fundamental analysis task for single-cell transcriptomics data is clustering with subsequent visualization of cell clusters. The genes responsible for the clustering are only inferred in a subsequent step. Clustering cells and genes together would be the remit of biclustering algorithms, which are often bogged down by the size of single-cell data. Here we present 'Correspondence Analysis based Biclustering on Networks' (CAbiNet) for joint clustering and visualization of single-cell RNA-sequencing data. CAbiNet performs efficient co-clustering of cells and their respective marker genes and jointly visualizes the biclusters in a non-linear embedding for easy and interactive visual exploration of the data.
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Affiliation(s)
- Yan Zhao
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055, Guangdong, P.R. China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, P.R. China
| | - Clemens Kohl
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Daniel Rosebrock
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Qinan Hu
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055, Guangdong, P.R. China
- Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology,1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, P.R. China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, P.R. China
| | - Yuhui Hu
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055, Guangdong, P.R. China
- Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology,1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, P.R. China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, P.R. China
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
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31
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Park JH, Hothi P, de Lomana ALG, Pan M, Calder R, Turkarslan S, Wu WJ, Lee H, Patel AP, Cobbs C, Huang S, Baliga NS. Gene regulatory network topology governs resistance and treatment escape in glioma stem-like cells. SCIENCE ADVANCES 2024; 10:eadj7706. [PMID: 38848360 PMCID: PMC11160475 DOI: 10.1126/sciadv.adj7706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 05/03/2024] [Indexed: 06/09/2024]
Abstract
Poor prognosis and drug resistance in glioblastoma (GBM) can result from cellular heterogeneity and treatment-induced shifts in phenotypic states of tumor cells, including dedifferentiation into glioma stem-like cells (GSCs). This rare tumorigenic cell subpopulation resists temozolomide, undergoes proneural-to-mesenchymal transition (PMT) to evade therapy, and drives recurrence. Through inference of transcriptional regulatory networks (TRNs) of patient-derived GSCs (PD-GSCs) at single-cell resolution, we demonstrate how the topology of transcription factor interaction networks drives distinct trajectories of cell-state transitions in PD-GSCs resistant or susceptible to cytotoxic drug treatment. By experimentally testing predictions based on TRN simulations, we show that drug treatment drives surviving PD-GSCs along a trajectory of intermediate states, exposing vulnerability to potentiated killing by siRNA or a second drug targeting treatment-induced transcriptional programs governing nongenetic cell plasticity. Our findings demonstrate an approach to uncover TRN topology and use it to rationally predict combinatorial treatments that disrupt acquired resistance in GBM.
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Affiliation(s)
| | - Parvinder Hothi
- Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA, USA
| | | | - Min Pan
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | - Wei-Ju Wu
- Institute for Systems Biology, Seattle, WA, USA
| | - Hwahyung Lee
- Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA, USA
| | - Anoop P. Patel
- Department of Neurosurgery, Preston Robert Tisch Brain Tumor Center, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Charles Cobbs
- Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA, USA
| | - Sui Huang
- Institute for Systems Biology, Seattle, WA, USA
| | - Nitin S. Baliga
- Institute for Systems Biology, Seattle, WA, USA
- Departments of Microbiology, Biology, and Molecular Engineering Sciences, University of Washington, Seattle, WA, USA
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32
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Edman NI, Phal A, Redler RL, Schlichthaerle T, Srivatsan SR, Ehnes DD, Etemadi A, An SJ, Favor A, Li Z, Praetorius F, Gordon M, Vincent T, Marchiano S, Blakely L, Lin C, Yang W, Coventry B, Hicks DR, Cao L, Bethel N, Heine P, Murray A, Gerben S, Carter L, Miranda M, Negahdari B, Lee S, Trapnell C, Zheng Y, Murry CE, Schweppe DK, Freedman BS, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha G, Ruohola-Baker H, Baker D. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. Cell 2024:S0092-8674(24)00534-8. [PMID: 38861993 DOI: 10.1016/j.cell.2024.05.025] [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: 12/16/2022] [Revised: 02/14/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024]
Abstract
Many growth factors and cytokines signal by binding to the extracellular domains of their receptors and driving association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. To enable systematic exploration of how receptor valency and geometry affect signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using repeat protein building blocks that can be modularly extended. By incorporating a de novo-designed fibroblast growth factor receptor (FGFR)-binding module into these scaffolds, we generated a series of synthetic signaling ligands that exhibit potent valency- and geometry-dependent Ca2+ release and mitogen-activated protein kinase (MAPK) pathway activation. The high specificity of the designed agonists reveals distinct roles for two FGFR splice variants in driving arterial endothelium and perivascular cell fates during early vascular development. Our designed modular assemblies should be broadly useful for unraveling the complexities of signaling in key developmental transitions and for developing future therapeutic applications.
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Affiliation(s)
- Natasha I Edman
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Ashish Phal
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Rachel L Redler
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - Thomas Schlichthaerle
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Sanjay R Srivatsan
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Devon Duron Ehnes
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Ali Etemadi
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Seong J An
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Andrew Favor
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Zhe Li
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Florian Praetorius
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Max Gordon
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Thomas Vincent
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Silvia Marchiano
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Leslie Blakely
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Chuwei Lin
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Wei Yang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Brian Coventry
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Derrick R Hicks
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Longxing Cao
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Neville Bethel
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Piper Heine
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Analisa Murray
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Stacey Gerben
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Marcos Miranda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Babak Negahdari
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Sangwon Lee
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98109, USA
| | - Ying Zheng
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Cardiovascular Biology, University of Washington, Seattle WA 98109, USA
| | - Charles E Murry
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Cardiovascular Biology, University of Washington, Seattle WA 98109, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; Department of Medicine/Cardiology, University of Washington, Seattle WA 98195, USA
| | - Devin K Schweppe
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Benjamin S Freedman
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; Kidney Research Institute, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA; Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Joseph Schlessinger
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98109, USA
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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33
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Holt M, Lin J, Cicka M, Wong A, Epelman S, Lavine KJ. Dissecting and Visualizing the Functional Diversity of Cardiac Macrophages. Circ Res 2024; 134:1791-1807. [PMID: 38843293 DOI: 10.1161/circresaha.124.323817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 06/11/2024]
Abstract
Cardiac macrophages represent a functionally diverse population of cells involved in cardiac homeostasis, repair, and remodeling. With recent advancements in single-cell technologies, it is possible to elucidate specific macrophage subsets based on transcriptional signatures and cell surface protein expression to gain a deep understanding of macrophage diversity in the heart. The use of fate-mapping technologies and parabiosis studies have provided insight into the ontogeny and dynamics of macrophages identifying subsets derived from embryonic and adult definitive hematopoietic progenitors that include tissue-resident and bone marrow monocyte-derived macrophages, respectively. Within the heart, these subsets have distinct tissue niches and functional roles in the setting of homeostasis and disease, with cardiac resident macrophages representing a protective cell population while bone marrow monocyte-derived cardiac macrophages have a context-dependent effect, triggering both proinflammatory tissue injury, but also promoting reparative functions. With the increased understanding of the clinical relevance of cardiac macrophage subsets, there has been an increasing need to detect and measure cardiac macrophage compositions in living animals and patients. New molecular tracers compatible with positron emission tomography/computerized tomography and positron emission tomography/ magnetic resonance imaging have enabled investigators to noninvasively and serially visualize cardiac macrophage subsets within the heart to define associations with disease and measure treatment responses. Today, advancements within this thriving field are poised to fuel an era of clinical translation.
