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Chen M, Wu Q, Shao N, Lai X, Lin H, Chen M, Wu Y, Chen J, Lin Q, Huang J, Chen X, Yan W, Chen S, Li H, Wu D, Yang M, Deng C. The significance of CD16+ monocytes in the occurrence and development of chronic thromboembolic pulmonary hypertension: insights from single-cell RNA sequencing. Front Immunol 2024; 15:1446710. [PMID: 39192976 PMCID: PMC11347785 DOI: 10.3389/fimmu.2024.1446710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 07/17/2024] [Indexed: 08/29/2024] Open
Abstract
Background Chronic thromboembolic pulmonary hypertension (CTEPH) is a serious pulmonary vascular disease characterized by residual thrombi in the pulmonary arteries and distal pulmonary microvascular remodeling. The pathogenesis of CTEPH remains unclear, but many factors such as inflammation, immunity, coagulation and angiogenesis may be involved. Monocytes are important immune cells that can differentiate into macrophages and dendritic cells and play an important role in thrombus formation. However, the distribution, gene expression profile and differentiation trajectory of monocyte subsets in CTEPH patients have not been systematically studied. This study aims to reveal the characteristics and functions of monocytes in CTEPH patients using single-cell sequencing technology, and to provide new insights for the diagnosis and treatment of CTEPH. Methods Single-cell RNA sequencing (scRNA-seq) were performed to analyze the transcriptomic features of peripheral blood mononuclear cells (PBMCs) from healthy controls, CTEPH patients and the tissues from CTEPH patients after the pulmonary endarterectomy (PEA). We established a CTEPH rat model with chronic pulmonary embolism caused by repeated injection of autologous thrombi through a central venous catheter, and used flow cytometry to detect the proportion changes of monocyte subsets in CTEPH patients and CTEPH rat model. We also observed the infiltration degree of macrophage subsets in thrombus tissue and their differentiation relationship with peripheral blood monocyte subsets by immunofluorescence staining. Results The results showed that the monocyte subsets in peripheral blood of CTEPH patients changed significantly, especially the proportion of CD16+ monocyte subset increased. This monocyte subset had unique functional features at the transcriptomic level, involving processes such as cell adhesion, T cell activation, coagulation response and platelet activation, which may play an important role in pulmonary artery thrombus formation and pulmonary artery intimal remodeling. In addition, we also found that the macrophage subsets in pulmonary endarterectomy tissue of CTEPH patients showed pro-inflammatory and lipid metabolism reprogramming features, which may be related to the persistence and insolubility of pulmonary artery thrombi and the development of pulmonary hypertension. Finally, we also observed that CD16+ monocyte subset in peripheral blood of CTEPH patients may be recruited to pulmonary artery intimal tissue and differentiate into macrophage subset with high expression of IL-1β, participating in disease progression. Conclusion CD16+ monocytes subset had significant gene expression changes in CTEPH patients, related to platelet activation, coagulation response and inflammatory response. And we also found that these cells could migrate to the thrombus and differentiate into macrophages with high expression of IL-1β involved in CTEPH disease progression. We believe that CD16+ monocytes are important participants in CTEPH and potential therapeutic targets.
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Affiliation(s)
- Maohe Chen
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
| | - Qiuxia Wu
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
| | - Nan Shao
- Division of Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xingyue Lai
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
| | - Huo Lin
- Department of Pulmonary and Critical Care Medicine, Shishi County Hospital, Shishi, China
| | - Min Chen
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
| | - Yijing Wu
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
| | - Jiafan Chen
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
| | - Qinghuang Lin
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
| | - Jiahui Huang
- Department of Respiratory and Critical Care Medicine, Fuqing City Hospital Affiliated to Fujian Medical University, Fuzhou, China
| | - Xiaoyun Chen
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
| | - Wei Yan
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
| | - Shi Chen
- Department of Respiratory and Critical Care, Wuhan No. 6 Hospital, Affiliated Hospital of Jianghan University, Wuhan, China
| | - Hongli Li
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
- Department of Respiratory and Critical Care Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Dawen Wu
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
- Department of Respiratory and Critical Care Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Minxia Yang
- Division of Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Chaosheng Deng
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
- Department of Respiratory and Critical Care Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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Yang J, Feng J, Lv J, Chu X, Wei Y, Zhang Y, Li J, Sun Y, Li G, Jiang T, Huang J, Fan X. PTBP1-mediated repression of neuron-specific CDC42 splicing constitutes a genomic alteration-independent, developmentally conserved vulnerability in IDH-wildtype glioblastoma. Funct Integr Genomics 2024; 24:135. [PMID: 39117866 DOI: 10.1007/s10142-024-01412-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 07/22/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024]
Abstract
Gene co-expression networks may encode hitherto inadequately recognized vulnerabilities for adult gliomas. By identifying evolutionally conserved gene co-expression modules around EGFR (EM) or PDGFRA (PM), we recently proposed an EM/PM classification scheme, which assigns IDH-wildtype glioblastomas (GBM) into the EM subtype committed in neural stem cell compartment, IDH-mutant astrocytomas and oligodendrogliomas into the PM subtype committed in early oligodendrocyte lineage. Here, we report the identification of EM/PM subtype-specific gene co-expression networks and the characterization of hub gene polypyrimidine tract-binding protein 1 (PTBP1) as a genomic alteration-independent vulnerability in IDH-wildtype GBM. Supervised by the EM/PM classification scheme, we applied weighted gene co-expression network analysis to identify subtype-specific global gene co-expression modules. These gene co-expression modules were characterized for their clinical relevance, cellular origin and conserved expression pattern during brain development. Using lentiviral vector-mediated constitutive or inducible knockdown, we characterized the effects of PTBP1 on the survival of IDH-wildtype GBM cells, which was complemented with the analysis of PTBP1-depedent splicing pattern and overexpression of splicing target neuron-specific CDC42 (CDC42-N) isoform. Transcriptomes of adult gliomas can be robustly assigned into 4 large gene co-expression modules that are prognostically relevant and are derived from either malignant cells of the EM/PM subtypes or tumor microenvironment. The EM subtype is associated with a malignant cell-intrinsic gene module involved in pre-mRNA splicing, DNA replication and damage response, and chromosome segregation, and a microenvironment-derived gene module predominantly involved in extracellular matrix organization and infiltrating immune cells. The PM subtype is associated with two malignant cell-intrinsic gene modules predominantly involved in transcriptional regulation and mRNA translation, respectively. Expression levels of these gene modules are independent prognostic factors and malignant cell-intrinsic gene modules are conserved during brain development. Focusing on the EM subtype, we identified PTBP1 as the most significant hub for the malignant cell-intrinsic gene module. PTBP1 is not altered in most glioma genomes. PTBP1 represses the conserved splicing of CDC42-N. PTBP1 knockdown or CDC42-N overexpression disrupts actin cytoskeleton dynamics, causing accumulation of reactive oxygen species and cell apoptosis. PTBP1-mediated repression of CDC42-N splicing represents a potential genomic alteration-independent, developmentally conserved vulnerability in IDH-wildtype GBM.
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Affiliation(s)
- Junjie Yang
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences , Beijing Normal University, Beijing, China
| | - Jing Feng
- Department of Pathology, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093, China
| | - Jing Lv
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences , Beijing Normal University, Beijing, China
| | - Xiaojing Chu
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences , Beijing Normal University, Beijing, China
| | - Yanfei Wei
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences , Beijing Normal University, Beijing, China
| | - Yunqiu Zhang
- Center of Growth Metabolism & Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jiuyi Li
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Yingyu Sun
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences , Beijing Normal University, Beijing, China
| | - Guanzhang Li
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Tao Jiang
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Jinyan Huang
- Biomedical Big Data Center, the First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Xiaolong Fan
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences , Beijing Normal University, Beijing, China.
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Yan J, Zeng Q, Wang X. RankCompV3: a differential expression analysis algorithm based on relative expression orderings and applications in single-cell RNA transcriptomics. BMC Bioinformatics 2024; 25:259. [PMID: 39112940 PMCID: PMC11304794 DOI: 10.1186/s12859-024-05889-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 07/30/2024] [Indexed: 08/11/2024] Open
Abstract
BACKGROUND Effective identification of differentially expressed genes (DEGs) has been challenging for single-cell RNA sequencing (scRNA-seq) profiles. Many existing algorithms have high false positive rates (FPRs) and often fail to identify weak biological signals. RESULTS We present a novel method for identifying DEGs in scRNA-seq data called RankCompV3. It is based on the comparison of relative expression orderings (REOs) of gene pairs which are determined by comparing the expression levels of a pair of genes in a set of single-cell profiles. The numbers of genes with consistently higher or lower expression levels than the gene of interest are counted in two groups in comparison, respectively, and the result is tabulated in a 3 × 3 contingency table which is tested by McCullagh's method to determine if the gene is dysregulated. In both simulated and real scRNA-seq data, RankCompV3 tightly controlled the FPR and demonstrated high accuracy, outperforming 11 other common single-cell DEG detection algorithms. Analysis with either regular single-cell or synthetic pseudo-bulk profiles produced highly concordant DEGs with the ground-truth. In addition, RankCompV3 demonstrates higher sensitivity to weak biological signals than other methods. The algorithm was implemented using Julia and can be called in R. The source code is available at https://github.com/pathint/RankCompV3.jl . CONCLUSIONS The REOs-based algorithm is a valuable tool for analyzing single-cell RNA profiles and identifying DEGs with high accuracy and sensitivity.
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Affiliation(s)
- Jing Yan
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, 350122, China
| | - Qiuhong Zeng
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, 350122, China
| | - Xianlong Wang
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, 350122, China.
- The Second Affiliated Hospital, Fujian Medical University, Quanzhou, 362000, China.
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104
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Tuersun A, Huo J, Lv Z, Zhang Y, Chen F, Zhao J, Feng W, Xu Z, Mao Z, Xue P, Lu A. Establishment of a chemokine-based prognostic model and identification of CXCL10+ M1 macrophages as predictors of neoadjuvant therapy efficacy in colorectal cancer. Front Immunol 2024; 15:1400722. [PMID: 39170612 PMCID: PMC11335547 DOI: 10.3389/fimmu.2024.1400722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 07/22/2024] [Indexed: 08/23/2024] Open
Abstract
Background Although neoadjuvant therapy has brought numerous benefits to patients, not all patients can benefit from it. Chemokines play a crucial role in the tumor microenvironment and are closely associated with the prognosis and treatment of colorectal cancer. Therefore, constructing a prognostic model based on chemokines will help risk stratification and providing a reference for the personalized treatment. Methods Employing LASSO-Cox predictive modeling, a chemokine-based prognostic model was formulated, harnessing the data from TCGA and GEO databases. Then, our exploration focused on the correlation between the chemokine signature and elements such as the immune landscape, somatic mutations, copy number variations, and drug sensitivity. CXCL10+M1 macrophages identified via scRNA-seq. Monocle2 showed cell pseudotime trajectories, CellChat characterized intercellular communication. CytoTRACE analyzed neoadjuvant therapy stemness, SCENIC detected cell type-specific regulation. Lastly, validation was performed through multiplex immunofluorescence experiments. Results A model based on 15 chemokines was constructed and validated. High-risk scores correlated with poorer prognosis and advanced TNM and clinical stages. Individuals presenting elevated risk scores demonstrated an increased propensity towards the development of chemotherapy resistance. Subsequent scRNA-seq data analysis indicated that patients with higher presence of CXCL10+ M1 macrophages in tumor tissues are more likely to benefit from neoadjuvant therapy. Conclusion We developed a chemokine-based prognostic model by integrating both single-cell and bulk RNA-seq data. Furthermore, we revealed epithelial cell heterogeneity in neoadjuvant outcomes and identified CXCL10+ M1 macrophages as potential therapy response predictors. These findings could significantly contribute to risk stratification and serve as a key guide for the advancement of personalized therapeutic approaches.
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Affiliation(s)
- Abudumaimaitijiang Tuersun
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Department of General Surgery, Second People’s Hospital, Kashi, Xinjiang Uygur Autonomous Region, China
| | - Jianting Huo
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zeping Lv
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yuchen Zhang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Fangqian Chen
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jingkun Zhao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Wenqing Feng
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhuoqing Xu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhihai Mao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Pei Xue
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Aiguo Lu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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105
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Nightingale R, Reehorst CM, Vukelic N, Papadopoulos N, Liao Y, Guleria S, Bell C, Vaillant F, Paul S, Luk IY, Dhillon AS, Jenkins LJ, Morrow RJ, Jackling FC, Chand AL, Chisanga D, Chen Y, Williams DS, Anderson RL, Ellis S, Meikle PJ, Shi W, Visvader JE, Pal B, Mariadason JM. Ehf controls mammary alveolar lineage differentiation and is a putative suppressor of breast tumorigenesis. Dev Cell 2024; 59:1988-2004.e11. [PMID: 38781975 DOI: 10.1016/j.devcel.2024.04.022] [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: 12/17/2022] [Revised: 03/03/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
The transcription factor EHF is highly expressed in the lactating mammary gland, but its role in mammary development and tumorigenesis is not fully understood. Utilizing a mouse model of Ehf deletion, herein, we demonstrate that loss of Ehf impairs mammary lobuloalveolar differentiation at late pregnancy, indicated by significantly reduced levels of milk genes and milk lipids, fewer differentiated alveolar cells, and an accumulation of alveolar progenitor cells. Further, deletion of Ehf increased proliferative capacity and attenuated prolactin-induced alveolar differentiation in mammary organoids. Ehf deletion also increased tumor incidence in the MMTV-PyMT mammary tumor model and increased the proliferative capacity of mammary tumor organoids, while low EHF expression was associated with higher tumor grade and poorer outcome in luminal A and basal human breast cancers. Collectively, these findings establish EHF as a non-redundant regulator of mammary alveolar differentiation and a putative suppressor of mammary tumorigenesis.
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Affiliation(s)
- Rebecca Nightingale
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Camilla M Reehorst
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Natalia Vukelic
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Nikolaos Papadopoulos
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Yang Liao
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Shalini Guleria
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Caroline Bell
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - François Vaillant
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Sudip Paul
- Metabolomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, VIC 3086, Australia
| | - Ian Y Luk
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Amardeep S Dhillon
- The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, VIC 3220, Australia
| | - Laura J Jenkins
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Riley J Morrow
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Felicity C Jackling
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia
| | - Ashwini L Chand
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - David Chisanga
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Yunshun Chen
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia; Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - David S Williams
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia; Department of Pathology, Austin Health, Heidelberg, VIC 3084, Australia
| | - Robin L Anderson
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Sarah Ellis
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Peter J Meikle
- Metabolomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, VIC 3086, Australia
| | - Wei Shi
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Jane E Visvader
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Bhupinder Pal
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia.
| | - John M Mariadason
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia; Department of Medicine, University of Melbourne, Parkville, VIC 3052, Australia.
