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Yang Q, Song W, Reheman H, Wang D, Qu J, Li Y. PANoptosis, an indicator of COVID-19 severity and outcomes. Brief Bioinform 2024; 25:bbae124. [PMID: 38555477 PMCID: PMC10981763 DOI: 10.1093/bib/bbae124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/21/2024] [Accepted: 03/02/2024] [Indexed: 04/02/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) has been wreaking havoc for 3 years. PANoptosis, a distinct and physiologically relevant inflammatory programmed cell death, perpetuates cytokine storm and multi-organ injuries in COVID-19. Although PANoptosis performs indispensable roles in host defense, further investigation is needed to elucidate the exact processes through which PANoptosis modulates immunological responses and prognosis in COVID-19. This study conducted a bioinformatics analysis of online single-cell RNA sequence (scRNA-seq) and bulk RNA-seq datasets to explore the potential of PANoptosis as an indicator of COVID-19 severity. The degree of PANoptosis in bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells (PBMC) indicated the severity of COVID-19. Single-cell transcriptomics identified pro-inflammatory monocytes as one of the primary sites of PANoptosis in COVID-19. The study subsequently demonstrated the immune and metabolic characteristics of this group of pro-inflammatory monocytes. In addition, the analysis illustrated that dexamethasone was likely to alleviate inflammation in COVID-19 by mitigating PANoptosis. Finally, the study showed that the PANoptosis-related genes could predict the intensive care unit admission (ICU) and outcomes of COVID-19 patients who are hospitalized.
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Affiliation(s)
- Qingyuan Yang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
| | - Wanmei Song
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
| | - Hanizaier Reheman
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
| | - Dan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jieming Qu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
| | - Yanan Li
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
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Chen X, Zhang Z, Qin Z, Zhu X, Wang K, Kang L, Li C, Wang H. Identification and validation of a novel signature based on macrophage marker genes for predicting prognosis and drug response in kidney renal clear cell carcinoma by integrated analysis of single cell and bulk RNA sequencing. Aging (Albany NY) 2024; 16:5676-5702. [PMID: 38517387 PMCID: PMC11006469 DOI: 10.18632/aging.205671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Abstract
Macrophages are found in a variety of tumors and play a critical role in shaping the tumor microenvironment, affecting tumor progression, metastasis, and drug resistance. However, the clinical relevance of marker genes associated with macrophage in kidney renal clear cell carcinoma (KIRC) has yet to be documented. In this study, we initiated a thorough examination of single-cell RNA sequencing (scRNA-seq) data for KIRC retrieved from the Gene Expression Omnibus (GEO) database and determined 244 macrophage marker genes (MMGs). Univariate analysis, LASSO regression, and multivariate regression analysis were performed to develop a five-gene prognostic signature in The Cancer Genome Atlas (TCGA) database, which could divide KIRC patients into low-risk (L-R) and high-risk (H-R) groups. Then, a nomogram was constructed to predict the survival rate of KIRC patients at 1, 3, and 5 years, which was well assessed by receiver operating characteristic curve (ROC), calibration curve, and decision curve analyses (DCA). Functional enrichment analysis showed that immune-related pathways (such as immunoglobulin complex, immunoglobulin receptor binding, and cytokine-cytokine receptor interaction) were mainly enriched in the H-R group. Additionally, in comparison to the L-R cohort, patients belonging to the H-R cohort exhibited increased immune cell infiltration, elevated expression of immune checkpoint genes (ICGs), and a higher tumor immune dysfunction and exclusion (TIDE) score. This means that patients in the H-R group may be less sensitive to immunotherapy than those in the L-R group. Finally, IFI30 was validated to increase the ability of KIRC cells to proliferate, invade and migrate in vitro. In summary, our team has for the first time developed and validated a predictive model based on macrophage marker genes to accurately predict overall survival (OS), immune characteristics, and treatment benefit in KIRC patients.