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Affiliation(s)
- Megan Holt
- Division of Cardiology, Department of Medicine, Center for Cardiovascular Research, Washington University School of Medicine (M.H., M.C., K.J.L.)
| | - Julia Lin
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada (J.L., A.W., S.E.)
- Department of Immunology, University of Toronto, ON, Canada (J.L., A.W., S.E.)
| | - Markus Cicka
- Division of Cardiology, Department of Medicine, Center for Cardiovascular Research, Washington University School of Medicine (M.H., M.C., K.J.L.)
| | - Anthony Wong
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada (J.L., A.W., S.E.)
- Department of Immunology, University of Toronto, ON, Canada (J.L., A.W., S.E.)
| | - Slava Epelman
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada (J.L., A.W., S.E.)
- Ted Rogers Centre for Heart Research, Translational Biology and Engineering Program, Toronto, ON, Canada (S.E.)
- Department of Immunology, University of Toronto, ON, Canada (J.L., A.W., S.E.)
- Peter Munk Cardiac Centre, University Health Network, Toronto, ON, Canada (S.E.)
| | - Kory J Lavine
- Division of Cardiology, Department of Medicine, Center for Cardiovascular Research, Washington University School of Medicine (M.H., M.C., K.J.L.)
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34
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Wang H, Du Y, Huang S, Sun X, Ye Y, Sun H, Chu X, Shan X, Yuan Y, Shen L, Bi Y. Single-cell analysis reveals a subpopulation of adipose progenitor cells that impairs glucose homeostasis. Nat Commun 2024; 15:4827. [PMID: 38844451 PMCID: PMC11156882 DOI: 10.1038/s41467-024-48914-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 05/10/2024] [Indexed: 06/09/2024] Open
Abstract
Adipose progenitor cells (APCs) are heterogeneous stromal cells and help to maintain metabolic homeostasis. However, the influence of obesity on human APC heterogeneity and the role of APC subpopulations on regulating glucose homeostasis remain unknown. Here, we find that APCs in human visceral adipose tissue contain four subsets. The composition and functionality of APCs are altered in patients with type 2 diabetes (T2D). CD9+CD55low APCs are the subset which is significantly increased in T2D patients. Transplantation of these cells from T2D patients into adipose tissue causes glycemic disturbance. Mechanistically, CD9+CD55low APCs promote T2D development through producing bioactive proteins to form a detrimental niche, leading to upregulation of adipocyte lipolysis. Depletion of pathogenic APCs by inducing intracellular diphtheria toxin A expression or using a hunter-killer peptide improves obesity-related glycemic disturbance. Collectively, our data provide deeper insights in human APC functionality and highlights APCs as a potential therapeutic target to combat T2D. All mice utilized in this study are male.
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Affiliation(s)
- Hongdong Wang
- Department of Endocrinology, Drum Tower Hospital Affiliated to Nanjing University Medical School, Branch of National Clinical Research Centre for Metabolic Diseases, Nanjing, China
| | - Yanhua Du
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shanshan Huang
- Department of Endocrinology, Drum Tower Hospital Affiliated to Nanjing University Medical School, Branch of National Clinical Research Centre for Metabolic Diseases, Nanjing, China
| | - Xitai Sun
- Department of General Surgery, Drum Tower Hospital Affiliated to Nanjing University Medical School, Nanjing, China
| | - Youqiong Ye
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haixiang Sun
- Department of Endocrinology, Drum Tower Hospital Affiliated to Nanjing University Medical School, Branch of National Clinical Research Centre for Metabolic Diseases, Nanjing, China
| | - Xuehui Chu
- Department of General Surgery, Drum Tower Hospital Affiliated to Nanjing University Medical School, Nanjing, China
| | - Xiaodong Shan
- Department of General Surgery, Drum Tower Hospital Affiliated to Nanjing University Medical School, Nanjing, China
| | - Yue Yuan
- Department of Endocrinology, Drum Tower Hospital Affiliated to Nanjing University Medical School, Branch of National Clinical Research Centre for Metabolic Diseases, Nanjing, China
| | - Lei Shen
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yan Bi
- Department of Endocrinology, Drum Tower Hospital Affiliated to Nanjing University Medical School, Branch of National Clinical Research Centre for Metabolic Diseases, Nanjing, China.
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Katznelson A, Hernandez B, Fahning H, Zhang J, Burton A, Torres-Padilla ME, Plachta N, Zaret KS, McCarthy RL. Heterochromatin protein ERH represses alternative cell fates during early mammalian differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597604. [PMID: 38895478 PMCID: PMC11185749 DOI: 10.1101/2024.06.06.597604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
During development, H3K9me3 heterochromatin is dynamically rearranged, silencing repeat elements and protein coding genes to restrict cell identity. Enhancer of Rudimentary Homolog (ERH) is an evolutionarily conserved protein originally characterized in fission yeast and recently shown to be required for H3K9me3 maintenance in human fibroblasts, but its function during development remains unknown. Here, we show that ERH is required for proper segregation of the inner cell mass and trophectoderm cell lineages during mouse development by repressing totipotent and alternative lineage programs. During human embryonic stem cell (hESC) differentiation into germ layer lineages, ERH is crucial for silencing naïve and pluripotency genes, transposable elements, and alternative lineage genes. Strikingly, ERH depletion in somatic cells reverts the H3K9me3 landscape to an hESC state and enables naïve and pluripotency gene and transposable element activation during iPSC reprogramming. Our findings reveal a role for ERH in initiation and maintenance of developmentally established gene repression.