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Bao M, Hua X, Chen X, An T, Mo H, Sun Z, Tao M, Yue G, Song J. PICALM Regulating the Generation of Amyloid β-Peptide to Promote Anthracycline-Induced Cardiotoxicity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401945. [PMID: 38935046 PMCID: PMC11348153 DOI: 10.1002/advs.202401945] [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: 03/08/2024] [Revised: 05/22/2024] [Indexed: 06/28/2024]
Abstract
Anthracyclines are chemotherapeutic drugs used to treat solid and hematologic malignancies. However, life-threatening cardiotoxicity, with cardiac dilation and heart failure, is a drawback. A combination of in vivo for single cell/nucleus RNA sequencing and in vitro approaches is used to elucidate the underlying mechanism. Genetic depletion and pharmacological blocking peptides on phosphatidylinositol binding clathrin assembly (PICALM) are used to evaluate the role of PICALM in doxorubicin-induced cardiotoxicity in vivo. Human heart tissue samples are used for verification. Patients with end-stage heart failure and chemotherapy-induced cardiotoxicity have thinner cell membranes compared to healthy controls do. Using the doxorubicin-induced cardiotoxicity mice model, it is possible to replicate the corresponding phenotype in patients. Cellular changes in doxorubicin-induced cardiotoxicity in mice, especially in cardiomyocytes, are identified using single cell/nucleus RNA sequencing. Picalm expression is upregulated only in cardiomyocytes with doxorubicin-induced cardiotoxicity. Amyloid β-peptide production is also increased after doxorubicin treatment, which leads to a greater increase in the membrane permeability of cardiomyocytes. Genetic depletion and pharmacological blocking peptides on Picalm reduce the generation of amyloid β-peptide. This alleviates the doxorubicin-induced cardiotoxicity in vitro and in vivo. In human heart tissue samples of patients with chemotherapy-induced cardiotoxicity, PICALM, and amyloid β-peptide are elevated as well.
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Affiliation(s)
- Mengni Bao
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant MaterialsAnimal Experimental CentreFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100037China
- State Key Laboratory of Cardiovascular DiseaseFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing10037China
- Shenzhen Key Laboratory of Cardiovascular DiseaseFuwai HospitalChinese Academy of Medical SciencesShenzhen518057China
| | - Xiumeng Hua
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant MaterialsAnimal Experimental CentreFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100037China
- State Key Laboratory of Cardiovascular DiseaseFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing10037China
- Department of Cardiovascular SurgeryFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing10037China
- The Cardiomyopathy Research GroupFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing10037China
| | - Xiao Chen
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant MaterialsAnimal Experimental CentreFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100037China
- State Key Laboratory of Cardiovascular DiseaseFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing10037China
- Department of Cardiovascular SurgeryFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing10037China
- The Cardiomyopathy Research GroupFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing10037China
| | - Tao An
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant MaterialsAnimal Experimental CentreFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100037China
- Department of CardiologyFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing10037China
| | - Han Mo
- Shenzhen Key Laboratory of Cardiovascular DiseaseFuwai HospitalChinese Academy of Medical SciencesShenzhen518057China
| | - Zhe Sun
- Shenzhen Key Laboratory of Cardiovascular DiseaseFuwai HospitalChinese Academy of Medical SciencesShenzhen518057China
| | - Menghao Tao
- State Key Laboratory of Cardiovascular DiseaseFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing10037China
| | - Guangxin Yue
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant MaterialsAnimal Experimental CentreFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100037China
| | - Jiangping Song
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant MaterialsAnimal Experimental CentreFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100037China
- State Key Laboratory of Cardiovascular DiseaseFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing10037China
- Shenzhen Key Laboratory of Cardiovascular DiseaseFuwai HospitalChinese Academy of Medical SciencesShenzhen518057China
- Department of Cardiovascular SurgeryFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing10037China
- The Cardiomyopathy Research GroupFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing10037China
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Zang X, Gu S, Wang W, Shi J, Gan J, Hu Q, Zhou C, Ding Y, He Y, Jiang L, Gu T, Xu Z, Huang S, Yang H, Meng F, Li Z, Cai G, Hong L, Wu Z. Dynamic intrauterine crosstalk promotes porcine embryo implantation during early pregnancy. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1676-1696. [PMID: 38748354 DOI: 10.1007/s11427-023-2557-x] [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: 01/18/2024] [Accepted: 02/21/2024] [Indexed: 08/09/2024]
Abstract
Dynamic crosstalk between the embryo and mother is crucial during implantation. Here, we comprehensively profile the single-cell transcriptome of pig peri-implantation embryos and corresponding maternal endometrium, identifying 4 different lineages in embryos and 13 cell types in the endometrium. Cell-specific gene expression characterizes 4 distinct trophectoderm subpopulations, showing development from undifferentiated trophectoderm to polar and mural trophectoderm. Dynamic expression of genes in different types of endometrial cells illustrates their molecular response to embryos during implantation. Then, we developed a novel tool, ExtraCellTalk, generating an overall dynamic map of maternal-foetal crosstalk using uterine luminal proteins as bridges. Through cross-species comparisons, we identified a conserved RBP4/STRA6 pathway in which embryonic-derived RBP4 could target the STRA6 receptor on stromal cells to regulate the interaction with other endometrial cells. These results provide insight into the maternal-foetal crosstalk during embryo implantation and represent a valuable resource for further studies to improve embryo implantation.
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Affiliation(s)
- Xupeng Zang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Shengchen Gu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Wenjing Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Junsong Shi
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, 527300, China
| | - Jianyu Gan
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Qun Hu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Chen Zhou
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Yue Ding
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Yanjuan He
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Lei Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Ting Gu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
- Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, 510520, China
| | - Zheng Xu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
- Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, 510520, China
| | - Sixiu Huang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
- Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, 510520, China
| | - Huaqiang Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
- Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, 510520, China
| | - Fanming Meng
- Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Zicong Li
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
- Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, 510520, China
| | - Gengyuan Cai
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
- Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, 510520, China
| | - Linjun Hong
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.
- Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, 510520, China.
| | - Zhenfang Wu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, 527300, China.
- Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, 510520, China.
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108
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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; 205:580-593. [PMID: 38887897 DOI: 10.1111/bjh.19585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [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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109
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Li Z, Li L, Yue M, Peng Q, Pu X, Zhou Y. Tracing Immunological Interaction in Trimethylamine N-Oxide Hydrogel-Derived Zwitterionic Microenvironment During Promoted Diabetic Wound Regeneration. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2402738. [PMID: 38885961 DOI: 10.1002/adma.202402738] [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: 02/22/2024] [Revised: 05/30/2024] [Indexed: 06/20/2024]
Abstract
The diabetic wound healing is challenging due to the sabotaged delicate balance of immune regulation via an undetermined pathophysiological mechanism, so it is crucial to decipher multicellular signatures underlying diabetic wound healing and seek therapeutic strategies. Here, this work develops a strategy using novel trimethylamine N-oxide (TMAO)-derived zwitterionic hydrogel to promote diabetic wound healing, and explore the multi-cellular ecosystem around zwitterionic hydrogel, mapping out an overview of different cells in the zwitterionic microenvironment by single-cell RNA sequencing. The diverse cellular heterogeneity is revealed, highlighting the critical role of macrophage and neutrophils in managing diabetic wound healing. It is found that polyzwitterionic hydrogel can upregulate Ccl3+ macrophages and downregulate S100a9+ neutrophils and facilitate their interactions compared with polyanionic and polycationic hydrogels, validating the underlying effect of zwitterionic microenvironment on the activation of adaptive immune system. Moreover, zwitterionic hydrogel inhibits the formation of neutrophil extracellular traps (NETs) and promotes angiogenesis, thus improving diabetic wound healing. These findings expand the horizons of the sophisticated orchestration of immune systems in zwitterion-directed diabetic wound repair and uncover new strategies of novel immunoregulatory biomaterials.
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Affiliation(s)
- Zheng Li
- Department of Prosthodontics, Peking University School and Hospital of Stomatology, Beijing, 100081, China
- National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices & Beijing Key Laboratory of Digital Stomatology & NHC Key Laboratory of Digital Stomatology, 22 Zhongguancun South Avenue, Haidian District, Beijing, 100081, P. R. China
| | - Longwei Li
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-Nano Energy and Sensor, Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, China
- School of Nanoscience and Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Muxin Yue
- Department of Prosthodontics, Peking University School and Hospital of Stomatology, Beijing, 100081, China
- National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices & Beijing Key Laboratory of Digital Stomatology & NHC Key Laboratory of Digital Stomatology, 22 Zhongguancun South Avenue, Haidian District, Beijing, 100081, P. R. China
- Institute of Medical Technology, Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing, 100191, P. R. China
| | - Qingyu Peng
- School of Mechanical and Material Engineering, North China University of Technology, Beijing, 100144, P. R. China
| | - Xiong Pu
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-Nano Energy and Sensor, Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, China
- School of Nanoscience and Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongsheng Zhou
- Department of Prosthodontics, Peking University School and Hospital of Stomatology, Beijing, 100081, China
- National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices & Beijing Key Laboratory of Digital Stomatology & NHC Key Laboratory of Digital Stomatology, 22 Zhongguancun South Avenue, Haidian District, Beijing, 100081, P. R. China
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110
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Cai A, Meng Y, Zhou H, Cai H, Shao X, Wang Q, Xu Y, Zhou Y, Zhou W, Chen L, Mou S. Podocyte Pathogenic Bone Morphogenetic Protein-2 Pathway and Immune Cell Behaviors in Primary Membranous Nephropathy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2404151. [PMID: 38785168 PMCID: PMC11304328 DOI: 10.1002/advs.202404151] [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: 04/19/2024] [Indexed: 05/25/2024]
Abstract
Primary membranous nephropathy (PMN) is one of the leading causes of end-stage renal disease, and the most frequent cause of massive proteinuria in nondiabetic adults, resulting in fatal complications. However, the underlying pathomechanisms of PMN remain largely unclear. Here, single-cell RNA sequencing is employed to analyze kidney biopsies from eleven PMN patients and seven healthy subjects. Profiling 44 060 cells from patients allowed us to characterize the cellular composition and cell-type-specific gene expression in the PMN kidney. The complement-induced BMP2/pSMAD1/COL4 pathway is identified as the pathogenic pathway in podocytes, bridging two key events, i.e., complement system activation and glomerular basement membrane thickening in PMN. Augmented infiltration and activation of myeloid leukocytes and B lymphocytes are found, profiling delicate crosstalk of immune cells in PMN kidneys. Overall, these results provide valuable insights into the roles of podocytes and immune cells in PMN, and comprehensive resources toward the complete understanding of PMN pathophysiology.
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Affiliation(s)
- Anxiang Cai
- Department of Nephrology, Ren Ji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Yiwei Meng
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghai200031China
- Institute of Molecular Medicine, Ren Ji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Hang Zhou
- Department of Nephrology, Ren Ji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Hong Cai
- Department of Nephrology, Ren Ji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Xinghua Shao
- Department of Nephrology, Ren Ji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Qin Wang
- Department of Nephrology, Ren Ji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Yao Xu
- Department of Nephrology, Ren Ji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Yin Zhou
- Department of Nephrology, Ren Ji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Wenyan Zhou
- Department of Nephrology, Ren Ji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghai200031China
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou310024China
- School of Life Science and TechnologyShanghai Tech UniversityShanghai201210China
| | - Shan Mou
- Department of Nephrology, Ren Ji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
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111
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Meng X, Zheng Y, Zhang L, Liu P, Liu Z, He Y. Single-Cell Analyses Reveal the Metabolic Heterogeneity and Plasticity of the Tumor Microenvironment during Head and Neck Squamous Cell Carcinoma Progression. Cancer Res 2024; 84:2468-2483. [PMID: 38718319 DOI: 10.1158/0008-5472.can-23-1344] [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: 05/04/2023] [Revised: 10/31/2023] [Accepted: 04/29/2024] [Indexed: 08/02/2024]
Abstract
Metabolic reprogramming is a hallmark of cancer. In addition to metabolic alterations in the tumor cells, multiple other metabolically active cell types in the tumor microenvironment (TME) contribute to the emergence of a tumor-specific metabolic milieu. Here, we defined the metabolic landscape of the TME during the progression of head and neck squamous cell carcinoma (HNSCC) by performing single-cell RNA sequencing on 26 human patient specimens, including normal tissue, precancerous lesions, early stage cancer, advanced-stage cancer, lymph node metastases, and recurrent tumors. The analysis revealed substantial heterogeneity at the transcriptional, developmental, metabolic, and functional levels in different cell types. SPP1+ macrophages were identified as a protumor and prometastatic macrophage subtype with high fructose and mannose metabolism, which was further substantiated by integrative analysis and validation experiments. An inhibitor of fructose metabolism reduced the proportion of SPP1+ macrophages, reshaped the immunosuppressive TME, and suppressed tumor growth. In conclusion, this work delineated the metabolic landscape of HNSCC at a single-cell resolution and identified fructose metabolism as a key metabolic feature of a protumor macrophage subpopulation. Significance: Fructose and mannose metabolism is a metabolic feature of a protumor and prometastasis macrophage subtype and can be targeted to reprogram macrophages and the microenvironment of head and neck squamous cell carcinoma.
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Affiliation(s)
- Xiaoyan Meng
- Department of Oral Maxillofacial & Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P.R. China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology Shanghai, Shanghai, P.R. China
| | - Yang Zheng
- Department of Oral Maxillofacial & Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P.R. China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology Shanghai, Shanghai, P.R. China
| | - Lingfang Zhang
- Suzhou Lingdian Biotechnology Co., Ltd., Suzhou, P.R. China
| | - Peipei Liu
- Suzhou Lingdian Biotechnology Co., Ltd., Suzhou, P.R. China
| | - Zhonglong Liu
- Department of Oral Maxillofacial & Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P.R. China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology Shanghai, Shanghai, P.R. China
| | - Yue He
- Department of Oral Maxillofacial & Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P.R. China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology Shanghai, Shanghai, P.R. China
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112
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Qian Y, Zou Q, Zhao M, Liu Y, Guo F, Ding Y. scRNMF: An imputation method for single-cell RNA-seq data by robust and non-negative matrix factorization. PLoS Comput Biol 2024; 20:e1012339. [PMID: 39116191 PMCID: PMC11338450 DOI: 10.1371/journal.pcbi.1012339] [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: 05/05/2024] [Revised: 08/21/2024] [Accepted: 07/19/2024] [Indexed: 08/10/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool in genomics research, enabling the analysis of gene expression at the individual cell level. However, scRNA-seq data often suffer from a high rate of dropouts, where certain genes fail to be detected in specific cells due to technical limitations. This missing data can introduce biases and hinder downstream analysis. To overcome this challenge, the development of effective imputation methods has become crucial in the field of scRNA-seq data analysis. Here, we propose an imputation method based on robust and non-negative matrix factorization (scRNMF). Instead of other matrix factorization algorithms, scRNMF integrates two loss functions: L2 loss and C-loss. The L2 loss function is highly sensitive to outliers, which can introduce substantial errors. We utilize the C-loss function when dealing with zero values in the raw data. The primary advantage of the C-loss function is that it imposes a smaller punishment for larger errors, which results in more robust factorization when handling outliers. Various datasets of different sizes and zero rates are used to evaluate the performance of scRNMF against other state-of-the-art methods. Our method demonstrates its power and stability as a tool for imputation of scRNA-seq data.