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Affiliation(s)
- Xiaoxu Chen
- Department of Oncology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Precision Medicine for Sex Hormones and Diseases (in Preparation), The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Zheyu Zhang
- Department of Oncology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Precision Medicine for Sex Hormones and Diseases (in Preparation), The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Zheng Qin
- Department of Oncology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Precision Medicine for Sex Hormones and Diseases (in Preparation), The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Xiao Zhu
- Department of Oncology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Precision Medicine for Sex Hormones and Diseases (in Preparation), The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Kaibin Wang
- Department of Oncology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Precision Medicine for Sex Hormones and Diseases (in Preparation), The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Lijuan Kang
- Department of Oncology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Precision Medicine for Sex Hormones and Diseases (in Preparation), The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Changying Li
- Department of Oncology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Precision Medicine for Sex Hormones and Diseases (in Preparation), The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Haitao Wang
- Department of Oncology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Precision Medicine for Sex Hormones and Diseases (in Preparation), The Second Hospital of Tianjin Medical University, Tianjin, China
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Zhou W, Lin Z, Tan W. Deciphering the molecular landscape: integrating single-cell transcriptomics to unravel myofibroblast dynamics and therapeutic targets in clear cell renal cell carcinomas. Front Immunol 2024; 15:1374931. [PMID: 38562930 PMCID: PMC10982338 DOI: 10.3389/fimmu.2024.1374931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Background Clear cell renal cell carcinomas (ccRCCs) epitomize the most formidable clinical subtype among renal neoplasms. While the impact of tumor-associated fibroblasts on ccRCC progression is duly acknowledged, a paucity of literature exists elucidating the intricate mechanisms and signaling pathways operative at the individual cellular level. Methods Employing single-cell transcriptomic analysis, we meticulously curated UMAP profiles spanning substantial ccRCC populations, delving into the composition and intrinsic signaling pathways of these cohorts. Additionally, Myofibroblasts were fastidiously categorized into discrete subpopulations, with a thorough elucidation of the temporal trajectory relationships between these subpopulations. We further probed the cellular interaction pathways connecting pivotal subpopulations with tumors. Our endeavor also encompassed the identification of prognostic genes associated with these subpopulations through Bulk RNA-seq, subsequently validated through empirical experimentation. Results A notable escalation in the nFeature and nCount of Myofibroblasts and EPCs within ccRCCs was observed, notably enriched in oxidation-related pathways. This phenomenon is postulated to be closely associated with the heightened metabolic activities of Myofibroblasts and EPCs. The Myofibroblasts subpopulation, denoted as C3 HMGA1+ Myofibroblasts, emerges as a pivotal subset, displaying low differentiation and positioning itself at the terminal point of the temporal trajectory. Intriguingly, these cells exhibit a high degree of interaction with tumor cells through the MPZ signaling pathway network, suggesting that Myofibroblasts may facilitate tumor progression via this pathway. Prognostic genes associated with C3 were identified, among which TUBB3 is implicated in potential resistance to tumor recurrence. Finally, experimental validation revealed that the knockout of the key gene within the MPZ pathway, MPZL1, can inhibit tumor activity, proliferation, invasion, and migration capabilities. Conclusion This investigation delves into the intricate mechanisms and interaction pathways between Myofibroblasts and ccRCCs at the single-cell level. We propose that targeting MPZL1 and the oxidative phosphorylation pathway could serve as potential key targets for treating the progression and recurrence of ccRCC. This discovery paves the way for new directions in the treatment and prognosis diagnosis of ccRCC in the future.