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36
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Yao J, Chu Q, Guo X, Shao W, Shang N, Luo K, Li X, Chen H, Cheng Q, Mo F, Zheng D, Xu F, Guo F, Zhu QH, Deng S, Chu C, Xu X, Liu H, Fan L. Spatiotemporal transcriptomic landscape of rice embryonic cells during seed germination. Dev Cell 2024:S1534-5807(24)00334-4. [PMID: 38848718 DOI: 10.1016/j.devcel.2024.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 02/15/2024] [Accepted: 05/14/2024] [Indexed: 06/09/2024]
Abstract
Characterizing cellular features during seed germination is crucial for understanding the complex biological functions of different embryonic cells in regulating seed vigor and seedling establishment. We performed spatially enhanced resolution omics sequencing (Stereo-seq) and single-cell RNA sequencing (scRNA-seq) to capture spatially resolved single-cell transcriptomes of germinating rice embryos. An automated cell-segmentation model, employing deep learning, was developed to accommodate the analysis requirements. The spatial transcriptomes of 6, 24, 36, and 48 h after imbibition unveiled both known and previously unreported embryo cell types, including two unreported scutellum cell types, corroborated by in situ hybridization and functional exploration of marker genes. Temporal transcriptomic profiling delineated gene expression dynamics in distinct embryonic cell types during seed germination, highlighting key genes involved in nutrient metabolism, biosynthesis, and signaling of phytohormones, reprogrammed in a cell-type-specific manner. Our study provides a detailed spatiotemporal transcriptome of rice embryo and presents a previously undescribed methodology for exploring the roles of different embryonic cells in seed germination.
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Affiliation(s)
- Jie Yao
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Hainan Institute, Zhejiang University, Sanya 572025, China
| | - Qinjie Chu
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Xing Guo
- BGI Research, Shenzhen 518103, China; BGI Research, Wuhan 430074, China
| | - Wenwen Shao
- BGI Research, Shenzhen 518103, China; BGI Research, Wuhan 430074, China
| | - Nianmin Shang
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Kang Luo
- College of Computer Science and Technology & Polytechnic Institute, Zhejiang University, Hangzhou 310015, Zhejiang, China
| | - Xiaohan Li
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Hongyu Chen
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Qing Cheng
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Fangyu Mo
- Hainan Institute, Zhejiang University, Sanya 572025, China
| | - Dihuai Zheng
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Fan Xu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Fu Guo
- Hainan Institute, Zhejiang University, Sanya 572025, China
| | - Qian-Hao Zhu
- CSIRO, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Shuiguang Deng
- College of Computer Science and Technology & Polytechnic Institute, Zhejiang University, Hangzhou 310015, Zhejiang, China
| | - Chengcai Chu
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xun Xu
- BGI Research, Shenzhen 518103, China
| | - Huan Liu
- BGI Research, Shenzhen 518103, China.
| | - Longjiang Fan
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Hainan Institute, Zhejiang University, Sanya 572025, China.
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37
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Puviindran V, Shimada E, Huang Z, Ma X, Ban GI, Xiang Y, Zhang H, Ou J, Wei X, Nakagawa M, Martin J, Diao Y, Alman BA. Single-cell transcriptomic analyses of mouse idh1 mutant growth plate chondrocytes reveal distinct cell populations responsible for longitudinal growth and enchondroma formation. RESEARCH SQUARE 2024:rs.3.rs-4451086. [PMID: 38883785 PMCID: PMC11178001 DOI: 10.21203/rs.3.rs-4451086/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Enchondromas are a common tumor in bone that can occur as multiple lesions in enchondromatosis, which is associated with deformity of the effected bone. These lesions harbor mutations in IDH and driving expression of a mutant Idh1 in Col2 expressing cells in mice causes an enchondromatosis phenotype. In this study we compared growth plates from E18.5 mice expressing a mutant Idh1 with control littermates using single cell RNA sequencing. Data from Col2 expressing cells were analyzed using UMAP and RNA pseudo-time analyses. A unique cluster of cells was identified in the mutant growth plates that expressed genes known to be upregulated in enchondromas. There was also a cluster of cells that was underrepresented in the mutant growth plates that expressed genes known to be important in longitudinal bone growth. Immunofluorescence showed that the genes from the unique cluster identified in the mutant growth plates were expressed in multiple growth plate anatomic zones, and pseudo-time analysis also suggested these cells could arise from multiple growth plate chondrocyte subpopulations. This data identifies subpopulations of cells in control and mutant growth plates, and supports the notion that a mutant Idh1 alters the subpopulations of growth plate chondrocytes, resulting a subpopulation of cells that become enchondromas at the expense of other populations that contribute to longitudinal growth.
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Affiliation(s)
| | | | | | - Xinyi Ma
- Duke University School of Medicine
| | - Ga I Ban
- Duke University School of Medicine
| | - Yu Xiang
- Duke University School of Medicine
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Schmidt M, Hansmann F, Loeffler-Wirth H, Zouboulis CC, Binder H, Schneider MR. A spatial portrait of the human sebaceous gland transcriptional program. J Biol Chem 2024:107442. [PMID: 38838779 DOI: 10.1016/j.jbc.2024.107442] [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: 03/30/2024] [Revised: 05/09/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024] Open
Abstract
Sebaceous glands (SG) and their oily secretion (sebum) are indispensable for maintaining skin structure and function, and their deregulation causes skin disorders including but not limited to acne. Recent studies also indicate that sebum may have important immunomodulatory activities and may influence whole-body energy metabolism. However, the progressive transcriptional changes of sebocytes that lead to sebum production have never been characterized in detail. Here, we exploited the high cellular resolution provided by sebaceous hyperplasia and integrated spatial transcriptomics, pseudotime analysis, RNA velocity, and functional enrichment to map the landscape of sebaceous differentiation by employing spatial transcriptomics. Our results were validated by comparison with published SG transcriptome data and further corroborated by assessing the protein expression pattern of a subset of the transcripts in the public repository Human Protein Atlas. Departing from four sebocyte differentiation stages generated by unsupervised clustering, we demonstrate consecutive modulation of cellular functions associable with specific gene sets, from cell proliferation and oxidative phosphorylation via lipid synthesis to cell death. Both validation methods confirmed the biological significance of our results. Our report is complemented by a freely available and browsable online tool. Our data provide the first high-resolution spatial portrait of the SG transcriptional landscape and deliver starting points for experimentally assessing novel candidate molecules for regulating SG homeostasis in health and disease.
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Affiliation(s)
- Maria Schmidt
- Interdisciplinary Institute for Bioinformatics (IZBI), University of Leipzig, Germany
| | - Florian Hansmann
- Institute for Veterinary Pathology, Veterinary Faculty, University of Leipzig, Germany
| | - Henry Loeffler-Wirth
- Interdisciplinary Institute for Bioinformatics (IZBI), University of Leipzig, Germany
| | - Christos C Zouboulis
- Departments of Dermatology, Venereology, Allergology and Immunology, Staedtisches Klinikum Dessau, Brandenburg Medical School Theodor Fontane and Faculty of Health Sciences Brandenburg, Dessau, Germany
| | - Hans Binder
- Interdisciplinary Institute for Bioinformatics (IZBI), University of Leipzig, Germany
| | - Marlon R Schneider
- Institute of Veterinary Physiology, Veterinary Faculty, University of Leipzig, Germany.