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Affiliation(s)
- Yuqing Qian
- Institute Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
| | - Quan Zou
- Institute Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
| | - Mengyuan Zhao
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yi Liu
- Institute Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
| | - Fei Guo
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Yijie Ding
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
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113
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Zhang H, Bi X, Yan P, Wang C. Neutrophil extracellular trap related risk score exhibits crucial prognostic value in skin cutaneous melanoma, associating with distinct immune characteristics. Skin Res Technol 2024; 30:e70008. [PMID: 39167030 PMCID: PMC11337913 DOI: 10.1111/srt.70008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024]
Abstract
BACKGROUND Neutrophil extracellular traps (NETs) are related to the prognosis of cancer patients. Nevertheless, the potential prognostic values of NETs in skin cutaneous melanoma (SKCM) remains largely unknown. MATERIALS AND METHODS The NET-related gene signature was constructed by LASSO Cox regression analysis using the TCGA-SKCM cohort. The overall survival (OS) and immune status in SKCM patients between the high- and low-NET score (high-score, low-score) groups were explored. The scRNA-seq dataset GSE115978 was used to understand the role of NET score in SKCM at single cell resolution. RESULTS A five NET genes-based signature (TLR2, CLEC6A, PDE4B, SLC22A4 and CYP4F3) was constructed as the NET-related prognostic model for SKCM. The OS of SKCM patients with low-score was better than that in patients with high-score. Additionally, NET score was negatively associated with infiltration of some immune cells (e.g. type I Macrophages, CD8-T cells, CD4-T cells). Moreover, patients with high-score had low stromal, immune and ESTIMATE scores. Furthermore, drug sensitivity analysis results showed that Lapatinib, Trametinib and Erlotinib may have better therapeutic advantages in patients with high-score. CONCLUSION We established a NET-related five gene signature in SKCM and found that the NET-related signature may exhibit a good predictive ability for SKCM prognosis. The NET score may not only predict the survival outcome and drug sensitivity in SKCM, but also reflect the immune conditions of SKCM patients.
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Affiliation(s)
- Haiyang Zhang
- Department of Hand and Foot SurgeryZibo Central HospitalZiboChina
| | - Xiaoqing Bi
- Dermatology&S.T.D. DepartmentZibo Central HospitalZiboChina
| | - Pengrong Yan
- Dermatology&S.T.D. DepartmentZibo Central HospitalZiboChina
| | - Congcong Wang
- Dermatology&S.T.D. DepartmentZibo Central HospitalZiboChina
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114
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Lause J, Ziegenhain C, Hartmanis L, Berens P, Kobak D. Compound models and Pearson residuals for single-cell RNA-seq data without UMIs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.02.551637. [PMID: 37577688 PMCID: PMC10418209 DOI: 10.1101/2023.08.02.551637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Recent work employed Pearson residuals from Poisson or negative binomial models to normalize UMI data. To extend this approach to non-UMI data, we model the additional amplification step with a compound distribution: we assume that sequenced RNA molecules follow a negative binomial distribution, and are then replicated following an amplification distribution. We show how this model leads to compound Pearson residuals, which yield meaningful gene selection and embeddings of Smart-seq2 datasets. Further, we suggest that amplification distributions across several sequencing protocols can be described by a broken power law. The resulting compound model captures previously unexplained overdispersion and zero-inflation patterns in non-UMI data.
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Ma Y, Li Q, Tang Y, Zhang Z, Liu R, Luo Q, Wang Y, Hu J, Chen Y, Li Z, Zhao C, Ran Y, Mu Y, Li Y, Xu X, Gong Y, He Z, Ba Y, Guo K, Dong K, Li X, Tan W, Zhu Y, Xiang Z, Xu H. The architecture of silk-secreting organs during the final larval stage of silkworms revealed by single-nucleus and spatial transcriptomics. Cell Rep 2024; 43:114460. [PMID: 38996068 DOI: 10.1016/j.celrep.2024.114460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/26/2024] [Accepted: 06/22/2024] [Indexed: 07/14/2024] Open
Abstract
Natural silks are renewable proteins with impressive mechanical properties and biocompatibility that are useful in various fields. However, the cellular and spatial organization of silk-secreting organs remains unclear. Here, we combined single-nucleus and spatially resolved transcriptomics to systematically map the cellular and spatial composition of the silk glands (SGs) of mulberry silkworms late in larval development. This approach allowed us to profile SG cell types and cell state dynamics and identify regulatory networks and cell-cell communication related to efficient silk protein synthesis; key markers were validated via transgenic approaches. Notably, we demonstrated the indispensable role of the ecdysone receptor (ultraspiracle) in regulating endoreplication in SG cells. Our atlas presents the results of spatiotemporal analysis of silk-secreting organ architecture late in larval development; this atlas provides a valuable reference for elucidating the mechanism of efficient silk protein synthesis and developing sustainable products made from natural silk.
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Affiliation(s)
- Yan Ma
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Qingjun Li
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Yiyun Tang
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Zhiyong Zhang
- Beijing SeekGene BioSciences Co., Ltd., Beijing 102206, China
| | - Rongpeng Liu
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Qin Luo
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Yuting Wang
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Jie Hu
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Yuqin Chen
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Zhiwei Li
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Chen Zhao
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Yiting Ran
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Yuanyuan Mu
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Yinghao Li
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Xiaoqing Xu
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Yuyan Gong
- Beijing SeekGene BioSciences Co., Ltd., Beijing 102206, China
| | - Zihan He
- Beijing SeekGene BioSciences Co., Ltd., Beijing 102206, China
| | - Yongbing Ba
- Shanghai OE Biotech. Co., Ltd., Shanghai 201212, China
| | - Kaiqi Guo
- Shanghai OE Biotech. Co., Ltd., Shanghai 201212, China
| | - Keshu Dong
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Xiao Li
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Wei Tan
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Yumeng Zhu
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Zhonghuai Xiang
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Hanfu Xu
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China.
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Huang X, Du G, Yang Y, Su P, Chen S, Cai C, Huang T, Zeng Y, Tao Y, Tian D, Zhang N. Advancing bladder cancer management: development of a prognostic model and personalized therapy. Front Immunol 2024; 15:1430792. [PMID: 39104534 PMCID: PMC11298345 DOI: 10.3389/fimmu.2024.1430792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/08/2024] [Indexed: 08/07/2024] Open
Abstract
Background Bladder cancer (BLCA) was recognized as a significant public health challenge due to its high incidence and mortality rates. The influence of molecular subtypes on treatment outcomes was well-acknowledged, necessitating further exploration of their characterization and application. This study was aimed at enhancing the understanding of BLCA by mapping its molecular heterogeneity and developing a robust prognostic model using single-cell and bulk RNA sequencing data. Additionally, immunological characteristics and personalized treatment strategies were investigated through the risk score. Methods Single-cell RNA sequencing (scRNA-seq) data from GSE135337 and bulk RNA-seq data from several sources, including GSE13507, GSE31684, GSE32894, GSE69795, and TCGA-BLCA, were utilized. Molecular subtypes, particularly the basal-squamous (Ba/Sq) subtype associated with poor prognosis, were identified. A prognostic model was constructed using LASSO and Cox regression analyses focused on genes linked with the Ba/Sq subtype. this model was validated across internal and external datasets to ensure predictive accuracy. High- and low-risk groups based on the risk score derived from TCGA-BLCA data were analyzed to examine their immune-related molecular profiles and treatment responses. Results Six molecular subtypes were identified, with the Ba/Sq subtype being consistently associated with poor prognosis. The prognostic model, based on basal-squamous subtype-related genes (BSSRGs), was shown to have strong predictive performance across diverse clinical settings with AUC values at 1, 3, and 5 years indicating robust predictability in training, testing, and entire datasets. Analysis of the different risk groups revealed distinct immune infiltration and microenvironments. Generally higher tumor mutation burden (TMB) scores and lower tumor immune dysfunction and exclusion (TIDE) scores were exhibited by the low-risk group, suggesting varied potentials for systemic drug response between the groups. Finally, significant differences in potential systemic drug response rates were also observed between risk groups. Conclusions The study introduced and validated a new prognostic model for BLCA based on BSSRGs, which was proven effective in prognosis prediction. The potential for personalized therapy, optimized by patient stratification and immune profiling, was highlighted by our risk score, aiming to improve treatment efficacy. This approach was promised to offer significant advancements in managing BLCA, tailoring treatments based on detailed molecular and immunological insights.
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Affiliation(s)
- Xiang Huang
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Guotu Du
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Ying Yang
- Department of Pathology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Peng Su
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Pathology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Shicheng Chen
- Department of Urology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Chongjiong Cai
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Urology, Renhuai People’s Hospital, Zunyi, China
| | - Tianyu Huang
- Department of Nursing, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yu Zeng
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yonggang Tao
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Demei Tian
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Neng Zhang
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
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Hu Q, Zhang B, Jing Y, Ma S, Hu L, Li J, Zheng Y, Xin Z, Peng J, Wang S, Cheng B, Qu J, Zhang W, Liu GH, Wang S. Single-nucleus transcriptomics uncovers a geroprotective role of YAP in primate gingival aging. Protein Cell 2024; 15:612-632. [PMID: 38577810 PMCID: PMC11259548 DOI: 10.1093/procel/pwae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 02/01/2024] [Indexed: 04/06/2024] Open
Abstract
Aging has a profound impact on the gingiva and significantly increases its susceptibility to periodontitis, a worldwide prevalent inflammatory disease. However, a systematic characterization and comprehensive understanding of the regulatory mechanism underlying gingival aging is still lacking. Here, we systematically dissected the phenotypic characteristics of gingiva during aging in primates and constructed the first single-nucleus transcriptomic landscape of gingival aging, by which a panel of cell type-specific signatures were elucidated. Epithelial cells were identified as the most affected cell types by aging in the gingiva. Further analyses pinpointed the crucial role of YAP in epithelial self-renew and homeostasis, which declined during aging in epithelial cells, especially in basal cells. The decline of YAP activity during aging was confirmed in the human gingival tissues, and downregulation of YAP in human primary gingival keratinocytes recapitulated the major phenotypic defects observed in the aged primate gingiva while overexpression of YAP showed rejuvenation effects. Our work provides an in-depth understanding of gingival aging and serves as a rich resource for developing novel strategies to combat aging-associated gingival diseases, with the ultimate goal of advancing periodontal health and promoting healthy aging.
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Affiliation(s)
- Qinchao Hu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510060, China
| | - Bin Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaobin Jing
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- International Center for Aging and Cancer, Hainan Medical University, Haikou 571199, China
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Lei Hu
- Salivary Gland Disease Center and Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Laboratory of Oral Health and Beijing Stomatological Hospital, Capital Medical University, Beijing 100050, China
| | - Jingyi Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Yandong Zheng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zijuan Xin
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Jianmin Peng
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510060, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuan Wu Hospital, Capital Medical University, Beijing 100053, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Bin Cheng
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510060, China
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuan Wu Hospital, Capital Medical University, Beijing 100053, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Songlin Wang
- Salivary Gland Disease Center and Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Laboratory of Oral Health and Beijing Stomatological Hospital, Capital Medical University, Beijing 100050, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
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Song YM, Ge JY, Ding M, Zheng YW. Key factor screening in mouse NASH model using single-cell sequencing combined with machine learning. Heliyon 2024; 10:e33597. [PMID: 39040415 PMCID: PMC11260934 DOI: 10.1016/j.heliyon.2024.e33597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/16/2024] [Accepted: 06/24/2024] [Indexed: 07/24/2024] Open
Abstract
Aims To identify and analyze genes closely related to the progression of nonalcoholic steatohepatitis (NASH) by employing a combination of single-cell RNA sequencing and machine-learning algorithms. Main methods Single-cell RNA sequencing (scRNA-seq) analysis was performed to find the cell population with the most significant differences between the Chow and NASH groups. This approach was used to validate the developmental trajectory of this cell population and investigate changes in cellular communication and important signaling pathways among these cells. Subsequently, high dimensional Weighted Gene Co-expression Network Analysis (hdWGCNA) was used to find the key modules in NASH. Machine learning analyses were performed to further identify core genes. Deep learning techniques were applied to elucidate the correlation between core genes and immune cells. The accuracy of this correlation was further confirmed using deep learning techniques, specifically Convolutional Neural Networks. Key findings By comparing scRNA-seq data between the Chow and NASH groups, we have observed a notable distinction existing in the Kupffer cell population. Signaling interactions between hepatic macrophages and other cells were significantly heightened in the NASH group. Through subsequent analysis of macrophage subtypes and key modules, we identified 150 genes tightly associated with NASH. Finally, we highlighted the 16 most significant core genes using multiple iterations of machine learning. Furthermore, we pointed out the close relationship between core genes and immune cells. Significances Using scRNA-seq analysis and machine learning, we can distinguish NASH-related genes from large genetic datasets, providing theoretical support in finding potential targets for the development of novel therapies.
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Affiliation(s)
- Yu-Mu Song
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, and South China Institute of Large Animal Models for Biomedicine, School of Pharmacy and Food Engineering, Wuyi University, Jiangmen, Guangdong, China
| | - Jian-Yun Ge
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, and South China Institute of Large Animal Models for Biomedicine, School of Pharmacy and Food Engineering, Wuyi University, Jiangmen, Guangdong, China
| | - Min Ding
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, and South China Institute of Large Animal Models for Biomedicine, School of Pharmacy and Food Engineering, Wuyi University, Jiangmen, Guangdong, China
- Institute of Regenerative Medicine, and Department of Dermatology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yun-Wen Zheng
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, and South China Institute of Large Animal Models for Biomedicine, School of Pharmacy and Food Engineering, Wuyi University, Jiangmen, Guangdong, China
- Institute of Regenerative Medicine, and Department of Dermatology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
- Department of Medical and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo Univ of Science, Noda, Chiba, Japan
- Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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Kong W, He J, Zhou Q, Zhou X, Wei X, Yang Y, Mei Y, Wang S, Zhang X, Yao B, Yue Y, Xu J, Jiang M, Xu C. Histone lactylation-related genes correlate with the molecular patterns and functions of cancer-associated fibroblasts and have significant clinical implications in clear cell renal cell carcinoma. Heliyon 2024; 10:e33554. [PMID: 39035489 PMCID: PMC11259888 DOI: 10.1016/j.heliyon.2024.e33554] [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: 11/27/2023] [Revised: 06/22/2024] [Accepted: 06/24/2024] [Indexed: 07/23/2024] Open
Abstract
Recent research emphasised the indispensable role of histone lactylation in the activation of hepatic stellate cells. The VHL mutation is extremely common in clear cell renal cell carcinoma, which normally causes a metabolic shift in cancer cells and increases lactate production, eventually creating a lactate-enriched tumour microenvironment. Cancer-associated fibroblasts (CAFs) promote tumour progression, which is also vital in clear cell renal cell carcinoma. Therefore, this study investigated histone lactylation in CAFs and its impact on patient survival. Multiomics technology was employed to determine the role of histone lactylation-related genes in the evolution of CAFs which correlated with the function and molecular signatures of CAFs. The results suggested that TIMP1 was the hub gene of histone lactylation-related genes in clear cell renal cell carcinoma.