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Affiliation(s)
- Wenqian Zhou
- Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhiheng Lin
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Wang Tan
- Xiangya Boai Rehabilitation Hospital, Changsha, Hunan, China
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Lin Z, Li X, Shi H, Cao R, Zhu L, Dang C, Sheng Y, Fan W, Yang Z, Wu S. Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses. Front Immunol 2024; 15:1351287. [PMID: 38482016 PMCID: PMC10933018 DOI: 10.3389/fimmu.2024.1351287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/13/2024] [Indexed: 04/13/2024] Open
Abstract
Background Cervical carcinoma (CC) represents a prevalent gynecological neoplasm, with a discernible rise in prevalence among younger cohorts observed in recent years. Nonetheless, the intrinsic cellular heterogeneity of CC remains inadequately investigated. Methods We utilized single-cell RNA sequencing (scRNA-seq) transcriptomic analysis to scrutinize the tumor epithelial cells derived from four specimens of cervical carcinoma (CC) patients. This method enabled the identification of pivotal subpopulations of tumor epithelial cells and elucidation of their contributions to CC progression. Subsequently, we assessed the influence of associated molecules in bulk RNA sequencing (Bulk RNA-seq) cohorts and performed cellular experiments for validation purposes. Results Through our analysis, we have discerned C3 PLP2+ Tumor Epithelial Progenitor Cells as a noteworthy subpopulation in cervical carcinoma (CC), exerting a pivotal influence on the differentiation and progression of CC. We have established an independent prognostic indicator-the PLP2+ Tumor EPCs score. By stratifying patients into high and low score groups based on the median score, we have observed that the high-score group exhibits diminished survival rates compared to the low-score group. The correlations observed between these groups and immune infiltration, enriched pathways, single-nucleotide polymorphisms (SNPs), drug sensitivity, among other factors, further underscore their impact on CC prognosis. Cellular experiments have validated the significant impact of ATF6 on the proliferation and migration of CC cell lines. Conclusion This study enriches our comprehension of the determinants shaping the progression of CC, elevates cognizance of the tumor microenvironment in CC, and offers valuable insights for prospective CC therapies. These discoveries contribute to the refinement of CC diagnostics and the formulation of optimal therapeutic approaches.
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Affiliation(s)
- Zhiheng Lin
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Xinhan Li
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Hengmei Shi
- Department of Obstetrics and Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Renshuang Cao
- Wangjing Hospital of Chinese Academy of Chinese Medical Sciences, Beijing, China
| | - Lijun Zhu
- Longhua Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Chunxiao Dang
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Yawen Sheng
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Weisen Fan
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | | | - Siyu Wu
- Department of Gynecology and Obstetrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Qingdao, China
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Li Y, Xu B, Zhang J, Liu X, Ganesan K, Shi G. Exploring the role of LIAS-related cuproptosis in systemic lupus erythematosus. Lupus 2023; 32:1598-1609. [PMID: 37903189 DOI: 10.1177/09612033231211429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
BACKGROUND Cuproptosis is a novel mode of cell death, which is strongly related to energy metabolism in mitochondria and regulated by protein lipoylation. Currently, the molecular mechanisms of cuproptosis-related genes (CRGs) involved in systemic lupus erythematosus (SLE) largely remained unclear, our study is aimed to explore the mechanisms of cuproptosis and CRGs involved in SLE. METHODS Bulk RNA-seq datasets were collected to display the expressions of CRGs in peripheral blood mononuclear cells (PBMCs) of SLE and healthy individuals, and then ROC analysis was used to establish the diagnostic models of CRGs. Next, the immune infiltration analyses were applied to reveal the difference of immune cells infiltration in LIAS-low and LIAS-high group. Additionally, WGCNA analysis was performed to find the gene modules significantly correlated with the LIAS expression level. We also performed the functional enrichment analyses for LIAS-related gene modules to determine the potential pathways involved in the development of SLE. Finally, scRNA-seq dataset was used to cluster immune cell subsets, reveal the activated pathways, and study cell-cell interactions in LIAS-low and LIAS-high cells. RESULT We found CDKN2A was significantly increased and LIAS was significantly decreased in SLE patients compared with healthy individuals. The AUC score showed that LIAS had a great diagnostic value than other CRGs. Additionally, the results of immune infiltration analyses showed that immune cells proportion were diverse in LIAS-low and LIAS-high samples. The gene sets related to LIAS expression level were involved in dephosphorylation of JAK1 by SHP1, phosphorylation of STAT2, cytokine signaling in immune system, expression of interferon-alpha and beta, inhibition of JAK kinase activity by SOCS1/3, and so on. Finally, the results of cell-cell communication showed that CCL- (CCL5 + CCR1) and ANNEXIN- (ANXA1 + FPR1) might play an essential role in the communication network between LIAS-low and LIAS-high cells. CONCLUSION Above findings inferred that LIAS-mediated cuproptosis might involve in a comprehensive cellular and molecular mechanism to cause the occurrence and development of SLE.