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Cheng D, Qiu K, Li D, Mao M, Rao Y, Song Y, Feng L, Shao X, Jiang C, Wang Y, Li L, Chen X, Wu S, Wang H, Liu J, Yu H, Zhang W, Chen F, Zhao Y, Ren J. Molecular and transcriptional basis of bidirectional CD4 + T cell exhaustion in oropharyngeal squamous cell carcinoma. MedComm (Beijing) 2024; 5:e572. [PMID: 38868329 PMCID: PMC11167179 DOI: 10.1002/mco2.572] [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: 08/14/2023] [Revised: 03/05/2024] [Accepted: 03/24/2024] [Indexed: 06/14/2024] Open
Abstract
Tumor-infiltrating CD4+ T cells orchestrate the adaptive immune response through remarkable plasticity, and the expression patterns of exhaustion-related inhibitory receptors in these cells differ significantly from those of CD8+ T cells. Thus, a better understanding of the molecular basis of CD4+ T cell exhaustion and their responses to immune checkpoint blockade (ICB) is required. Here, we integrated multiomics approaches to define the phenotypic and molecular profiles of exhausted CD4+ T cells in oropharyngeal squamous cell carcinoma (OPSCC). Two distinct immune-promoting (Module 1) and immunosuppressive (Module 2) functional modules in tumor-infiltrating CD4+ T cells were identified, and both the immune-promoting function of Module 1 cells and immunosuppressive function of Module 2 cells were positively associated with their corresponding exhaustion states. Furthermore, the application of ICBs targeting effector CD4+ T cells in Module 1 (αPD-1) and Treg cells in Module 2 (αCTLA-4) in mouse models could help reinvigorate the effector function of Module 1-exhausted CD4+ T cells and reduce the immunosuppressive function of Module 2-exhausted CD4+ T cells, ultimately promoting OPSCC tumor regression. Taken together, our study provides a crucial cellular basis for the selection of optimal ICB in treating OPSCC.
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Affiliation(s)
- Danni Cheng
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Ke Qiu
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Daibo Li
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Minzi Mao
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Yufang Rao
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Yao Song
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Lan Feng
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Xiuli Shao
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Chuanhuan Jiang
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Yan Wang
- Research Core FacilityWest China HospitalSichuan UniversityChengduChina
| | - Li Li
- Institute of Clinical PathologyWest China HospitalSichuan UniversityChengduSichuanChina
| | - Xuemei Chen
- Research Core FacilityWest China HospitalSichuan UniversityChengduChina
| | - Sisi Wu
- Research Core FacilityWest China HospitalSichuan UniversityChengduChina
| | - Haiyang Wang
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Jun Liu
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Haopeng Yu
- West China Biomedical Big Data CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Wei Zhang
- West China Biomedical Big Data CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Fei Chen
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Yu Zhao
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
- West China Biomedical Big Data CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Jianjun Ren
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
- West China Biomedical Big Data CenterWest China HospitalSichuan UniversityChengduSichuanChina
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40
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Walzer KA, Tandel J, Byerly JH, Daniels AM, Gullicksrud JA, Whelan EC, Carro SD, Krespan E, Beiting DP, Striepen B. Transcriptional control of the Cryptosporidium life cycle. Nature 2024; 630:174-180. [PMID: 38811723 DOI: 10.1038/s41586-024-07466-1] [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: 06/07/2023] [Accepted: 04/25/2024] [Indexed: 05/31/2024]
Abstract
The parasite Cryptosporidium is a leading agent of diarrhoeal disease in young children, and a cause and consequence of chronic malnutrition1,2. There are no vaccines and only limited treatment options3. The parasite infects enterocytes, in which it engages in asexual and sexual replication4, both of which are essential to continued infection and transmission. However, their molecular mechanisms remain largely unclear5. Here we use single-cell RNA sequencing to reveal the gene expression programme of the entire Cryptosporidium parvum life cycle in culture and in infected animals. Diverging from the prevailing model6, we find support for only three intracellular stages: asexual type-I meronts, male gamonts and female gametes. We reveal a highly organized program for the assembly of components at each stage. Dissecting the underlying regulatory network, we identify the transcription factor Myb-M as the earliest determinant of male fate, in an organism that lacks genetic sex determination. Conditional expression of this factor overrides the developmental program and induces widespread maleness, while conditional deletion ablates male development. Both have a profound impact on the infection. A large set of stage-specific genes now provides the opportunity to understand, engineer and disrupt parasite sex and life cycle progression to advance the development of vaccines and treatments.
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Affiliation(s)
- Katelyn A Walzer
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jayesh Tandel
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jessica H Byerly
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Abigail M Daniels
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jodi A Gullicksrud
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eoin C Whelan
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stephen D Carro
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elise Krespan
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel P Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Boris Striepen
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Kim HS, Xiao Y, Chen X, He S, Im J, Willner MJ, Finlayson MO, Xu C, Zhu H, Choi SJ, Mosharov EV, Kim H, Xu B, Leong KW. Chronic Opioid Treatment Arrests Neurodevelopment and Alters Synaptic Activity in Human Midbrain Organoids. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400847. [PMID: 38549185 PMCID: PMC11151039 DOI: 10.1002/advs.202400847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Indexed: 06/06/2024]
Abstract
Understanding the impact of long-term opioid exposure on the embryonic brain is critical due to the surging number of pregnant mothers with opioid dependency. However, this has been limited by human brain inaccessibility and cross-species differences in animal models. Here, a human midbrain model is established that uses hiPSC-derived midbrain organoids to assess cell-type-specific responses to acute and chronic fentanyl treatment and fentanyl withdrawal. Single-cell mRNA sequencing of 25,510 cells from organoids in different treatment groups reveals that chronic fentanyl treatment arrests neuronal subtype specification during early midbrain development and alters synaptic activity and neuron projection. In contrast, acute fentanyl treatment increases dopamine release but does not significantly alter gene expression related to cell lineage development. These results provide the first examination of the effects of opioid exposure on human midbrain development at the single-cell level.