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Affiliation(s)
- Weiyu Kong
- Department of Urology, Suzhou Ninth People's Hospital, Soochow University, Suzhou, 215000, China
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Jiaxin He
- National Experimental Teaching Center of Basic Medical Science, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Qinyao Zhou
- National Experimental Teaching Center of Basic Medical Science, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Xin Zhou
- National Experimental Teaching Center of Basic Medical Science, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Xiyi Wei
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Yonglin Yang
- The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, China
| | - Yiwen Mei
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Shuai Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Xi Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Bing Yao
- National Experimental Teaching Center of Basic Medical Science, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Yulin Yue
- Department of Clinical Laboratory, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Jiali Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Minjun Jiang
- Department of Urology, Suzhou Ninth People's Hospital, Soochow University, Suzhou, 215000, China
| | - Chen Xu
- Department of Urology, Suzhou Ninth People's Hospital, Soochow University, Suzhou, 215000, China
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Pfaltzgraff NG, Liu B, de Rooij DG, Page DC, Mikedis MM. Destabilization of mRNAs enhances competence to initiate meiosis in mouse spermatogenic cells. Development 2024; 151:dev202740. [PMID: 38884383 PMCID: PMC11273298 DOI: 10.1242/dev.202740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/07/2024] [Indexed: 06/18/2024]
Abstract
The specialized cell cycle of meiosis transforms diploid germ cells into haploid gametes. In mammals, diploid spermatogenic cells acquire the competence to initiate meiosis in response to retinoic acid. Previous mouse studies revealed that MEIOC interacts with RNA-binding proteins YTHDC2 and RBM46 to repress mitotic genes and to promote robust meiotic gene expression in spermatogenic cells that have initiated meiosis. Here, we have used the enhanced resolution of scRNA-seq and bulk RNA-seq of developmentally synchronized spermatogenesis to define how MEIOC molecularly supports early meiosis in spermatogenic cells. We demonstrate that MEIOC mediates transcriptomic changes before meiotic initiation, earlier than previously appreciated. MEIOC, acting with YTHDC2 and RBM46, destabilizes its mRNA targets, including the transcriptional repressors E2f6 and Mga, in mitotic spermatogonia. MEIOC thereby derepresses E2F6- and MGA-repressed genes, including Meiosin and other meiosis-associated genes. This confers on spermatogenic cells the molecular competence to, in response to retinoic acid, fully activate the transcriptional regulator STRA8-MEIOSIN, which is required for the meiotic G1/S phase transition and for meiotic gene expression. We conclude that, in mice, mRNA decay mediated by MEIOC-YTHDC2-RBM46 enhances the competence of spermatogenic cells to initiate meiosis.
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Affiliation(s)
- Natalie G. Pfaltzgraff
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Bingrun Liu
- Whitehead Institute, Cambridge, MA 02142, USA
| | | | - David C. Page
- Whitehead Institute, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Maria M. Mikedis
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Whitehead Institute, Cambridge, MA 02142, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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He X, Long Q, Zhong Y, Zhang Y, Qian B, Huang S, Chang L, Qi Z, Li L, Wang X, Yang X, Dong Gao W, Ye X, Zhao Q. Short-chain fatty acids regulate erastin-induced cardiomyocyte ferroptosis and ferroptosis-related genes. Front Pharmacol 2024; 15:1409321. [PMID: 39070785 PMCID: PMC11272585 DOI: 10.3389/fphar.2024.1409321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/07/2024] [Indexed: 07/30/2024] Open
Abstract
Background Ferroptosis has been proven to contribute to the progression of myocardial ischemia/reperfusion (I/R) injury and can be inhibited or promoted by ATF3. Short-chain fatty acids (SCFAs) have shown benefits in various cardiovascular diseases with anti-inflammatory and antioxidant effects. However, the impact of SCFAs on ferroptosis in ischemic-stimulated cardiomyocytes remains unknown. This study aimed to investigate the effect of SCFAs on cardiomyocyte ferroptosis, the expression of ATF3, and its potential upstream regulators. Methods and results The expression of ATF3, ferroptosis pathway geneset (FPG), and geneset of potential regulators for ATF3 (GPRA, predicted by the PROMO database) was explored in the public human myocardial infarction single-cell RNA-seq (sma) dataset. Cardiomyocyte data was extracted from the dataset and re-clustered to explore the FPG, ATF3, and GPRA expression patterns in cardiomyocyte subclusters. A dose-dependent toxic experiment was run to detect the suitable dose for SCFA treatment. The erastin-induced ferroptosis model and hypoxia-reoxygenation (H/R) model (10 h of hypoxia followed by 6 h of reoxygenation) were adopted to assess the effect of SCFAs via the CCK8 assay. Gene expression was examined via RT-PCR and western blot. Ferroptosis markers, including lipid peroxides and Fe2+, were detected using the liperfluo and ferroOrange probes, respectively. In the sma dataset, upregulated ferroptosis pathway genes were mainly found in the infarction-stimulated cardiac cells (border zone and fibrotic zone), particularly the cardiomyocytes and adipocytes. The ATF3 and some of its potential transcription factors (VDR, EGR3, PAX5, and SP1) can be regulated by SCFA. SCFA can attenuate erastin-induced lipid peroxidation in cardiomyocytes. SCFA treatment can also reverse erastin-induced Fe2+ increase but may strengthen the Fe2+ in the H/R model. We also precisely defined a ferroptosis subcluster of cardiomyocytes (CM09) that highly expressed FPG, ATF3, and GPRA. Conclusion The ATF3 and the ferroptosis pathway are elevated in cardiomyocytes of injury-related cardiac regions (border zone, ischemic zone, and fibrotic zone). SCFA can attenuate cardiomyocyte ferroptosis and regulate the expression of ATF3. Our study offers novel insights into the potential targets of SCFAs in the cardiovascular system.
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Affiliation(s)
- Xiaojun He
- Department of Cardiovascular Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qiang Long
- Department of Cardiovascular Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yiming Zhong
- Department of Cardiovascular Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yecen Zhang
- Department of Cardiovascular Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Bei Qian
- Department of Cardiovascular Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Shixing Huang
- Department of Cardiovascular Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Lan Chang
- Department of Cardiovascular Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhaoxi Qi
- Department of Cardiovascular Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Lihui Li
- Department of Cardiovascular Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xinming Wang
- Department of Cardiovascular Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaomei Yang
- Department of Anesthesiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Cardiology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Wei Dong Gao
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Xiaofeng Ye
- Department of Cardiovascular Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qiang Zhao
- Department of Cardiovascular Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Chen Z, Yu M, Zhang B, Jin L, Yu Q, Liu S, Zhou B, Yan J, Zhang W, Li X, Xu Y, Xiao Y, Zhou J, Fan J, Hung MC, Ye Q, Li H, Guo L. SIGLEC15, negatively correlated with PD-L1 in HCC, could induce CD8+ T cell apoptosis to promote immune evasion. Oncoimmunology 2024; 13:2376264. [PMID: 38988824 PMCID: PMC11236293 DOI: 10.1080/2162402x.2024.2376264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 07/01/2024] [Indexed: 07/12/2024] Open
Abstract
Functional roles of SIGLEC15 in hepatocellular carcinoma (HCC) were not clear, which was recently found to be an immune inhibitor with similar structure of inhibitory B7 family members. SIGLEC15 expression in HCC was explored in public databases and further examined by PCR analysis. SIGLEC15 and PD-L1 expression patterns were examined in HCC samples through immunohistochemistry. SIGLEC15 expression was knocked-down or over-expressed in HCC cell lines, and CCK8 tests were used to examine cell proliferative ability in vitro. Influences of SIGLEC15 expression on tumor growth were examined in immune deficient and immunocompetent mice respectively. Co-culture system of HCC cell lines and Jurkat cells, flow cytometry analysis of tumor infiltrated immune cells and further sequencing analyses were performed to investigate how SIGLEC15 could affect T cells in vitro and in vivo. We found SIGLEC15 was increased in HCC tumor tissues and was negatively correlated with PD-L1 in HCC samples. In vitro and in vivo models demonstrated inhibition of SIGLEC15 did not directly influence tumor proliferation. However, SIGLEC15 could promoted HCC immune evasion in immune competent mouse models. Knock-out of Siglec15 could inhibit tumor growth and reinvigorate CD8+ T cell cytotoxicity. Anti-SIGLEC15 treatment could effectively inhibit tumor growth in mouse models with or without mononuclear phagocyte deletion. Bulk and single-cell RNA sequencing data of treated mouse tumors demonstrated SIGLEC15 could interfere CD8+ T cell viability and induce cell apoptosis. In all, SIGLEC15 was negatively correlated with PD-L1 in HCC and mainly promote HCC immune evasion through inhibition of CD8+ T cell viability and cytotoxicity.
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Affiliation(s)
- Zheng Chen
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, P.R. China
| | - Mincheng Yu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, P.R. China
| | - Bo Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, P.R. China
| | - Lei Jin
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, P.R. China
| | - Qiang Yu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, P.R. China
| | - Shuang Liu
- Neurosurgery Department of Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Binghai Zhou
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, P.R. China
| | - Jiuliang Yan
- Department of Pancreatic Surgery, Shanghai General Hospital and Shanghai Key Laboratory of Pancreatic Disease, Institute of Pancreatic Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Wentao Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, P.R. China
| | - Xiaoqiang Li
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen, P.R. China
| | - Yongfeng Xu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, P.R. China
| | - Yongsheng Xiao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, P.R. China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, P.R. China
| | - Jia Fan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, P.R. China
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences, Research Center for Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung, TX, Taiwan
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Qinghai Ye
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, P.R. China
| | - Hui Li
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, P.R. China
- Shanghai Medical College and Zhongshan Hospital Immunotherapy Translational Research Center, Shanghai, P.R. China
| | - Lei Guo
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, P.R. China
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Zhou J, Guruvayurappan K, Toneyan S, Chen HV, Chen AR, Koo P, McVicker G. Analysis of single-cell CRISPR perturbations indicates that enhancers act multiplicatively and provides limited evidence for epistatic-like interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.26.538501. [PMID: 37163096 PMCID: PMC10168320 DOI: 10.1101/2023.04.26.538501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A single gene may have multiple enhancers, but how they work in concert to regulate transcription is poorly understood. To analyze enhancer interactions throughout the genome, we developed a generalized linear modeling framework, GLiMMIRS, for interrogating enhancer effects from single-cell CRISPR experiments. We applied GLiMMIRS to a published dataset and tested for interactions between 46,166 enhancer pairs and corresponding genes, including 264 'high-confidence' enhancer pairs. We found that enhancer effects combine multiplicatively but with limited evidence for further interactions. Only 31 enhancer pairs exhibited significant interactions (FDR < 0.1), of which none came from the high confidence subset and 20 were driven by outlier expression values. Additional analyses of a second CRISPR dataset and in silico enhancer perturbations with Enformer both support a multiplicative model of enhancer effects without interactions. Altogether, our results indicate that enhancer interactions are uncommon or have small effects that are difficult to detect.
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Affiliation(s)
- Jessica Zhou
- Integrative Biology Laboratory, Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724
| | - Karthik Guruvayurappan
- Integrative Biology Laboratory, Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA
- School of Biological Sciences, University of California San Diego, La Jolla, CA, 92037, USA
- Halicioglu Data Science Institute, University of California San Diego, La Jolla, CA, 92093, USA
- Memorial Sloan Kettering Cancer Center, 1275 York Avenue New York NY 10065
| | - Shushan Toneyan
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724
| | - Hsiuyi V. Chen
- Integrative Biology Laboratory, Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA
- Current address: A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore 138648, Singapore
| | - Aaron R. Chen
- Integrative Biology Laboratory, Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA
- Current address: Renaissance School of Medicine at Stony Brook University, Stony Brook, NY, 11794, USA
| | - Peter Koo
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724
| | - Graham McVicker
- Integrative Biology Laboratory, Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA
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Jin C, Chen Y, Wang Y, Li J, Liang J, Zheng S, Zhang L, Li Q, Wang Y, Ling F, Li Y, Zheng Y, Nie Q, Feng Q, Wang J, Yang H. Single-cell RNA sequencing reveals special basal cells and fibroblasts in idiopathic pulmonary fibrosis. Sci Rep 2024; 14:15778. [PMID: 38982264 PMCID: PMC11233624 DOI: 10.1038/s41598-024-66947-5] [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: 03/30/2024] [Accepted: 07/05/2024] [Indexed: 07/11/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is the most predominant type of idiopathic interstitial pneumonia and has an increasing incidence, poor prognosis, and unclear pathogenesis. In order to investigate the molecular mechanisms underlying IPF further, we performed single-cell RNA sequencing analysis on three healthy controls and five IPF lung tissue samples. The results revealed a significant shift in epithelial cells (ECs) phenotypes in IPF, which may be attributed to the differentiation of alveolar type 2 cells to basal cells. In addition, several previously unrecognized basal cell subtypes were preliminarily identified, including extracellular matrix basal cells, which were increased in the IPF group. We identified a special population of fibroblasts that highly expressed extracellular matrix-related genes, POSTN, CTHRC1, COL3A1, COL5A2, and COL12A1. We propose that the close interaction between ECs and fibroblasts through ligand-receptor pairs may have a critical function in IPF development. Collectively, these outcomes provide innovative perspectives on the complexity and diversity of basal cells and fibroblasts in IPF and contribute to the understanding of possible mechanisms in pathological lung fibrosis.
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Affiliation(s)
- Chengji Jin
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Yahong Chen
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Yujie Wang
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Jia Li
- The Second Affiliated Clinical College, Hainan Medical University, Haikou, 570100, China
| | - Jin Liang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Shaomao Zheng
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Lipeng Zhang
- The Second Affiliated Clinical College, Hainan Medical University, Haikou, 570100, China
| | - Qiaoyu Li
- The Second Affiliated Clinical College, Hainan Medical University, Haikou, 570100, China
| | - Yongchao Wang
- Singleron Biotechnologies, Yaogu Avenue 11, Nanjing, 211800, China
| | - Fayu Ling
- Department of Thoracic Surgery, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Yongjie Li
- Department of Thoracic Surgery, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Yu Zheng
- The Second Affiliated Clinical College, Hainan Medical University, Haikou, 570100, China
| | - Qiuli Nie
- The Second Affiliated Clinical College, Hainan Medical University, Haikou, 570100, China
| | - Qiong Feng
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Jing Wang
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China.
- NHC Key Laboratory of Tropical Disease Control, Hainan Medical University, Haikou, 571199, China.
| | - Huiling Yang
- School of Pharmacy, Guangdong Medical University, Dongguan, 523808, China.