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Affiliation(s)
- Yan Li
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Municipal Clinical Research Center for Immune Diseases, Xiamen, China
- Xiamen Key Laboratory of Rheumatology and Clinical Immunology, Xiamen, China
| | - Bojun Xu
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jimin Zhang
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Municipal Clinical Research Center for Immune Diseases, Xiamen, China
- Xiamen Key Laboratory of Rheumatology and Clinical Immunology, Xiamen, China
| | - Xiaoyan Liu
- Department of Dermatology, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Kumar Ganesan
- School of Chinese Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Guixiu Shi
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Municipal Clinical Research Center for Immune Diseases, Xiamen, China
- Xiamen Key Laboratory of Rheumatology and Clinical Immunology, Xiamen, China
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Tan Z, Chen X, Zuo J, Fu S, Wang J, Wang H. Integrating Bulk and Single-Cell RNA Sequencing Reveals Heterogeneity, Tumor Microenvironment, and Immunotherapeutic Efficacy Based on Sialylation-Related Genes in Bladder Cancer. J Inflamm Res 2023; 16:3399-3417. [PMID: 37600224 PMCID: PMC10438438 DOI: 10.2147/jir.s418433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023] Open
Abstract
Background As known abnormal sialylation exerts crucial roles in the growth, metastasis, and immune evasion of cancers, but the molecular characteristics and roles in bladder cancer (BLCA) remain unclear. This study intends to establish BLCA risk stratification based on sialylation-related genes and elucidate its role in prognosis, tumor microenvironment, and immunotherapy of BLCA. Methods Bulk RNA-seq and scRNA-seq data were downloaded from open-access databases. The scRNA-seq data were processed using the R package "Seurat" to identify the core cell types. The tumor sub-typing of BLCA samples was performed by the R package "ConsensusClusterPlus" in the bulk RNA-seq data. Signature genes were identified by the R package "limma" and univariate regression analysis to calculate risk scores using the R package "GSVA" and establish risk stratification of BLCA patients. Finally, the differences in clinicopathological characteristics, tumor microenvironment, and immunotherapy efficacy between the different groups were investigated. Results 5 core cell types were identified in the scRNA-seq dataset, with monocytes and macrophages presenting the greatest percentage, sialylation-related gene expression, and sialylation scores. The bulk RNA-seq samples were classified into 3 tumor subtypes based on 19 prognosis-related sialylation genes. The 10 differential expressed genes (DEGs) with the smallest p-values were collected as signature genes, and the risk score was calculated, with the samples divided into high and low-risk score groups. The results showed that patients in the high-risk score group exhibited worse survival outcomes, higher tumor grade, more advanced stage, more frequency of gene mutations, higher expression levels of immune checkpoints, and lower immunotherapy response. Conclusion We established a novel risk stratification of BLCA from a glycomics perspective, which demonstrated good accuracy in determining the prognostic outcome, clinicopathological characteristics, immune microenvironment, and immunotherapy efficacy of patients, and we are proposing to apply it to direct the choice of clinical treatment options for patients.