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Affiliation(s)
- Hye Sung Kim
- Department of Biomedical EngineeringColumbia UniversityNew YorkNY10027USA
- Institute of Tissue Regeneration Engineering (ITREN)Dankook UniversityCheonan31116Republic of Korea
- Mechanobiology Dental Medicine Research CenterDankook UniversityCheonan31116Republic of Korea
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative MedicineDankook UniversityCheonan31116Republic of Korea
| | - Yang Xiao
- Department of Biomedical EngineeringColumbia UniversityNew YorkNY10027USA
| | - Xuejing Chen
- Department of Biomedical EngineeringColumbia UniversityNew YorkNY10027USA
- Department of PhysicsTsinghua UniversityBeijing100084China
| | - Siyu He
- Department of Biomedical EngineeringColumbia UniversityNew YorkNY10027USA
| | - Jongwon Im
- Department of Biomedical EngineeringColumbia UniversityNew YorkNY10027USA
| | - Moshe J. Willner
- Department of Biomedical EngineeringColumbia UniversityNew YorkNY10027USA
| | - Michael O. Finlayson
- Single Cell Analysis CoreJP Sulzberger Columbia Genome CenterColumbia University Irving Medical CenterNew YorkNY10032USA
| | - Cong Xu
- Department of Biomedical EngineeringColumbia UniversityNew YorkNY10027USA
| | - Huixiang Zhu
- Department of PsychiatryColumbia University Medical CenterNew YorkNY10032USA
| | - Se Joon Choi
- Department of PsychiatryColumbia University Medical CenterNew YorkNY10032USA
- Division of Molecular TherapeuticsNew York State Psychiatric InstituteNew YorkNY10032USA
| | - Eugene V. Mosharov
- Department of PsychiatryColumbia University Medical CenterNew YorkNY10032USA
- Division of Molecular TherapeuticsNew York State Psychiatric InstituteNew YorkNY10032USA
| | - Hae‐Won Kim
- Institute of Tissue Regeneration Engineering (ITREN)Dankook UniversityCheonan31116Republic of Korea
- Mechanobiology Dental Medicine Research CenterDankook UniversityCheonan31116Republic of Korea
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative MedicineDankook UniversityCheonan31116Republic of Korea
| | - Bin Xu
- Department of PsychiatryColumbia University Medical CenterNew YorkNY10032USA
| | - Kam W. Leong
- Department of Biomedical EngineeringColumbia UniversityNew YorkNY10027USA
- Department of Systems BiologyColumbia University Irving Medical CenterNew YorkNY10032USA
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42
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Zhao BJ, Song SY, Zhao WM, Xu HB, Peng K, Shan XS, Chen QC, Liu H, Liu HY, Ji FH. The effect of sevoflurane exposure on cell-type-specific changes in the prefrontal cortex in young mice. J Neurochem 2024; 168:1080-1096. [PMID: 38317263 DOI: 10.1111/jnc.16068] [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: 09/25/2023] [Revised: 12/29/2023] [Accepted: 01/18/2024] [Indexed: 02/07/2024]
Abstract
Sevoflurane, the predominant pediatric anesthetic, has been linked to neurotoxicity in young mice, although the underlying mechanisms remain unclear. This study focuses on investigating the impact of neonatal sevoflurane exposure on cell-type-specific alterations in the prefrontal cortex (PFC) of young mice. Neonatal mice were subjected to either control treatment (60% oxygen balanced with nitrogen) or sevoflurane anesthesia (3% sevoflurane in 60% oxygen balanced with nitrogen) for 2 hours on postnatal days (PNDs) 6, 8, and 10. Behavioral tests and single-nucleus RNA sequencing (snRNA-seq) of the PFC were conducted from PNDs 31 to 37. Mechanistic exploration included clustering analysis, identification of differentially expressed genes (DEGs), enrichment analyses, single-cell trajectory analysis, and genome-wide association studies (GWAS). Sevoflurane anesthesia resulted in sociability and cognition impairments in mice. Novel specific marker genes identified 8 distinct cell types in the PFC. Most DEGs between the control and sevoflurane groups were unique to specific cell types. Re-defining 15 glutamatergic neuron subclusters based on layer identity revealed their altered expression profiles. Notably, sevoflurane disrupted the trajectory from oligodendrocyte precursor cells (OPCs) to oligodendrocytes (OLs). Validation of disease-relevant candidate genes across the main cell types demonstrated their association with social dysfunction and working memory impairment. Behavioral results and snRNA-seq collectively elucidated the cellular atlas in the PFC of young male mice, providing a foundation for further mechanistic studies on developmental neurotoxicity induced by anesthesia.
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Affiliation(s)
- Bao-Jian Zhao
- Department of Anesthesiology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Institute of Anesthesiology, Soochow University, Suzhou, Jiangsu, China
- Department of Anesthesiology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Shao-Yong Song
- Department of Anesthesiology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Institute of Anesthesiology, Soochow University, Suzhou, Jiangsu, China
- Department of Pain Medicine, Dushu Lake Hospital Affiliated of Soochow University, Suzhou, Jiangsu, China
| | - Wei-Ming Zhao
- Department of Anesthesiology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Institute of Anesthesiology, Soochow University, Suzhou, Jiangsu, China
| | - Han-Bing Xu
- Department of Anesthesiology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Institute of Anesthesiology, Soochow University, Suzhou, Jiangsu, China
| | - Ke Peng
- Department of Anesthesiology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Institute of Anesthesiology, Soochow University, Suzhou, Jiangsu, China
| | - Xi-Sheng Shan
- Department of Anesthesiology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Institute of Anesthesiology, Soochow University, Suzhou, Jiangsu, China
| | - Qing-Cai Chen
- Department of Anesthesiology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Institute of Anesthesiology, Soochow University, Suzhou, Jiangsu, China
| | - Hong Liu
- Department of Anesthesiology and Pain Medicine, University of California Davis Health, Sacramento, California, USA
| | - Hua-Yue Liu
- Department of Anesthesiology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Institute of Anesthesiology, Soochow University, Suzhou, Jiangsu, China
- Ambulatory Surgery Center, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Fu-Hai Ji
- Department of Anesthesiology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Institute of Anesthesiology, Soochow University, Suzhou, Jiangsu, China
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43
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Choksi SP, Byrnes LE, Konjikusic MJ, Tsai BWH, Deleon R, Lu Q, Westlake CJ, Reiter JF. An alternative cell cycle coordinates multiciliated cell differentiation. Nature 2024; 630:214-221. [PMID: 38811726 DOI: 10.1038/s41586-024-07476-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 04/26/2024] [Indexed: 05/31/2024]
Abstract
The canonical mitotic cell cycle coordinates DNA replication, centriole duplication and cytokinesis to generate two cells from one1. Some cells, such as mammalian trophoblast giant cells, use cell cycle variants like the endocycle to bypass mitosis2. Differentiating multiciliated cells, found in the mammalian airway, brain ventricles and reproductive tract, are post-mitotic but generate hundreds of centrioles, each of which matures into a basal body and nucleates a motile cilium3,4. Several cell cycle regulators have previously been implicated in specific steps of multiciliated cell differentiation5,6. Here we show that differentiating multiciliated cells integrate cell cycle regulators into a new alternative cell cycle, which we refer to as the multiciliation cycle. The multiciliation cycle redeploys many canonical cell cycle regulators, including cyclin-dependent kinases (CDKs) and their cognate cyclins. For example, cyclin D1, CDK4 and CDK6, which are regulators of mitotic G1-to-S progression, are required to initiate multiciliated cell differentiation. The multiciliation cycle amplifies some aspects of the canonical cell cycle, such as centriole synthesis, and blocks others, such as DNA replication. E2F7, a transcriptional regulator of canonical S-to-G2 progression, is expressed at high levels during the multiciliation cycle. In the multiciliation cycle, E2F7 directly dampens the expression of genes encoding DNA replication machinery and terminates the S phase-like gene expression program. Loss of E2F7 causes aberrant acquisition of DNA synthesis in multiciliated cells and dysregulation of multiciliation cycle progression, which disrupts centriole maturation and ciliogenesis. We conclude that multiciliated cells use an alternative cell cycle that orchestrates differentiation instead of controlling proliferation.