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Zhang C, Xiao D, Shu L, Gong M, Liu X, Jiang X. Single-cell RNA sequencing uncovers cellular heterogeneity and the progression of heterotopic ossification of the elbow. Front Pharmacol 2024; 15:1434146. [PMID: 39045052 PMCID: PMC11264200 DOI: 10.3389/fphar.2024.1434146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 06/13/2024] [Indexed: 07/25/2024] Open
Abstract
Heterotopic ossification of the elbow (HOE) is a complicated pathologic process characterized by extra bone formation in the elbow. Bone formation is a complex developmental process involving the differentiation of mesenchymal stem cells into osteoblasts. The aim of this study was to explore the cellular origin and progression of HOE by single-cell RNA sequencing. We identified 13 clusters of cells in HOE and further analyzed the subclusters for 4 of the main cell types. Six subclusters of osteoblasts, nine subclusters of chondrocytes, six subclusters of fibroblasts, and five subclusters of mononuclear phagocytes (MPs) were identified and analyzed. The new findings on osterix (OSX) and SOX9 expression in osteoblast subclusters and chondrocyte subclusters indicate that HOE is mediated through endochondral ossification. Further identification of the corresponding signature gene sets of distinct subclusters indicated that subclusters of osteoblasts_3, osteoblasts_4, osteoblasts_5, and osteoblasts_6 are relatively more mature during the osteoblastic progression of HOE. The trajectory analysis of the osteoblasts demonstrated that some genes were gradually downregulated, such as CRYAB, CCL3, SFRP4, WIF1, and IGFBP3, while other critical genes were upregulated, such as VCAN, IGFBP4, FSTL1, POSTN, MDK, THBS2, and ALPL, suggesting that these factors may participate in HOE progression. Cell-cell communication networks revealed extensive molecular interactions among the 13 HOE clusters. Ligand-receptor pairs for IL6, COL24A1, COL22A1, VWF, FZD6, FGF2, and NOTCH1 were identified, suggesting that multiple signaling pathways may be involved in HOE. In conclusion, this study provided the cellular atlas for HOE. We have established a greater extent of the heterogeneity of HOE cells than previously known through transcriptomic analysis at the single-cell level. We have observed gradual patterns of signature gene expression during the differentiation and maturation progression of osteoblasts from stem cells in HOE with higher resolution. The cell heterogeneity of HOE deserves further investigation to pave the way for identification of potential targets for HOE early diagnosis and therapeutic treatment.
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Affiliation(s)
- Chi Zhang
- Department of Orthopedics, Peking University International Hospital, Beijing, China
- Biomedical Engineering Department, Institute of Advanced Clinical Medicine, Peking University, Beijing, China
| | - Dan Xiao
- Department of Orthopedic Surgery, Beijing Jishuitan Hospital, Beijing, China
| | - Li Shu
- Department of Orthopedics, Peking University International Hospital, Beijing, China
| | - Maoqi Gong
- Department of Orthopedic Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Xinghua Liu
- Department of Orthopedic Surgery, Beijing Jishuitan Hospital, Beijing, China
| | - Xieyuan Jiang
- Department of Orthopedic Surgery, Beijing Jishuitan Hospital, Beijing, China
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Schnell J, Miao Z, Achieng M, Fausto CC, Wang V, Kuyper FD, Thornton ME, Grubbs B, Kim J, Lindström NO. Stepwise developmental mimicry generates proximal-biased kidney organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601028. [PMID: 39005387 PMCID: PMC11244853 DOI: 10.1101/2024.06.28.601028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The kidney maintains body fluid homeostasis by reabsorbing essential compounds and excreting waste. Proximal tubule cells, crucial for renal reabsorption of a range of sugars, ions, and amino acids, are highly susceptible to damage, leading to pathologies necessitating dialysis and kidney transplants. While human pluripotent stem cell-derived kidney organoids are used for modeling renal development, disease, and injury, the formation of proximal nephron cells in these 3D structures is incomplete. Here, we describe how to drive the development of proximal tubule precursors in kidney organoids by following a blueprint of in vivo human nephrogenesis. Transient manipulation of the PI3K signaling pathway activates Notch signaling in the early nephron and drives nephrons toward a proximal precursor state. These "proximal-biased" (PB) organoid nephrons proceed to generate proximal nephron precursor cells. Single-cell transcriptional analyses across the organoid nephron differentiation, comparing control and PB types, confirm the requirement of transient Notch signaling for proximal development. Indicative of functional maturity, PB organoids demonstrate dextran and albumin uptake, akin to in vivo proximal tubules. Moreover, PB organoids are highly sensitive to nephrotoxic agents, display an injury response, and drive expression of HAVCR1 / KIM1 , an early proximal-specific marker of kidney injury. Injured PB organoids show evidence of collapsed tubules, DNA damage, and upregulate the injury-response marker SOX9 . The PB organoid model therefore has functional relevance and potential for modeling mechanisms underpinning nephron injury. These advances improve the use of iPSC-derived kidney organoids as tools to understand developmental nephrology, model disease, test novel therapeutics, and for understanding human renal physiology.
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Mao Z, Gao Z, Long R, Guo H, Chen L, Huan S, Yin G. Mitotic catastrophe heterogeneity: implications for prognosis and immunotherapy in hepatocellular carcinoma. Front Immunol 2024; 15:1409448. [PMID: 39015573 PMCID: PMC11250588 DOI: 10.3389/fimmu.2024.1409448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 06/17/2024] [Indexed: 07/18/2024] Open
Abstract
Background and aims The mitotic catastrophe (MC) pathway plays an important role in hepatocellular carcinoma (HCC) progression and tumor microenvironment (TME) regulation. However, the mechanisms linking MC heterogeneity to immune evasion and treatment response remain unclear. Methods Based on 94 previously published highly correlated genes for MC, HCC patients' data from the Cancer Genome Atlas (TCGA) and changes in immune signatures and prognostic stratification were studied. Time and spatial-specific differences for MCGs were assessed by single-cell RNA sequencing and spatial transcriptome (ST) analysis. Multiple external databases (GEO, ICGC) were employed to construct an MC-related riskscore model. Results Identification of two MC-related subtypes in HCC patients from TCGA, with clear differences in immune signatures and prognostic risk stratification. Spatial mapping further associates low MC tumor regions with significant immune escape-related signaling. Nomogram combining MC riskscore and traditional indicators was validated great effect for early prediction of HCC patient outcomes. Conclusion MC heterogeneity enables immune escape and therapy resistance in HCC. The MC gene signature serves as a reliable prognostic indicator for liver cancer. By revealing clear immune and spatial heterogeneity of HCC, our integrated approach provides contextual therapeutic strategies for optimal clinical decision-making.
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Affiliation(s)
- Zun Mao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhixiang Gao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ruyu Long
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Huimin Guo
- Department of Gastroenterology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Long Chen
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Sheng Huan
- Department of Anesthesiology and Perioperative Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Guoping Yin
- Department of Anesthesiology, Nanjing Second Hospital, Nanjing, China
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Xu D, Zhuang X, Ma H, Li Z, Wei L, Luo J, Han H. Altered tumor microenvironment heterogeneity of penile cancer during progression from non-lymphatic to lymphatic metastasis. Cancer Med 2024; 13:e70025. [PMID: 39003681 PMCID: PMC11246611 DOI: 10.1002/cam4.70025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024] Open
Abstract
BACKGROUND Lymphatic metastasis is the major challenge in the treatment of penile cancer. The prognosis of individuals with lymphatic metastasis is extremely poor. Therefore, early identification of disease progression and lymphatic metastasis is an urgent task for researchers in penile cancer worldwide. METHODS In this study, using single-cell RNA sequencing, an immune landscape was established for the cancer ecosystem based on 46,861 cells from six patients with penile cancer (four with lymphatic metastasis [stage IV] and two without lymphatic metastasis [stage I]). Using bulk RNA sequencing, the discrepancy between the cancers and their respective metastatic lymph nodes was depicted based on seven patients with penile cancer. RESULTS The interaction between epithelial cells, fibroblasts, and endothelial cells, and the functional cooperation among invasion, epithelial-mesenchymal transition, and angiogenesis were found to be important landscapes in the penile cancer ecosystem, playing important roles in progression of cancer and lymph node metastasis. CONCLUSIONS This study is the first to investigate the altered tumor microenvironment heterogeneity of penile cancer as it evolves from non-lymphatic to lymphatic metastasis and provides insights into the mechanisms underlying malignant progression, the premetastatic niche, and lymphatic metastasis in penile cancer.
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Affiliation(s)
- Da‐Ming Xu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouP. R. China
- Department of UrologySun Yat‐sen University Cancer CenterGuangzhouP. R. China
| | - Xiao‐Yu Zhuang
- Department of AnesthesiologySecond Affiliated Hospital of Shantou University Medical CollegeShantouP. R. China
| | - Hua‐Li Ma
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouP. R. China
- Department of RadiologySun Yat‐sen University Cancer CenterGuangzhouP. R. China
| | - Zai‐Shang Li
- Department of Urology, Shenzhen People's HospitalThe Second Clinic Medical College of Jinan UniversityShenzhenP. R. China
| | - Li‐Chao Wei
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouP. R. China
- Department of UrologySun Yat‐sen University Cancer CenterGuangzhouP. R. China
| | - Jun‐Hang Luo
- Department of Urology, First Affiliated HospitalSun Yat‐sen UniversityGuangzhouP. R. China
- Institute of Precision Medicine, First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouP. R. China
| | - Hui Han
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouP. R. China
- Department of UrologySun Yat‐sen University Cancer CenterGuangzhouP. R. China
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129
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Sun H, Han X, Du Z, Chen G, Guo T, Xie F, Gu W, Shi Z. Machine learning for the identification of neoantigen-reactive CD8 + T cells in gastrointestinal cancer using single-cell sequencing. Br J Cancer 2024; 131:387-402. [PMID: 38849478 PMCID: PMC11263575 DOI: 10.1038/s41416-024-02737-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND It appears that tumour-infiltrating neoantigen-reactive CD8 + T (Neo T) cells are the primary driver of immune responses to gastrointestinal cancer in patients. However, the conventional method is very time-consuming and complex for identifying Neo T cells and their corresponding T cell receptors (TCRs). METHODS By mapping neoantigen-reactive T cells from the single-cell transcriptomes of thousands of tumour-infiltrating lymphocytes, we developed a 26-gene machine learning model for the identification of neoantigen-reactive T cells. RESULTS In both training and validation sets, the model performed admirably. We discovered that the majority of Neo T cells exhibited notable differences in the biological processes of amide-related signal pathways. The analysis of potential cell-to-cell interactions, in conjunction with spatial transcriptomic and multiplex immunohistochemistry data, has revealed that Neo T cells possess potent signalling molecules, including LTA, which can potentially engage with tumour cells within the tumour microenvironment, thereby exerting anti-tumour effects. By sequencing CD8 + T cells in tumour samples of patients undergoing neoadjuvant immunotherapy, we determined that the fraction of Neo T cells was significantly and positively linked with the clinical benefit and overall survival rate of patients. CONCLUSION This method expedites the identification of neoantigen-reactive TCRs and the engineering of neoantigen-reactive T cells for therapy.
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Affiliation(s)
- Hongwei Sun
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiao Han
- KangChen Bio-tech., Ltd, ShangHai, China
| | - Zhengliang Du
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Geer Chen
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Tonglei Guo
- Data and Analysis Center for Genetic Diseases, Beijing Chigene Translational Medicine Research Center Co, Ltd, Tongzhou District, Beijing, China
| | - Fei Xie
- Data and Analysis Center for Genetic Diseases, Beijing Chigene Translational Medicine Research Center Co, Ltd, Tongzhou District, Beijing, China
| | - Weiyue Gu
- Data and Analysis Center for Genetic Diseases, Beijing Chigene Translational Medicine Research Center Co, Ltd, Tongzhou District, Beijing, China
- Chineo Medical Technology Co., Ltd, Beijing, 100101, China
| | - Zhiwen Shi
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
- Data and Analysis Center for Genetic Diseases, Beijing Chigene Translational Medicine Research Center Co, Ltd, Tongzhou District, Beijing, China.
- Chineo Medical Technology Co., Ltd, Beijing, 100101, China.
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Sun Y, Dong L, Kang L, Zhong W, Jackson D, Yang F. Progressive meristem and single-cell transcriptomes reveal the regulatory mechanisms underlying maize inflorescence development and sex differentiation. MOLECULAR PLANT 2024; 17:1019-1037. [PMID: 38877701 DOI: 10.1016/j.molp.2024.06.007] [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: 12/07/2023] [Revised: 05/23/2024] [Accepted: 06/11/2024] [Indexed: 06/16/2024]
Abstract
Maize develops separate ear and tassel inflorescences with initially similar morphology but ultimately different architecture and sexuality. The detailed regulatory mechanisms underlying these changes still remain largely unclear. In this study, through analyzing the time-course meristem transcriptomes and floret single-cell transcriptomes of ear and tassel, we revealed the regulatory dynamics and pathways underlying inflorescence development and sex differentiation. We identified 16 diverse gene clusters with differential spatiotemporal expression patterns and revealed biased regulation of redox, programmed cell death, and hormone signals during meristem differentiation between ear and tassel. Notably, based on their dynamic expression patterns, we revealed the roles of two RNA-binding proteins in regulating inflorescence meristem activity and axillary meristem formation. Moreover, using the transcriptional profiles of 53 910 single cells, we uncovered the cellular heterogeneity between ear and tassel florets. We found that multiple signals associated with either enhanced cell death or reduced growth are responsible for tassel pistil suppression, while part of the gibberellic acid signal may act non-cell-autonomously to regulate ear stamen arrest during sex differentiation. We further showed that the pistil-protection gene SILKLESS 1 (SK1) functions antagonistically to the known pistil-suppression genes through regulating common molecular pathways, and constructed a regulatory network for pistil-fate determination. Collectively, our study provides a deep understanding of the regulatory mechanisms underlying inflorescence development and sex differentiation in maize, laying the foundation for identifying new regulators and pathways for maize hybrid breeding and improvement.
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Affiliation(s)
- Yonghao Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Liang Dong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lu Kang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wanshun Zhong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - David Jackson
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; School of Agriculture, Sun Yat-Sen University, Shenzhen 518107, China.
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131
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Gu L, Chen H, Sun M, Chen Y, Shi Q, Chang J, Wei J, Ma W, Bao X, Wang R. Unraveling dynamic immunological landscapes in intracerebral hemorrhage: insights from single-cell and spatial transcriptomic profiling. MedComm (Beijing) 2024; 5:e635. [PMID: 38988493 PMCID: PMC11233862 DOI: 10.1002/mco2.635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 07/12/2024] Open
Abstract
Intracerebral hemorrhage (ICH) poses a formidable challenge in stroke management, with limited therapeutic options, particularly in the realm of immune-targeted interventions. Clinical trials targeting immune responses post-ICH have encountered setbacks, potentially attributable to the substantial cellular heterogeneity and intricate intercellular networks within the brain. Here, we present a pioneering investigation utilizing single-cell RNA sequencing and spatial transcriptome profiling at hyperacute (1 h), acute (24 h), and subacute (7 days) intervals post-ICH, aimed at unraveling the dynamic immunological landscape and spatial distributions within the cerebral tissue. Our comprehensive analysis revealed distinct cell differentiation patterns among myeloid and lymphocyte populations, along with delineated spatial distributions across various brain regions. Notably, we identified a subset of lymphocytes characterized by the expression of Spp1 and Lyz2, termed macrophage-associated lymphocytes, which exhibited close interactions with myeloid cells. Specifically, we observed prominent interactions between Lgmn+Macro-T cells and microglia through the spp1-cd44 pathway during the acute phase post-ICH in the choroid plexus. These findings represent a significant advancement in our understanding of immune cell dynamics at single-cell resolution across distinct post-ICH time points, thereby laying the groundwork for exploring critical temporal windows and informing the development of targeted therapeutic strategies.