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Affiliation(s)
- Zhiyong Tan
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Urological Disease Clinical Medical Center of Yunnan Province, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Scientific and Technological Innovation Team of Basic and Clinical Research of Bladder Cancer in Yunnan Universities, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
| | - Xiaorong Chen
- Department of Kidney Transplantation, the Third Hospital of Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Jieming Zuo
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Urological Disease Clinical Medical Center of Yunnan Province, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Scientific and Technological Innovation Team of Basic and Clinical Research of Bladder Cancer in Yunnan Universities, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
| | - Shi Fu
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Urological Disease Clinical Medical Center of Yunnan Province, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Scientific and Technological Innovation Team of Basic and Clinical Research of Bladder Cancer in Yunnan Universities, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
| | - Jiansong Wang
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Urological Disease Clinical Medical Center of Yunnan Province, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Scientific and Technological Innovation Team of Basic and Clinical Research of Bladder Cancer in Yunnan Universities, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
| | - Haifeng Wang
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Urological Disease Clinical Medical Center of Yunnan Province, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Scientific and Technological Innovation Team of Basic and Clinical Research of Bladder Cancer in Yunnan Universities, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
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Luo J, Wu X, Cheng Y, Chen G, Wang J, Song X. Expression quantitative trait locus studies in the era of single-cell omics. Front Genet 2023; 14:1182579. [PMID: 37284065 PMCID: PMC10239882 DOI: 10.3389/fgene.2023.1182579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/26/2023] [Indexed: 06/08/2023] Open
Abstract
Genome-wide association studies have revealed that the regulation of gene expression bridges genetic variants and complex phenotypes. Profiling of the bulk transcriptome coupled with linkage analysis (expression quantitative trait locus (eQTL) mapping) has advanced our understanding of the relationship between genetic variants and gene regulation in the context of complex phenotypes. However, bulk transcriptomics has inherited limitations as the regulation of gene expression tends to be cell-type-specific. The advent of single-cell RNA-seq technology now enables the identification of the cell-type-specific regulation of gene expression through a single-cell eQTL (sc-eQTL). In this review, we first provide an overview of sc-eQTL studies, including data processing and the mapping procedure of the sc-eQTL. We then discuss the benefits and limitations of sc-eQTL analyses. Finally, we present an overview of the current and future applications of sc-eQTL discoveries.
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Affiliation(s)
- Jie Luo
- State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro‐products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yuan Cheng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guang Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro‐products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jian Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro‐products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xijiao Song
- State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro‐products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Li X, Gibson G, Qiu P. Gene representation in scRNA-seq is correlated with common motifs at the 3' end of transcripts. Front Bioinform 2023; 3:1120290. [PMID: 37255988 PMCID: PMC10226423 DOI: 10.3389/fbinf.2023.1120290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/02/2023] [Indexed: 06/01/2023] Open
Abstract
One important characteristic of single-cell RNA sequencing (scRNA-seq) data is its high sparsity, where the gene-cell count data matrix contains high proportion of zeros. The sparsity has motivated widespread discussions on dropouts and missing data, as well as imputation algorithms of scRNA-seq analysis. Here, we aim to investigate whether there exist genes that are more prone to be under-detected in scRNA-seq, and if yes, what commonalities those genes may share. From public data sources, we gathered paired bulk RNA-seq and scRNA-seq data from 53 human samples, which were generated in diverse biological contexts. We derived pseudo-bulk gene expression by averaging the scRNA-seq data across cells. Comparisons of the paired bulk and pseudo-bulk gene expression profiles revealed that there indeed exists a collection of genes that are frequently under-detected in scRNA-seq compared to bulk RNA-seq. This result was robust to randomization when unpaired bulk and pseudo-bulk gene expression profiles were compared. We performed motif search to the last 350 bp of the identified genes, and observed an enrichment of poly(T) motif. The poly(T) motif toward the tails of those genes may be able to form hairpin structures with the poly(A) tails of their mRNA transcripts, making it difficult for their mRNA transcripts to be captured during scRNA-seq library preparation, which is a mechanistic conjecture of why certain genes may be more prone to be under-detected in scRNA-seq.