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Affiliation(s)
- Semil P Choksi
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Lauren E Byrnes
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Mia J Konjikusic
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Benedict W H Tsai
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Rachel Deleon
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Quanlong Lu
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Christopher J Westlake
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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44
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Lian X, Zhong L, Bai Y, Guang X, Tang S, Guo X, Wei T, Yang F, Zhang Y, Huang G, Zhang J, Shao L, Lei G, Li Z, Sahu SK, Zhang S, Liu H, Hu F. Spatiotemporal transcriptomic atlas of rhizome formation in Oryza longistaminata. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1652-1668. [PMID: 38345936 PMCID: PMC11123419 DOI: 10.1111/pbi.14294] [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: 10/10/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/22/2024]
Abstract
Rhizomes are modified stems that grow underground and produce new individuals genetically identical to the mother plant. Recently, a breakthrough has been made in efforts to convert annual grains into perennial ones by utilizing wild rhizomatous species as donors, yet the developmental biology of this organ is rarely studied. Oryza longistaminata, a wild rice species featuring strong rhizomes, provides a valuable model for exploration of rhizome development. Here, we first assembled a double-haplotype genome of O. longistaminata, which displays a 48-fold improvement in contiguity compared to the previously published assembly. Furthermore, spatiotemporal transcriptomics was performed to obtain the expression profiles of different tissues in O. longistaminata rhizomes and tillers. Two spatially reciprocal cell clusters, the vascular bundle 2 cluster and the parenchyma 2 cluster, were determined to be the primary distinctions between the rhizomes and tillers. We also captured meristem initiation cells in the sunken area of parenchyma located at the base of internodes, which is the starting point for rhizome initiation. Trajectory analysis further indicated that the rhizome is regenerated through de novo generation. Collectively, these analyses revealed a spatiotemporal transcriptional transition underlying the rhizome initiation, providing a valuable resource for future perennial crop breeding.
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Affiliation(s)
- Xiaoping Lian
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Liyuan Zhong
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Yixuan Bai
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Xuanmin Guang
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Sijia Tang
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Xing Guo
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Tong Wei
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Feng Yang
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Yujiao Zhang
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Guangfu Huang
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Jing Zhang
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Lin Shao
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Guijie Lei
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Zheng Li
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Shilai Zhang
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Huan Liu
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Fengyi Hu
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
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Fan L, Liu J, Hu W, Chen Z, Lan J, Zhang T, Zhang Y, Wu X, Zhong Z, Zhang D, Zhang J, Qin R, Chen H, Zong Y, Zhang J, Chen B, Jiang J, Cheng J, Zhou J, Gao Z, Liu Z, Chai Y, Fan J, Wu P, Chen Y, Zhu Y, Wang K, Yuan Y, Huang P, Zhang Y, Feng H, Song K, Zeng X, Zhu W, Hu X, Yin W, Chen W, Wang J. Targeting pro-inflammatory T cells as a novel therapeutic approach to potentially resolve atherosclerosis in humans. Cell Res 2024; 34:407-427. [PMID: 38491170 PMCID: PMC11143203 DOI: 10.1038/s41422-024-00945-0] [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: 09/24/2023] [Accepted: 02/24/2024] [Indexed: 03/18/2024] Open
Abstract
Atherosclerosis (AS), a leading cause of cardio-cerebrovascular disease worldwide, is driven by the accumulation of lipid contents and chronic inflammation. Traditional strategies primarily focus on lipid reduction to control AS progression, leaving residual inflammatory risks for major adverse cardiovascular events (MACEs). While anti-inflammatory therapies targeting innate immunity have reduced MACEs, many patients continue to face significant risks. Another key component in AS progression is adaptive immunity, but its potential role in preventing AS remains unclear. To investigate this, we conducted a retrospective cohort study on tumor patients with AS plaques. We found that anti-programmed cell death protein 1 (PD-1) monoclonal antibody (mAb) significantly reduces AS plaque size. With multi-omics single-cell analyses, we comprehensively characterized AS plaque-specific PD-1+ T cells, which are activated and pro-inflammatory. We demonstrated that anti-PD-1 mAb, when captured by myeloid-expressed Fc gamma receptors (FcγRs), interacts with PD-1 expressed on T cells. This interaction turns the anti-PD-1 mAb into a substitute PD-1 ligand, suppressing T-cell functions in the PD-1 ligands-deficient context of AS plaques. Further, we conducted a prospective cohort study on tumor patients treated with anti-PD-1 mAb with or without Fc-binding capability. Our analysis shows that anti-PD-1 mAb with Fc-binding capability effectively reduces AS plaque size, while anti-PD-1 mAb without Fc-binding capability does not. Our work suggests that T cell-targeting immunotherapy can be an effective strategy to resolve AS in humans.
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Affiliation(s)
- Lin Fan
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, Zhejiang, China
| | - Junwei Liu
- Department of Cell Biology, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Wei Hu
- Department of Cell Biology, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
- Kidney Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zexin Chen
- Center of Clinical Epidemiology and Biostatistics and Department of Scientific Research, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jie Lan
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, China
- Department of Bioinformatics, The Basic Medical School of Chongqing Medical University, Chongqing, China
| | - Tongtong Zhang
- Department of Cell Biology, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Hepatobiliary and Pancreatic Surgery, The Center for Integrated Oncology and Precision Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yang Zhang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xianpeng Wu
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Zhiwei Zhong
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Danyang Zhang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jinlong Zhang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Rui Qin
- Department of Cell Biology, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
- The MOE Frontier Science Center for Brain Science & Brain-machine Integration, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hui Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, China
| | - Yunfeng Zong
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jianmin Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Bing Chen
- Department of Vascular Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jun Jiang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jifang Cheng
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jingyi Zhou
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhiwei Gao
- Department of Vascular Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhenjie Liu
- Department of Vascular Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Chai
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Junqiang Fan
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Pin Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yinxuan Chen
- Department of Cell Biology, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuefeng Zhu
- Department of Vascular Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Kai Wang
- Department of Respiratory, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Yuan
- Department of Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Pintong Huang
- Department of Ultrasound in Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Zhang
- Department of Ultrasound in Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Huiqin Feng
- Department of Clinical Research Center, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Kaichen Song
- Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xun Zeng
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Wei Zhu
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Xinyang Hu
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China.
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, Zhejiang, China.
| | - Weiwei Yin
- Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Wei Chen
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China.
- Department of Cell Biology, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China.
- Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China.
- The MOE Frontier Science Center for Brain Science & Brain-machine Integration, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Jian'an Wang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China.