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Affiliation(s)
- Lingui Gu
- Department of NeurosurgeryPeking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Hualin Chen
- Department of NeurosurgeryPeking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Mingjiang Sun
- Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical UniversityBeijingChina
| | - Yihao Chen
- Department of NeurosurgeryPeking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Qinglei Shi
- Research Institute of Big Data, Chinese University of Hong Kong (Shenzhen) School of MedicineShenzhenChina
| | - Jianbo Chang
- Department of NeurosurgeryPeking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Junji Wei
- Department of NeurosurgeryPeking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Wenbin Ma
- Department of NeurosurgeryPeking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Xinjie Bao
- Department of NeurosurgeryPeking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- State Key Laboratory of Common Mechanism Research for Major DiseasesBeijingChina
| | - Renzhi Wang
- Department of NeurosurgeryPeking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- School of MedicineThe Chinese University of Hong KongShenzhenGuangdongChina
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132
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Patel JR, Joel MZ, Lee KK, Kambala A, Cornman H, Oladipo O, Taylor M, Imo BU, Ma EZ, Manjunath J, Kollhoff AL, Deng J, Parthasarathy V, Cravero K, Marani M, Szeto M, Zhao R, Sankararaman S, Li R, Henry S, Pritchard T, Rebecca V, Kwatra MM, Ho WJ, Dong X, Kang S, Kwatra SG. Single-Cell RNA Sequencing Reveals Dysregulated POSTN+WNT5A+ Fibroblast Subclusters in Prurigo Nodularis. J Invest Dermatol 2024; 144:1568-1578.e5. [PMID: 38246584 DOI: 10.1016/j.jid.2023.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/17/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024]
Abstract
Prurigo nodularis (PN) is an intensely pruritic, inflammatory skin disease with a poorly understood pathogenesis. We performed single-cell transcriptomic profiling of 28,695 lesional and nonlesional PN cells. Lesional PN has increased dysregulated fibroblasts (FBs) and myofibroblasts. FBs in lesional PN were shifted toward a cancer-associated FB-like phenotype, with POSTN+WNT5A+ cancer-associated FBs increased in PN and similarly so in squamous cell carcinoma. A multicenter cohort study revealed an increased risk of squamous cell carcinoma and cancer-associated FB-associated malignancies (breast and colorectal) in patients with PN. Systemic fibroproliferative diseases (renal sclerosis and idiopathic pulmonary fibrosis) were upregulated in patients with PN. Ligand-receptor analyses demonstrated an FB neuronal axis with FB-derived WNT5A and periostin interactions with neuronal receptors melanoma cell adhesion molecule and ITGAV. These findings identify a pathogenic and targetable POSTN+WNT5A+ FB subpopulation that may predispose cancer-associated FB-associated malignancies in patients with PN.
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Affiliation(s)
- Jay R Patel
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Marina Z Joel
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kevin K Lee
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Anusha Kambala
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hannah Cornman
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Olusola Oladipo
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Matthew Taylor
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brenda Umenita Imo
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Emily Z Ma
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jaya Manjunath
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alexander L Kollhoff
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - June Deng
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Varsha Parthasarathy
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Karen Cravero
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Melika Marani
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mindy Szeto
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ryan Zhao
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sreenidhi Sankararaman
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ruixiang Li
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Shanae Henry
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Thomas Pritchard
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Vito Rebecca
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Madan M Kwatra
- Department of Anesthesiology, Duke University School of Medicine, Durham, North Carolina, USA; Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Won Jin Ho
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Xinzhong Dong
- The Solomon H. Snyder Department of Neuroscience, Center for Sensory Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sewon Kang
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Shawn G Kwatra
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
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133
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Wang J, Wen S, Chen M, Xie J, Lou X, Zhao H, Chen Y, Zhao M, Shi G. Regulation of endocrine cell alternative splicing revealed by single-cell RNA sequencing in type 2 diabetes pathogenesis. Commun Biol 2024; 7:778. [PMID: 38937540 PMCID: PMC11211498 DOI: 10.1038/s42003-024-06475-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 06/19/2024] [Indexed: 06/29/2024] Open
Abstract
The prevalent RNA alternative splicing (AS) contributes to molecular diversity, which has been demonstrated in cellular function regulation and disease pathogenesis. However, the contribution of AS in pancreatic islets during diabetes progression remains unclear. Here, we reanalyze the full-length single-cell RNA sequencing data from the deposited database to investigate AS regulation across human pancreatic endocrine cell types in non-diabetic (ND) and type 2 diabetic (T2D) individuals. Our analysis demonstrates the significant association between transcriptomic AS profiles and cell-type-specificity, which could be applied to distinguish the clustering of major endocrine cell types. Moreover, AS profiles are enabled to clearly define the mature subset of β-cells in healthy controls, which is completely lost in T2D. Further analysis reveals that RNA-binding proteins (RBPs), heterogeneous nuclear ribonucleoproteins (hnRNPs) and FXR1 family proteins are predicted to induce the functional impairment of β-cells through regulating AS profiles. Finally, trajectory analysis of endocrine cells suggests the β-cell identity shift through dedifferentiation and transdifferentiation of β-cells during the progression of T2D. Together, our study provides a mechanism for regulating β-cell functions and suggests the significant contribution of AS program during diabetes pathogenesis.
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Affiliation(s)
- Jin Wang
- Department of Endocrinology & Metabolism, Medical Center for Comprehensive Weight Control, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Shiyi Wen
- Department of Endocrinology & Metabolism, Medical Center for Comprehensive Weight Control, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Minqi Chen
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou, Guangdong, China
| | - Jiayi Xie
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou, Guangdong, China
| | - Xinhua Lou
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Haihan Zhao
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yanming Chen
- Department of Endocrinology & Metabolism, Medical Center for Comprehensive Weight Control, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Diabetology & Guangzhou Municipal Key Laboratory of Mechanistic and Translational Obesity Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Meng Zhao
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou, Guangdong, China.
| | - Guojun Shi
- Department of Endocrinology & Metabolism, Medical Center for Comprehensive Weight Control, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.
- Guangdong Provincial Key Laboratory of Diabetology & Guangzhou Municipal Key Laboratory of Mechanistic and Translational Obesity Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.
- State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.
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134
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Hashemi E, McCarthy C, Rao S, Malarkannan S. Transcriptomic diversity of innate lymphoid cells in human lymph nodes compared to BM and spleen. Commun Biol 2024; 7:769. [PMID: 38918571 PMCID: PMC11199704 DOI: 10.1038/s42003-024-06450-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 06/12/2024] [Indexed: 06/27/2024] Open
Abstract
Innate lymphoid cells (ILCs) are largely tissue-resident, mostly described within the mucosal tissues. However, their presence and functions in the human draining lymph nodes (LNs) are unknown. Our study unravels the tissue-specific transcriptional profiles of 47,287 CD127+ ILCs within the human abdominal and thoracic LNs. LNs contain a higher frequency of CD127+ ILCs than in BM or spleen. We define independent stages of ILC development, including EILP and pILC in the BM. These progenitors exist in LNs in addition to naïve ILCs (nILCs) that can differentiate into mature ILCs. We define three ILC1 and four ILC3 sub-clusters in the LNs. ILC1 and ILC3 subsets have clusters with high heat shock protein-encoding genes. We identify previously unrecognized regulons, including the BACH2 family for ILC1 and the ATF family for ILC3. Our study is the comprehensive characterization of ILCs in LNs, providing an in-depth understanding of ILC-mediated immunity in humans.
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Affiliation(s)
- Elaheh Hashemi
- Blood Research Institute, Versiti, Milwaukee, WI, USA
- Department of Microbiology and Immunology, Medical College of Wisconsin (MCW), Milwaukee, WI, USA
| | | | - Sridhar Rao
- Blood Research Institute, Versiti, Milwaukee, WI, USA
- Division of Hematology, Oncology, and Bone Marrow Transplantation, Department of Pediatrics, MCW, Milwaukee, WI, USA
- Department of Cell Biology, Neurobiology, and Anatomy, MCW, Milwaukee, WI, USA
| | - Subramaniam Malarkannan
- Blood Research Institute, Versiti, Milwaukee, WI, USA.
- Department of Microbiology and Immunology, Medical College of Wisconsin (MCW), Milwaukee, WI, USA.
- Division of Hematology, Oncology, and Bone Marrow Transplantation, Department of Pediatrics, MCW, Milwaukee, WI, USA.
- Division of Hematology and Oncology, Department of Medicine, MCW, Milwaukee, WI, USA.
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135
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He W, Yao C, Wang K, Duan Z, Wang S, Xie L. Single-cell landscape of immunological responses in elderly patients with sepsis. Immun Ageing 2024; 21:40. [PMID: 38909272 PMCID: PMC11193269 DOI: 10.1186/s12979-024-00446-z] [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: 04/30/2024] [Accepted: 06/11/2024] [Indexed: 06/24/2024]
Abstract
Sepsis is a dysregulated host response to severe infections, and immune dysfunction plays a crucial role in its pathogenesis. Elderly patients, a special population influenced by immunosenescence, are more susceptible to sepsis and have a worse prognosis. However, the immunopathogenic mechanisms underlying sepsis in elderly patients remain unclear. Here, we performed single-cell RNA sequencing of peripheral blood samples from young and old subjects and patients with sepsis. By exploring the transcriptional profiles of immune cells, we analyzed immune cell compositions, phenotype shifts, expression heterogeneities, and intercellular communication. In elderly patients with sepsis, innate immune cells (e.g., monocytes and DCs) exhibit decreased antigen presentation, presenting an overactive inflammatory and senescent phenotype. However, the immunophenotype of T cells shifted to characterize effector, memory, and exhaustion. Moreover, we identified strong interferon-γ responses of T cells in both aging and sepsis groups and a deranged inflammaging status in elderly sepsis patients. Tregs in elderly patients with sepsis showed increased abundance and enhanced immunosuppressive effects. In addition, metabolism-associated pathways were upregulated in T cells in elderly patients with sepsis, and the lysine metabolism pathway was enriched in Tregs. Cell-cell interaction analysis showed that the expression profile of ligand-receptor pairs was probably associated with aggravated immune dysfunction in elderly patients with sepsis. A novel HLA-KIR interaction was observed between Tregs and CD8 + T cells. These findings illustrate the immunological hallmarks of sepsis in elderly patients, and highlight that immunosuppressive and metabolic regulatory pathways may undergo important alterations in elderly patients with sepsis.
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Affiliation(s)
- Wanxue He
- Department of Pulmonary and Critical Care Medicine, Xuanwu Hospital Capital Medical University, Beijing, China
- College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Chen Yao
- College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Kaifei Wang
- College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Zhimei Duan
- College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Shuo Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Lixin Xie
- College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China.
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136
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Li S, Yang M, Shen H, Ding L, Lyu X, Lin K, Ong J, Du P. Capturing totipotency in human cells through spliceosomal repression. Cell 2024; 187:3284-3302.e23. [PMID: 38843832 DOI: 10.1016/j.cell.2024.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 09/01/2023] [Accepted: 05/03/2024] [Indexed: 06/23/2024]
Abstract
The cleavage of zygotes generates totipotent blastomeres. In human 8-cell blastomeres, zygotic genome activation (ZGA) occurs to initiate the ontogenesis program. However, capturing and maintaining totipotency in human cells pose significant challenges. Here, we realize culturing human totipotent blastomere-like cells (hTBLCs). We find that splicing inhibition can transiently reprogram human pluripotent stem cells into ZGA-like cells (ZLCs), which subsequently transition into stable hTBLCs after long-term passaging. Distinct from reported 8-cell-like cells (8CLCs), both ZLCs and hTBLCs widely silence pluripotent genes. Interestingly, ZLCs activate a particular group of ZGA-specific genes, and hTBLCs are enriched with pre-ZGA-specific genes. During spontaneous differentiation, hTBLCs re-enter the intermediate ZLC stage and further generate epiblast (EPI)-, primitive endoderm (PrE)-, and trophectoderm (TE)-like lineages, effectively recapitulating human pre-implantation development. Possessing both embryonic and extraembryonic developmental potency, hTBLCs can autonomously generate blastocyst-like structures in vitro without external cell signaling. In summary, our study provides key criteria and insights into human cell totipotency.
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Affiliation(s)
- Shiyu Li
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Min Yang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hui Shen
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Li Ding
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xuehui Lyu
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Kexin Lin
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jennie Ong
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Peng Du
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Beijing Advanced Center of RNA Biology, Peking University, Beijing 100871, China.
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137
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Iamsawat S, Yu R, Kim S, Dvorina N, Qiu K, Choi J, Baldwin WM, Min B. Single-Cell Analysis Uncovers Striking Cellular Heterogeneity of Lung-Infiltrating Regulatory T Cells during Eosinophilic versus Neutrophilic Allergic Airway Inflammation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1867-1876. [PMID: 38647384 PMCID: PMC11147735 DOI: 10.4049/jimmunol.2300646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 03/28/2024] [Indexed: 04/25/2024]
Abstract
Allergic airway inflammation results from uncontrolled immune responses to environmental Ags. Although it is well established that allergic immune responses exhibit a high degree of diversity, driven by primary effector cell types such as eosinophils, neutrophils, or CD4 T cells with distinct effector signatures, the mechanisms responsible for such pathogenesis remain elusive. Foxp3+ regulatory T cells (Tregs) are essential immune regulators during chronic inflammation, including allergic airway inflammation. Emerging evidence suggests that Tregs infiltrating inflamed tissues exhibit distinct phenotypes dependent on the specific tissue sites and can display heterogeneity and tissue residency. Whether diverse allergic airway inflammatory responses influence infiltrating Treg heterogeneity or Treg lung residency has not been explored. We employed an unbiased single-cell RNA sequencing approach to investigate lung-infiltrating Tregs in models of eosinophilic and neutrophilic airway inflammation. We found that lung-infiltrating Tregs are highly heterogeneous, and that Tregs displaying lung-resident phenotypes are significantly different depending on the types of inflammation. Treg expression of ST2, a receptor for alarmin IL-33, was predominantly associated with eosinophilic inflammation and tissue residency. Nevertheless, Treg-specific ST2 deficiency did not affect the development of eosinophilic allergic inflammation or the generation of lung-resident Tregs. These results uncover a stark heterogeneity among Tregs infiltrating the lungs during allergic airway inflammation. The results indicate that varying types of inflammation may give rise to phenotypically distinct lung-resident Tregs, underscoring a (to our knowledge) novel mechanism by which inflammatory cues may shape the composition of infiltrating Tregs, allowing them to regulate inflammatory responses through tissue-adapted mechanisms.