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, Zhejiang, China.
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46
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Zhang S, Sun A, Qian JM, Lin S, Xing W, Yang Y, Zhu HZ, Zhou XY, Guo YS, Liu Y, Meng Y, Jin SL, Song W, Li CP, Li Z, Jin S, Wang JH, Dong MQ, Gao C, Chen C, Bai Y, Liu JJG. Pro-CRISPR PcrIIC1-associated Cas9 system for enhanced bacterial immunity. Nature 2024; 630:484-492. [PMID: 38811729 DOI: 10.1038/s41586-024-07486-x] [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: 10/13/2023] [Accepted: 04/29/2024] [Indexed: 05/31/2024]
Abstract
The CRISPR system is an adaptive immune system found in prokaryotes that defends host cells against the invasion of foreign DNA1. As part of the ongoing struggle between phages and the bacterial immune system, the CRISPR system has evolved into various types, each with distinct functionalities2. Type II Cas9 is the most extensively studied of these systems and has diverse subtypes. It remains uncertain whether members of this family can evolve additional mechanisms to counter viral invasions3,4. Here we identify 2,062 complete Cas9 loci, predict the structures of their associated proteins and reveal three structural growth trajectories for type II-C Cas9. We found that novel associated genes (NAGs) tended to be present within the loci of larger II-C Cas9s. Further investigation revealed that CbCas9 from Chryseobacterium species contains a novel β-REC2 domain, and forms a heterotetrameric complex with an NAG-encoded CRISPR-Cas-system-promoting (pro-CRISPR) protein of II-C Cas9 (PcrIIC1). The CbCas9-PcrIIC1 complex exhibits enhanced DNA binding and cleavage activity, broader compatibility for protospacer adjacent motif sequences, increased tolerance for mismatches and improved anti-phage immunity, compared with stand-alone CbCas9. Overall, our work sheds light on the diversity and 'growth evolutionary' trajectories of II-C Cas9 proteins at the structural level, and identifies many NAGs-such as PcrIIC1, which serves as a pro-CRISPR factor to enhance CRISPR-mediated immunity.
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Affiliation(s)
- Shouyue Zhang
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ao Sun
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jing-Mei Qian
- State Key Laboratory of Plant Genomics, CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuo Lin
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Wenjing Xing
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yun Yang
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Han-Zhou Zhu
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xin-Yi Zhou
- State Key Laboratory of Plant Genomics, CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yan-Shuo Guo
- State Key Laboratory of Plant Genomics, CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yun Liu
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yu Meng
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shu-Lin Jin
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Wenhao Song
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Cheng-Ping Li
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhaofu Li
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shuai Jin
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Jian-Hua Wang
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Caixia Gao
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Chunlai Chen
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Yang Bai
- State Key Laboratory of Plant Genomics, CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, China.
| | - Jun-Jie Gogo Liu
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
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Liu C, Xie J, Lin B, Tian W, Wu Y, Xin S, Hong L, Li X, Liu L, Jin Y, Tang H, Deng X, Zou Y, Zheng S, Fang W, Cheng J, Dai X, Bao X, Zhao P. Pan-Cancer Single-Cell and Spatial-Resolved Profiling Reveals the Immunosuppressive Role of APOE+ Macrophages in Immune Checkpoint Inhibitor Therapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401061. [PMID: 38569519 PMCID: PMC11186051 DOI: 10.1002/advs.202401061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/13/2024] [Indexed: 04/05/2024]
Abstract
The heterogeneity of macrophages influences the response to immune checkpoint inhibitor (ICI) therapy. However, few studies explore the impact of APOE+ macrophages on ICI therapy using single-cell RNA sequencing (scRNA-seq) and machine learning methods. The scRNA-seq and bulk RNA-seq data are Integrated to construct an M.Sig model for predicting ICI response based on the distinct molecular signatures of macrophage and machine learning algorithms. Comprehensive single-cell analysis as well as in vivo and in vitro experiments are applied to explore the potential mechanisms of the APOE+ macrophage in affecting ICI response. The M.Sig model shows clear advantages in predicting the efficacy and prognosis of ICI therapy in pan-cancer patients. The proportion of APOE+ macrophages is higher in ICI non-responders of triple-negative breast cancer compared with responders, and the interaction and longer distance between APOE+ macrophages and CD8+ exhausted T (Tex) cells affecting ICI response is confirmed by multiplex immunohistochemistry. In a 4T1 tumor-bearing mice model, the APOE inhibitor combined with ICI treatment shows the best efficacy. The M.Sig model using real-world immunotherapy data accurately predicts the ICI response of pan-cancer, which may be associated with the interaction between APOE+ macrophages and CD8+ Tex cells.
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Affiliation(s)
- Chuan Liu
- Department of Medical OncologyThe First Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhou310003China
| | - Jindong Xie
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Bo Lin
- College of Computer Science and TechnologyZhejiang UniversityHangzhou310053China
- Innovation Centre for InformationBinjiang Institute of Zhejiang UniversityHangzhou310053China
| | - Weihong Tian
- Changzhou Third People's HospitalChangzhou Medical CenterNanjing Medical UniversityChangzhou213000China
| | - Yifan Wu
- School of softwareZhejiang UniversityNingbo315100China
| | - Shan Xin
- Department of GeneticsYale School of medicineNew HavenCT06510USA
| | - Libing Hong
- Department of Medical OncologyThe First Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhou310003China
| | - Xin Li
- Department Chronic Inflammation and CancerGerman Cancer Research Center (DKFZ)69120HeidelbergGermany
| | - Lulu Liu
- Department of Medical OncologyThe First Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhou310003China
| | - Yuzhi Jin
- Department of Medical OncologyThe First Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhou310003China
| | - Hailin Tang
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Xinpei Deng
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Yutian Zou
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Shaoquan Zheng
- Breast Disease CenterThe First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510060China
| | - Weijia Fang
- Department of Medical OncologyThe First Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhou310003China
| | - Jinlin Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious DiseasesNational Clinical Research Center for Infectious DiseasesNational Medical Center for Infectious DiseasesCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesThe First Affiliated HospitalZhejiang University School of MedicineZhejiang UniversityHangzhou310003China
| | - Xiaomeng Dai
- Department of Medical OncologyThe First Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhou310003China
| | - Xuanwen Bao
- Department of Medical OncologyThe First Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhou310003China
| | - Peng Zhao
- Department of Medical OncologyThe First Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhou310003China
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Lenz G. Heterogeneity generating capacity in tumorigenesis and cancer therapeutics. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167226. [PMID: 38734320 DOI: 10.1016/j.bbadis.2024.167226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/26/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Cells of multicellular organisms generate heterogeneity in a controlled and transient fashion during embryogenesis, which can be reactivated in pathologies such as cancer. Although genomic heterogeneity is an important part of tumorigenesis, continuous generation of phenotypic heterogeneity is central for the adaptation of cancer cells to the challenges of tumorigenesis and response to therapy. Here I discuss the capacity of generating heterogeneity, hereafter called cell hetness, in cancer cells both as the activation of hetness oncogenes and inactivation of hetness tumor suppressor genes, which increase the generation of heterogeneity, ultimately producing an increase in adaptability and cell fitness. Transcriptomic high hetness states in therapy-tolerant cell states denote its importance in cancer resistance to therapy. The definition of the concept of hetness will allow the understanding of its origins, its control during embryogenesis, its loss of control in tumorigenesis and cancer therapeutics and its active targeting.