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Affiliation(s)
- Supinya Iamsawat
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Rongzhen Yu
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Sohee Kim
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Nina Dvorina
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH
| | - Kevin Qiu
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Jaehyuk Choi
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL
- Center for Human Immunobiology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - William M Baldwin
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH
| | - Booki Min
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL
- Center for Human Immunobiology, Northwestern University Feinberg School of Medicine, Chicago, IL
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138
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Wu F, Du H, Overbey E, Kim J, Makhijani P, Martin N, Lerner CA, Nguyen K, Baechle J, Valentino TR, Fuentealba M, Bartleson JM, Halaweh H, Winer S, Meydan C, Garrett-Bakelman F, Sayed N, Melov S, Muratani M, Gerencser AA, Kasler HG, Beheshti A, Mason CE, Furman D, Winer DA. Single-cell analysis identifies conserved features of immune dysfunction in simulated microgravity and spaceflight. Nat Commun 2024; 15:4795. [PMID: 38862487 PMCID: PMC11166937 DOI: 10.1038/s41467-023-42013-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 09/27/2023] [Indexed: 06/13/2024] Open
Abstract
Microgravity is associated with immunological dysfunction, though the mechanisms are poorly understood. Here, using single-cell analysis of human peripheral blood mononuclear cells (PBMCs) exposed to short term (25 hours) simulated microgravity, we characterize altered genes and pathways at basal and stimulated states with a Toll-like Receptor-7/8 agonist. We validate single-cell analysis by RNA sequencing and super-resolution microscopy, and against data from the Inspiration-4 (I4) mission, JAXA (Cell-Free Epigenome) mission, Twins study, and spleens from mice on the International Space Station. Overall, microgravity alters specific pathways for optimal immunity, including the cytoskeleton, interferon signaling, pyroptosis, temperature-shock, innate inflammation (e.g., Coronavirus pathogenesis pathway and IL-6 signaling), nuclear receptors, and sirtuin signaling. Microgravity directs monocyte inflammatory parameters, and impairs T cell and NK cell functionality. Using machine learning, we identify numerous compounds linking microgravity to immune cell transcription, and demonstrate that the flavonol, quercetin, can reverse most abnormal pathways. These results define immune cell alterations in microgravity, and provide opportunities for countermeasures to maintain normal immunity in space.
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Grants
- R01 MH117406 NIMH NIH HHS
- T32 AG000266 NIA NIH HHS
- This work was supported in part through funds derived from the Buck Institute for Research on Aging (D.A.W., D.F.), and the Huiying Memorial Foundation (D.A.W.). T.V. and J.B. are funded by a T32 NIH fellowship grant (NIA T32 AG000266). C.E.M. thanks the Scientific Computing Unit (SCU) at WCM, the WorldQuant Foundation, NASA (NNX14AH50G, NNX17AB26G, 80NSSC22K0254, NNH18ZTT001N-FG2, 80NSSC22K0254, NNX16AO69A), the National Institutes of Health (R01MH117406), and LLS (MCL7001-18, LLS 9238-16).
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Affiliation(s)
- Fei Wu
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Huixun Du
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Eliah Overbey
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA
| | - JangKeun Kim
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Priya Makhijani
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
- Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Nicolas Martin
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Chad A Lerner
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Khiem Nguyen
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Jordan Baechle
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | | | | | | | - Heather Halaweh
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Shawn Winer
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Francine Garrett-Bakelman
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Nazish Sayed
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Simon Melov
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Masafumi Muratani
- Transborder Medical Research Center, University of Tsukuba, Ibaraki, 305-8575, Japan
- Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | | | | | - Afshin Beheshti
- Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94043, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA.
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10021, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10021, USA.
| | - David Furman
- Buck Institute for Research on Aging, Novato, CA, 94945, USA.
- Stanford 1000 Immunomes Project, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Research in Translational Medicine, Universidad Austral, CONICET, Pilar, Buenos Aires, Argentina.
| | - Daniel A Winer
- Buck Institute for Research on Aging, Novato, CA, 94945, USA.
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
- Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Division of Cellular & Molecular Biology, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON, M5G 1L7, Canada.
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Liu S, Zhang S, Dong H, Jin X, Sun J, Zhou H, Jin Y, Li Y, Wu G. CD63 + tumor-associated macrophages drive the progression of hepatocellular carcinoma through the induction of epithelial-mesenchymal transition and lipid reprogramming. BMC Cancer 2024; 24:698. [PMID: 38849760 PMCID: PMC11157766 DOI: 10.1186/s12885-024-12472-7] [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: 11/01/2023] [Accepted: 06/03/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Tumor-associated macrophages (TAMs) constitute a substantial part of human hepatocellular carcinoma (HCC). The present study was devised to explore TAM diversity and their roles in HCC progression. METHODS Through the integration of multiple 10 × single-cell transcriptomic data derived from HCC samples and the use of consensus nonnegative matrix factorization (an unsupervised clustering algorithm), TAM molecular subtypes and expression programs were evaluated in detail. The roles played by these TAM subtypes in HCC were further probed through pseudotime, enrichment, and intercellular communication analyses. Lastly, vitro experiments were performed to validate the relationship between CD63, which is an inflammatory TAM expression program marker, and tumor cell lines. RESULTS We found that the inflammatory expression program in TAMs had a more obvious interaction with HCC cells, and CD63, as a marker gene of the inflammatory expression program, was associated with poor prognosis of HCC patients. Both bulk RNA-seq and vitro experiments confirmed that higher TAM CD63 expression was associated with the growth of HCC cells as well as their epithelial-mesenchymal transition, metastasis, invasion, and the reprogramming of lipid metabolism. CONCLUSIONS These analyses revealed that the TAM inflammatory expression program in HCC is closely associated with malignant tumor cells, with the hub gene CD63 thus representing an ideal target for therapeutic intervention in this cancer type.
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Affiliation(s)
- Shiqi Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Shuairan Zhang
- Department of Gastroenterology, The First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Hang Dong
- Phase I Clinical Trails Center, The People's Hospital of China Medical University, Shenyang, People's Republic of China
| | - Xiuli Jin
- Department of Gastroenterology, The First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Jing Sun
- Department of Gastroenterology, The First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Haonan Zhou
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Yifan Jin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Yiling Li
- Department of Gastroenterology, The First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China.
| | - Gang Wu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China.
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140
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Chen J, Chen R, Huang J. A pan-cancer single-cell transcriptional analysis of antigen-presenting cancer-associated fibroblasts in the tumor microenvironment. Front Immunol 2024; 15:1372432. [PMID: 38903527 PMCID: PMC11187094 DOI: 10.3389/fimmu.2024.1372432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024] Open
Abstract
Background Cancer-associated fibroblasts (CAFs) are the primary stromal cells found in tumor microenvironment, and display high plasticity and heterogeneity. By using single-cell RNA-seq technology, researchers have identified various subpopulations of CAFs, particularly highlighting a recently identified subpopulation termed antigen-presenting CAFs (apCAFs), which are largely unknown. Methods We collected datasets from public databases for 9 different solid tumor types to analyze the role of apCAFs in the tumor microenvironment. Results Our data revealed that apCAFs, likely originating mainly from normal fibroblast, are commonly found in different solid tumor types and generally are associated with anti-tumor effects. apCAFs may be associated with the activation of CD4+ effector T cells and potentially promote the survival of CD4+ effector T cells through the expression of C1Q molecules. Moreover, apCAFs exhibited highly enrichment of transcription factors RUNX3 and IKZF1, along with increased glycolytic metabolism. Conclusions Taken together, these findings offer novel insights into a deeper understanding of apCAFs and the potential therapeutic implications for apCAFs targeted immunotherapy in cancer.
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Affiliation(s)
- Juntao Chen
- Shenshan Medical Center, Memorial Hospital of Sun Yat-Sen University, Shanwei, China
| | - Renhui Chen
- Department of Otolaryngology-Head and Neck Surgery, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jingang Huang
- Medical Research Center, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
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141
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Hua H, Wang Y, Wang X, Wang S, Zhou Y, Liu Y, Liang Z, Ren H, Lu S, Wu S, Jiang Y, Pu Y, Zheng X, Tang C, Shen Z, Li C, Du Y, Deng H. Remodeling ceramide homeostasis promotes functional maturation of human pluripotent stem cell-derived β cells. Cell Stem Cell 2024; 31:850-865.e10. [PMID: 38697109 DOI: 10.1016/j.stem.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 03/21/2024] [Accepted: 04/12/2024] [Indexed: 05/04/2024]
Abstract
Human pluripotent stem cell-derived β cells (hPSC-β cells) show the potential to restore euglycemia. However, the immature functionality of hPSC-β cells has limited their efficacy in application. Here, by deciphering the continuous maturation process of hPSC-β cells post transplantation via single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq), we show that functional maturation of hPSC-β cells is an orderly multistep process during which cells sequentially undergo metabolic adaption, removal of negative regulators of cell function, and establishment of a more specialized transcriptome and epigenome. Importantly, remodeling lipid metabolism, especially downregulating the metabolic activity of ceramides, the central hub of sphingolipid metabolism, is critical for β cell maturation. Limiting intracellular accumulation of ceramides in hPSC-β cells remarkably enhanced their function, as indicated by improvements in insulin processing and glucose-stimulated insulin secretion. In summary, our findings provide insights into the maturation of human pancreatic β cells and highlight the importance of ceramide homeostasis in function acquisition.
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Affiliation(s)
- Huijuan Hua
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yaqi Wang
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China
| | | | - Shusen Wang
- Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, China
| | - Yunlu Zhou
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yinan Liu
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zhen Liang
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Huixia Ren
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Sufang Lu
- Hangzhou Reprogenix Bioscience, Hangzhou, China
| | | | - Yong Jiang
- Hangzhou Reprogenix Bioscience, Hangzhou, China
| | - Yue Pu
- Hangzhou Reprogenix Bioscience, Hangzhou, China
| | - Xiang Zheng
- Hangzhou Repugene Technology, Hangzhou, China
| | - Chao Tang
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zhongyang Shen
- Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, China
| | - Cheng Li
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China.
| | - Yuanyuan Du
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
| | - Hongkui Deng
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; Changping Laboratory, Beijing, China.
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142
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Wang J, Li H, Xue Y, Zhang Y, Ma X, Zhou C, Rong L, Zhang Y, Wang Y, Fang Y. Cell communication pathway prognostic model identified detrimental neurodevelopmental pathways in neuroblastoma. Neoplasia 2024; 52:100997. [PMID: 38669760 PMCID: PMC11061340 DOI: 10.1016/j.neo.2024.100997] [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: 03/10/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024]
Abstract
Neurodevelopmental cell communication plays a crucial role in neuroblastoma prognosis. However, determining the impact of these communication pathways on prognosis is challenging due to limited sample sizes and patchy clinical survival information of single cell RNA-seq data. To address this, we have developed the cell communication pathway prognostic model (CCPPM) in this study. CCPPM involves the identification of communication pathways through single-cell RNA-seq data, screening of prognosis-significant pathways using bulk RNA-seq data, conducting functional and attribute analysis of these pathways, and analyzing the post-effects of communication within these pathways. By employing the CCPPM, we have identified ten communication pathways significantly influencing neuroblastoma, all related to axongenesis and neural projection development, especially the BMP7-(BMPR1B-ACVR2B) communication pathway was found to promote tumor cell migration by activating the transcription factor SMAD1 and regulating UNK and MYCBP2. Notably, BMP7 expression was higher in neuroblastoma samples with distant metastases. In summary, CCPPM offers a novel approach to studying the influence of cell communication pathways on disease prognosis and identified detrimental communication pathways related to neurodevelopment.
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Affiliation(s)
- Jiali Wang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Huimin Li
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yao Xue
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yidan Zhang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaopeng Ma
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Chunlei Zhou
- Department of Pathology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Liucheng Rong
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yixuan Zhang
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, School of Pharmacy, Nanjing Medical University, Nanjing, China; International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing, China; Gusu School, Nanjing Medical University, Suzhou, China.
| | - Yaping Wang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China.
| | - Yongjun Fang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China.
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143
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Chen H, Zuo H, Huang J, Liu J, Jiang L, Jiang C, Zhang S, Hu Q, Lai H, Yin B, Yang G, Mai G, Li B, Chi H. Unravelling infiltrating T-cell heterogeneity in kidney renal clear cell carcinoma: Integrative single-cell and spatial transcriptomic profiling. J Cell Mol Med 2024; 28:e18403. [PMID: 39031800 PMCID: PMC11190954 DOI: 10.1111/jcmm.18403] [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: 03/26/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 07/15/2024] Open
Abstract
Kidney renal clear cell carcinoma (KIRC) pathogenesis intricately involves immune system dynamics, particularly the role of T cells within the tumour microenvironment. Through a multifaceted approach encompassing single-cell RNA sequencing, spatial transcriptome analysis and bulk transcriptome profiling, we systematically explored the contribution of infiltrating T cells to KIRC heterogeneity. Employing high-density weighted gene co-expression network analysis (hdWGCNA), module scoring and machine learning, we identified a distinct signature of infiltrating T cell-associated genes (ITSGs). Spatial transcriptomic data were analysed using robust cell type decomposition (RCTD) to uncover spatial interactions. Further analyses included enrichment assessments, immune infiltration evaluations and drug susceptibility predictions. Experimental validation involved PCR experiments, CCK-8 assays, plate cloning assays, wound-healing assays and Transwell assays. Six subpopulations of infiltrating and proliferating T cells were identified in KIRC, with notable dynamics observed in mid- to late-stage disease progression. Spatial analysis revealed significant correlations between T cells and epithelial cells across varying distances within the tumour microenvironment. The ITSG-based prognostic model demonstrated robust predictive capabilities, implicating these genes in immune modulation and metabolic pathways and offering prognostic insights into drug sensitivity for 12 KIRC treatment agents. Experimental validation underscored the functional relevance of PPIB in KIRC cell proliferation, invasion and migration. Our study comprehensively characterizes infiltrating T-cell heterogeneity in KIRC using single-cell RNA sequencing and spatial transcriptome data. The stable prognostic model based on ITSGs unveils infiltrating T cells' prognostic potential, shedding light on the immune microenvironment and offering avenues for personalized treatment and immunotherapy.