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Affiliation(s)
- Guido Lenz
- Departamento de Biofísica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
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49
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Li X, Mara AB, Musial SC, Kolling FW, Gibbings SL, Gerebtsov N, Jakubzick CV. Coordinated chemokine expression defines macrophage subsets across tissues. Nat Immunol 2024; 25:1110-1122. [PMID: 38698086 DOI: 10.1038/s41590-024-01826-9] [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: 05/18/2023] [Accepted: 03/20/2024] [Indexed: 05/05/2024]
Abstract
Lung-resident macrophages, which include alveolar macrophages and interstitial macrophages (IMs), exhibit a high degree of diversity, generally attributed to different activation states, and often complicated by the influx of monocytes into the pool of tissue-resident macrophages. To gain a deeper insight into the functional diversity of IMs, here we perform comprehensive transcriptional profiling of resident IMs and reveal ten distinct chemokine-expressing IM subsets at steady state and during inflammation. Similar IM subsets that exhibited coordinated chemokine signatures and differentially expressed genes were observed across various tissues and species, indicating conserved specialized functional roles. Other macrophage types shared specific IM chemokine profiles, while also presenting their own unique chemokine signatures. Depletion of CD206hi IMs in Pf4creR26EYFP+DTR and Pf4creR26EYFPCx3cr1DTR mice led to diminished inflammatory cell recruitment, reduced tertiary lymphoid structure formation and fewer germinal center B cells in models of allergen- and infection-driven inflammation. These observations highlight the specialized roles of IMs, defined by their coordinated chemokine production, in regulating immune cell influx and organizing tertiary lymphoid tissue architecture.
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Affiliation(s)
- Xin Li
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Arlind B Mara
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Shawn C Musial
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Fred W Kolling
- Dartmouth Cancer Center, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | | | - Nikita Gerebtsov
- Lab for Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Claudia V Jakubzick
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, NH, USA.
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Fu W, Liao Q, Shi Y, Liu W, Ren H, Xu C, Zeng C. Transient induction of actin cytoskeletal remodeling associated with dedifferentiation, proliferation, and redifferentiation stimulates cardiac regeneration. Acta Pharm Sin B 2024; 14:2537-2553. [PMID: 38828141 PMCID: PMC11143747 DOI: 10.1016/j.apsb.2024.01.021] [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: 11/02/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 06/05/2024] Open
Abstract
The formation of new and functional cardiomyocytes requires a 3-step process: dedifferentiation, proliferation, and redifferentiation, but the critical genes required for efficient dedifferentiation, proliferation, and redifferentiation remain unknown. In our study, a circular trajectory using single-nucleus RNA sequencing of the pericentriolar material 1 positive (PCM1+) cardiomyocyte nuclei from hearts 1 and 3 days after surgery-induced myocardial infarction (MI) on postnatal Day 1 was reconstructed and demonstrated that actin remodeling contributed to the dedifferentiation, proliferation, and redifferentiation of cardiomyocytes after injury. We identified four top actin-remodeling regulators, namely Tmsb4x, Tmsb10, Dmd, and Ctnna3, which we collectively referred to as 2D2P. Transiently expressed changes of 2D2P, using a polycistronic non-integrating lentivirus driven by Tnnt2 (cardiac-specific troponin T) promoters (Tnnt2-2D2P-NIL), efficiently induced transiently proliferative activation and actin remodeling in postnatal Day 7 cardiomyocytes and adult hearts. Furthermore, the intramyocardial delivery of Tnnt2-2D2P-NIL resulted in a sustained improvement in cardiac function without ventricular dilatation, thickened septum, or fatal arrhythmia for at least 4 months. In conclusion, this study highlights the importance of actin remodeling in cardiac regeneration and provides a foundation for new gene-cocktail-therapy approaches to improve cardiac repair and treat heart failure using a novel transient and cardiomyocyte-specific viral construct.
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Affiliation(s)
- Wenbin Fu
- Department of Cardiology, Daping Hospital, the Third Military Medical University (Army Medical University), Chongqing 400042, China
- Key Laboratory of Geriatric Cardiovascular and Cerebrovascular Disease Research, Ministry of Education of China, Chongqing 400042, China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing 400042, China
| | - Qiao Liao
- Department of Cardiology, Daping Hospital, the Third Military Medical University (Army Medical University), Chongqing 400042, China
- Key Laboratory of Geriatric Cardiovascular and Cerebrovascular Disease Research, Ministry of Education of China, Chongqing 400042, China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing 400042, China
| | - Yu Shi
- Department of Cardiology, Daping Hospital, the Third Military Medical University (Army Medical University), Chongqing 400042, China
- Key Laboratory of Geriatric Cardiovascular and Cerebrovascular Disease Research, Ministry of Education of China, Chongqing 400042, China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing 400042, China
| | - Wujian Liu
- Department of Cardiology, Daping Hospital, the Third Military Medical University (Army Medical University), Chongqing 400042, China
- Key Laboratory of Geriatric Cardiovascular and Cerebrovascular Disease Research, Ministry of Education of China, Chongqing 400042, China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing 400042, China
| | - Hongmei Ren
- Department of Cardiology, Daping Hospital, the Third Military Medical University (Army Medical University), Chongqing 400042, China
- Key Laboratory of Geriatric Cardiovascular and Cerebrovascular Disease Research, Ministry of Education of China, Chongqing 400042, China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing 400042, China
| | - Chunmei Xu
- Department of Cardiology, Daping Hospital, the Third Military Medical University (Army Medical University), Chongqing 400042, China
- Key Laboratory of Geriatric Cardiovascular and Cerebrovascular Disease Research, Ministry of Education of China, Chongqing 400042, China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing 400042, China
| | - Chunyu Zeng
- Department of Cardiology, Daping Hospital, the Third Military Medical University (Army Medical University), Chongqing 400042, China
- Key Laboratory of Geriatric Cardiovascular and Cerebrovascular Disease Research, Ministry of Education of China, Chongqing 400042, China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing 400042, China
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, the Third Military Medical University, Chongqing 400042, China
- Cardiovascular Research Center, Chongqing College, University of Chinese Academy of Sciences, Chongqing 400042, China
- State Key Laboratory of Trauma and Chemical Poisoning, Chongqing 400042, China
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