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Affiliation(s)
- Haiqing Chen
- Department of General Surgery (Hepatopancreatobiliary Surgery), The Affiliated HospitalSouthwest Medical UniversityLuzhouChina
- School of Clinical Medicine, The Affiliated HospitalSouthwest Medical UniversityLuzhouChina
| | - Haoyuan Zuo
- Department of General Surgery (Hepatopancreatobiliary Surgery), The Affiliated HospitalSouthwest Medical UniversityLuzhouChina
- Department of General Surgery (Hepatopancreatobiliary Surgery)Deyang People's HospitalDeyangChina
| | - Jinbang Huang
- School of Clinical Medicine, The Affiliated HospitalSouthwest Medical UniversityLuzhouChina
| | - Jie Liu
- Department of General Surgery (Hepatopancreatobiliary Surgery), The Affiliated HospitalSouthwest Medical UniversityLuzhouChina
- Department of General SurgeryDazhou Central HospitalDazhouChina
| | - Lai Jiang
- School of Clinical Medicine, The Affiliated HospitalSouthwest Medical UniversityLuzhouChina
| | - Chenglu Jiang
- School of Clinical Medicine, The Affiliated HospitalSouthwest Medical UniversityLuzhouChina
| | - Shengke Zhang
- School of Clinical Medicine, The Affiliated HospitalSouthwest Medical UniversityLuzhouChina
| | - Qingwen Hu
- School of Clinical Medicine, The Affiliated HospitalSouthwest Medical UniversityLuzhouChina
| | - Haotian Lai
- School of Clinical Medicine, The Affiliated HospitalSouthwest Medical UniversityLuzhouChina
| | - Bangchao Yin
- Department of PathologySixth People's Hospital of YibinYibinChina
| | - Guanhu Yang
- Department of Specialty MedicineOhio UniversityAthensOhioUSA
| | - Gang Mai
- Department of General Surgery (Hepatopancreatobiliary Surgery), The Affiliated HospitalSouthwest Medical UniversityLuzhouChina
- Department of General Surgery (Hepatopancreatobiliary Surgery)Deyang People's HospitalDeyangChina
| | - Bo Li
- Department of General Surgery (Hepatopancreatobiliary Surgery), The Affiliated HospitalSouthwest Medical UniversityLuzhouChina
| | - Hao Chi
- School of Clinical Medicine, The Affiliated HospitalSouthwest Medical UniversityLuzhouChina
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144
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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 PMCID: PMC11565582 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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145
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Guo H, Zhang L, Guo H, Cui X, Fan Y, Li T, Qi X, Yan T, Chen A, Shi F, Zeng F. Single-cell transcriptome atlas reveals somatic cell embryogenic differentiation features during regeneration. PLANT PHYSIOLOGY 2024; 195:1414-1431. [PMID: 38401160 DOI: 10.1093/plphys/kiae107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 12/15/2023] [Accepted: 01/16/2024] [Indexed: 02/26/2024]
Abstract
Understanding somatic cell totipotency remains a challenge facing scientific inquiry today. Plants display remarkable cell totipotency expression, illustrated by single-cell differentiation during somatic embryogenesis (SE) for plant regeneration. Determining cell identity and exploring gene regulation in such complex heterogeneous somatic cell differentiation have been major challenges. Here, we performed high-throughput single-cell sequencing assays to define the precise cellular landscape and revealed the modulation mode of marker genes during embryogenic differentiation in cotton (Gossypium hirsutum L.) as the crop for biotechnology application. We demonstrated that nonembryogenic calli (NEC) and primary embryogenic calli (PEC) tissues were composed of heterogeneous cells that could be partitioned into four broad populations with six distinct cell clusters. Enriched cell clusters and cell states were identified in NEC and PEC samples, respectively. Moreover, a broad repertoire of new cluster-specific genes and associated expression modules were identified. The energy metabolism, signal transduction, environmental adaptation, membrane transport pathways, and a series of transcription factors were preferentially enriched in cell embryogenic totipotency expression. Notably, the SE-ASSOCIATED LIPID TRANSFER PROTEIN (SELTP) gene dose-dependently marked cell types with distinct embryogenic states and exhibited a parabolic curve pattern along the somatic cell embryogenic differentiation trajectory, suggesting that SELTP could serve as a favorable quantitative cellular marker for detecting embryogenic expression at the single-cell level. In addition, RNA velocity and Scissor analysis confirmed the pseudo-temporal model and validated the accuracy of the scRNA-seq data, respectively. This work provides valuable marker-genes resources and defines precise cellular taxonomy and trajectory atlases for somatic cell embryogenic differentiation in plant regeneration.
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Affiliation(s)
- Huihui Guo
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Li Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Haixia Guo
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Xiwang Cui
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Yupeng Fan
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Tongtong Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Xiushan Qi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Tongdi Yan
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Aiyun Chen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Fengjuan Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Fanchang Zeng
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
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Lazarov O, Disouky A, Sanborn M, Mostafa M, Sabitha K, Schantz A, Kim N, Pawlowski S, Honer W, Bennett D, Zhou Y, Keene C, Maienschein-Cline M, Rehman J. A roadmap to human hippocampal neurogenesis in adulthood, aging and AD. RESEARCH SQUARE 2024:rs.3.rs-4469965. [PMID: 38854131 PMCID: PMC11160907 DOI: 10.21203/rs.3.rs-4469965/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
In the rodent, hippocampal neurogenesis plays critical roles in learning and memory1,2, is tightly regulated by inhibitory neurons3-7 and contributes to memory dysfunction in Alzheimer's disease (AD) mouse models8-10. In contrast, the mechanisms regulating neurogenesis in the adult human hippocampus, the dynamic shifts in the transcriptomic and epigenomic profiles in aging and AD and putative niche interactions within the cellular environment, remain largely unknown. Using single nuclei multi-omics of postmortem human hippocampi we map the molecular mechanisms of hippocampal neurogenesis across aging, cognitive decline, and AD neuropathology. Transcriptomic and epigenetic profiling of neural stem cells (NSCs), neuroblasts and immature neurons suggests that the earliest shift in the characteristics of neurogenesis takes place in NSCs in aging. Cognitive impairment was associated with changes in neuroblast profile. In AD, there was a widespread cessation of the transcription machinery in immature neurons, with robust downregulation of genes regulating ribosomal and mitochondrial function. Further, there was substantial loss of parvalbumin+ inhibitory neurons in the hippocampus in aging. The number of the rest of inhibitory neurons were reduced as a function of age and diagnosis. Notably, a similar system-level effect was observed between immature and inhibitory neurons in the transition from aging to AD, manifested by common molecular pathways that were ultimately lost in AD. The numbers of neuroblasts, immature and GABAergic neurons inversely correlated with extent of neuropathology. Using CellChat and NeuronChat, we inferred the ligands and receptors by which neurogenic cells communicate with their cellular environment. Loss of synaptic adhesion molecules and neurotransmitters, either sent or received by neurogenic cells, was observed in AD. Together, this study delineates the molecular mechanisms and dynamics of human neurogenesis, functional association with inhibitory neurons and a mechanism of hippocampal hyperexcitability in AD.
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Affiliation(s)
| | | | | | | | - K Sabitha
- The University of Illinois at Chicago
| | | | | | | | | | | | - Yi Zhou
- Institute of Neuroscience, Chinese Academy of Sciences
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Purvis GSD, McNeill E, Wright B, Channon KM, Greaves DR. Ly6C hi Monocytes Are Metabolically Reprogrammed in the Blood during Inflammatory Stimulation and Require Intact OxPhos for Chemotaxis and Monocyte to Macrophage Differentiation. Cells 2024; 13:916. [PMID: 38891050 PMCID: PMC11171939 DOI: 10.3390/cells13110916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/16/2024] [Accepted: 05/22/2024] [Indexed: 06/20/2024] Open
Abstract
Acute inflammation is a rapid and dynamic process involving the recruitment and activation of multiple cell types in a coordinated and precise manner. Here, we investigate the origin and transcriptional reprogramming of monocytes using a model of acute inflammation, zymosan-induced peritonitis. Monocyte trafficking and adoptive transfer experiments confirmed that monocytes undergo rapid phenotypic change as they exit the blood and give rise to monocyte-derived macrophages that persist during the resolution of inflammation. Single-cell transcriptomics revealed significant heterogeneity within the surface marker-defined CD11b+Ly6G-Ly6Chi monocyte populations within the blood and at the site of inflammation. We show that two major transcriptional reprogramming events occur during the initial six hours of Ly6Chi monocyte mobilisation, one in the blood priming monocytes for migration and a second at the site of inflammation. Pathway analysis revealed an important role for oxidative phosphorylation (OxPhos) during both these reprogramming events. Experimentally, we demonstrate that OxPhos via the intact mitochondrial electron transport chain is essential for murine and human monocyte chemotaxis. Moreover, OxPhos is needed for monocyte-to-macrophage differentiation and macrophage M(IL-4) polarisation. These new findings from transcriptional profiling open up the possibility that shifting monocyte metabolic capacity towards OxPhos could facilitate enhanced macrophage M2-like polarisation to aid inflammation resolution and tissue repair.
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Affiliation(s)
- Gareth S. D. Purvis
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK;
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (E.M.); (B.W.); (K.M.C.)
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Eileen McNeill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (E.M.); (B.W.); (K.M.C.)
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Benjamin Wright
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (E.M.); (B.W.); (K.M.C.)
| | - Keith M. Channon
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (E.M.); (B.W.); (K.M.C.)
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
- British Heart Foundation Centre of Research Excellence, University of Oxford, Oxford OX3 9DU, UK
| | - David R. Greaves
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK;
- British Heart Foundation Centre of Research Excellence, University of Oxford, Oxford OX3 9DU, UK
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148
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Tang X, Chen C, Yan S, Yang A, Deng Y, Chen B, Gu J. Single-Nucleus RNA-Seq Reveals Spermatogonial Stem Cell Developmental Pattern in Shaziling Pigs. Biomolecules 2024; 14:607. [PMID: 38927011 PMCID: PMC11202124 DOI: 10.3390/biom14060607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/19/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024] Open
Abstract
Normal testicular development ensures the process of spermatogenesis, which is a complex biological process. The sustained high productivity of spermatogenesis throughout life is predominantly attributable to the constant proliferation and differentiation of spermatogonial stem cells (SSCs). The self-renewal and differentiation processes of SSCs are strictly regulated by the SSC niche. Therefore, understanding the developmental pattern of SSCs is crucial for spermatogenesis. The Shaziling pig is a medium-sized indigenous pig breed originating from central China. It is renowned for its superior meat quality and early male sexual maturity. The spermatogenic ability of the boars is of great economic importance to the pig industry. To investigate testicular development, particularly the pattern of SSC development in Shaziling pigs, we used single-cell transcriptomics to identify gene expression patterns in 82,027 individual cells from nine Shaziling pig testes at three key postnatal developmental stages. We generated an unbiased cell developmental atlas of Shaziling pig testicular tissues. We elucidated the complex processes involved in the development of SSCs within their niche in the Shaziling pig. Specifically, we identified potential marker genes and cellular signaling pathways that regulate SSC self-renewal and maintenance. Additionally, we proposed potential novel marker genes for SSCs that could be used for SSC isolation and sorting in Shaziling pigs. Furthermore, by immunofluorescence staining of testicular tissues of different developmental ages using marker proteins (UCHL1 and KIT), the developmental pattern of the spermatogonia of Shaziling pigs was intensively studied. Our research enhances the comprehension of the development of SSCs and provides a valuable reference for breeding Shaziling pigs.
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Affiliation(s)
- Xiangwei Tang
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (X.T.); (C.C.); (A.Y.); (Y.D.)
| | - Chujie Chen
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (X.T.); (C.C.); (A.Y.); (Y.D.)
| | - Saina Yan
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China;
| | - Anqi Yang
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (X.T.); (C.C.); (A.Y.); (Y.D.)
- School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Yanhong Deng
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (X.T.); (C.C.); (A.Y.); (Y.D.)
| | - Bin Chen
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (X.T.); (C.C.); (A.Y.); (Y.D.)
| | - Jingjing Gu
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (X.T.); (C.C.); (A.Y.); (Y.D.)
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149
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Liu Q, Peng F, Liu H, Sun Q, Chen H, Xu X, Hu Z, Zhou X, Jin K, Xie J, Huang Y, Huang W, Yang Y. Overactivated MX1 Positive Natural Killer Cells Promote the Progression of Sepsis-Induced Acute Respiratory Distress Syndrome. J Inflamm Res 2024; 17:3187-3200. [PMID: 38779429 PMCID: PMC11110828 DOI: 10.2147/jir.s460259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
Background Natural killer (NK) cells are key regulators of immune defense in sepsis-induced acute respiratory distress syndrome (ARDS), yet the characteristics of NK cell clusters in ARDS remain poorly understood. Methods A prospective and observational study enrolled septic patients with ARDS or not was conducted to determine the percentage of NK cells via flow cytometry. The transcriptomes of peripheral blood mononuclear cells (PBMCs) from healthy controls, patients with sepsis only, and patients with sepsis-induced ARDS were profiled. Vitro experiments were performed to confirm the mechanism mediating MX1+NK cell infiltration. Results A total of 115 septic patients were analyzed, among whom 63 patients developed ARDS and 52 patients did not. Decreased NK percentages were found in sepsis with ARDS patients (%, 7.46±4.40 vs 11.65±6.88, P=0.0001) compared with sepsis-only patients. A lower percentage of NK cells showed a significant increase in 28-day mortality. Single-cell sequencing analysis revealed distinct characteristics of NK cells in sepsis-induced ARDS, notably the identification of a unique cluster defined as MX1+NK cells. Flow cytometry analysis showed an elevated percentage of MX1+NK cells specifically in individuals with sepsis-induced ARDS, compared with patients with sepsis only. Pseudo-time analysis showed that MX1+NK cells were characterized by upregulation of type I interferon-induced genes and other pro-inflammatory genes. MX1+NK cells can respond to type I interferons and secrete type I interferons themselves. Ligand-receptor interaction analysis also revealed extensive interaction between MX1+NK cells and T/B cells, leading to an uncontrolled inflammatory response in ARDS. Conclusion MX1+NK cells can respond to type I interferons and secrete type I interferons themselves, promoting the development of sepsis-induced ARDS. Interfering with the infiltration of MX1+NK cells could be a therapeutic approach for this disease. Due to the limited sample size, a larger sample size was needed for further exploration.
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Affiliation(s)
- Qingxiang Liu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210009, People’s Republic of China
| | - Fei Peng
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210009, People’s Republic of China
| | - Haitao Liu
- School of Life Science, Fudan University, Shanghai, 200000, People’s Republic of China
| | - Qin Sun
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210009, People’s Republic of China
| | - Hui Chen
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210009, People’s Republic of China
| | - Xinyi Xu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210009, People’s Republic of China
| | - Zihan Hu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210009, People’s Republic of China
| | - Xing Zhou
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210009, People’s Republic of China
| | - Kai Jin
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210009, People’s Republic of China
| | - Jianfeng Xie
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210009, People’s Republic of China
| | - Yingzi Huang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210009, People’s Republic of China
| | - Wei Huang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210009, People’s Republic of China
| | - Yi Yang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210009, People’s Republic of China
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150
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Li W, Yao C, Guo H, Ni X, Zhu R, Wang Y, Yu B, Feng X, Gu Z, Da Z. Macrophages communicate with mesangial cells through the CXCL12/DPP4 axis in lupus nephritis pathogenesis. Cell Death Dis 2024; 15:344. [PMID: 38762508 PMCID: PMC11102518 DOI: 10.1038/s41419-024-06708-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/20/2024]
Abstract
Lupus nephritis (LN) occurs in 50% of cases of systemic lupus erythematosus (SLE) and is one of the most serious complications that can occur during lupus progression. Mesangial cells (MCs) are intrinsic cells in the kidney that can regulate capillary blood flow, phagocytose apoptotic cells, and secrete vasoactive substances and growth factors. Previous studies have shown that various types of inflammatory cells can activate MCs for hyperproliferation, leading to disruption of the filtration barrier and impairment of renal function in LN. Here, we characterized the heterogeneity of kidney cells of LN mice by single-nucleus RNA sequencing (snRNA-seq) and revealed the interaction between macrophages and MCs through the CXC motif chemokine ligand 12 (CXCL12)/dipeptidyl peptidase 4 (DPP4) axis. In culture, macrophages modulated the proliferation and migration of MCs through this ligand-receptor interaction. In LN mice, treatment with linagliptin, a DPP4 inhibitor, effectively inhibited MC proliferation and reduced urinary protein levels. Together, our findings indicated that targeting the CXCL12/DPP4 axis with linagliptin treatment may serve as a novel strategy for the treatment of LN via the CXCL12/DPP4 axis.
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Affiliation(s)
- Weiwei Li
- Department of Rheumatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China
| | - Chun Yao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education; Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu, China
| | - Haixia Guo
- Department of Rheumatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China
| | - Xi'an Ni
- Department of Rheumatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China
| | - Ran Zhu
- Department of Rheumatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China
| | - Yongjun Wang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education; Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu, China
| | - Bin Yu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education; Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu, China
| | - Xuebing Feng
- Department of Rheumatology and Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Zhifeng Gu
- Department of Rheumatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China
| | - Zhanyun Da
- Department of Rheumatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China.
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