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Affiliation(s)
- Xinling Li
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
| | - Greg Gibson
- School of Biological Sciences, and Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA, United States
| | - Peng Qiu
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
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Massaiu I, Campodonico J, Mapelli M, Salvioni E, Valerio V, Moschetta D, Myasoedova VA, Cappellini MD, Pompilio G, Poggio P, Agostoni P. Dysregulation of Iron Metabolism-Linked Genes at Myocardial Tissue and Cell Levels in Dilated Cardiomyopathy. Int J Mol Sci 2023; 24:ijms24032887. [PMID: 36769209 PMCID: PMC9918212 DOI: 10.3390/ijms24032887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/19/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
In heart failure, the biological and clinical connection between abnormal iron homeostasis, myocardial function, and prognosis is known; however, the expression profiles of iron-linked genes both at myocardial tissue and single-cell level are not well defined. Through publicly available bulk and single-nucleus RNA sequencing (RNA-seq) datasets of left ventricle samples from adult non-failed (NF) and dilated cardiomyopathy (DCM) subjects, we aim to evaluate the altered iron metabolism in a diseased condition, at the whole cardiac tissue and single-cell level. From the bulk RNA-seq data, we found 223 iron-linked genes expressed at the myocardial tissue level and 44 differentially expressed between DCM and NF subjects. At the single-cell level, at least 18 iron-linked expressed genes were significantly regulated in DCM when compared to NF subjects. Specifically, the iron metabolism in DCM cardiomyocytes is altered at several levels, including: (1) imbalance of Fe3+ internalization (SCARA5 down-regulation) and reduction of internal conversion from Fe3+ to Fe2+ (STEAP3 down-regulation), (2) increase of iron consumption to produce hemoglobin (HBA1/2 up-regulation), (3) higher heme synthesis and externalization (ALAS2 and ABCG2 up-regulation), (4) lower cleavage of heme to Fe2+, biliverdin and carbon monoxide (HMOX2 down-regulation), and (5) positive regulation of hepcidin (BMP6 up-regulation).
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Affiliation(s)
| | | | | | | | | | - Donato Moschetta
- Centro Cardiologico Monzino, IRCCS, 20138 Milan, Italy
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, 20122 Milan, Italy
| | | | - Maria Domenica Cappellini
- UOC General Medicine, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Giulio Pompilio
- Centro Cardiologico Monzino, IRCCS, 20138 Milan, Italy
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy
| | - Paolo Poggio
- Centro Cardiologico Monzino, IRCCS, 20138 Milan, Italy
- Correspondence: (P.P.); (P.A.); Tel.: +39-02-5800-2853 (P.P.); +39-02-5800-2488 (P.A.)
| | - Piergiuseppe Agostoni
- Centro Cardiologico Monzino, IRCCS, 20138 Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
- Correspondence: (P.P.); (P.A.); Tel.: +39-02-5800-2853 (P.P.); +39-02-5800-2488 (P.A.)
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10
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Chen S, Yan X, Zheng R, Li M. Bubble: a fast single-cell RNA-seq imputation using an autoencoder constrained by bulk RNA-seq data. Brief Bioinform 2023; 24:6960616. [PMID: 36567258 DOI: 10.1093/bib/bbac580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/10/2022] [Accepted: 11/28/2022] [Indexed: 12/27/2022] Open
Abstract
Single-cell RNA-sequencing technology (scRNA-seq) brings research to single-cell resolution. However, a major drawback of scRNA-seq is large sparsity, i.e. expressed genes with no reads due to technical noise or limited sequence depth during the scRNA-seq protocol. This phenomenon is also called 'dropout' events, which likely affect downstream analyses such as differential expression analysis, the clustering and visualization of cell subpopulations, cellular trajectory inference, etc. Therefore, there is a need to develop a method to identify and impute these dropout events. We propose Bubble, which first identifies dropout events from all zeros based on expression rate and coefficient of variation of genes within cell subpopulation, and then leverages an autoencoder constrained by bulk RNA-seq data to only impute those values. Unlike other deep learning-based imputation methods, Bubble fuses the matched bulk RNA-seq data as a constraint to reduce the introduction of false positive signals. Using simulated and several real scRNA-seq datasets, we demonstrate that Bubble enhances the recovery of missing values, gene-to-gene and cell-to-cell correlations, and reduces the introduction of false positive signals. Regarding some crucial downstream analyses of scRNA-seq data, Bubble facilitates the identification of differentially expressed genes, improves the performance of clustering and visualization, and aids the construction of cellular trajectory. More importantly, Bubble provides fast and scalable imputation with minimal memory usage.
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Affiliation(s)
- Siqi Chen
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
| | - Xuhua Yan
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
| | - Ruiqing Zheng
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
| | - Min Li
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
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11
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Sun J, Zhang J, Bian Q, Wang X. Effects of Dlx2 overexpression on the genes associated with the maxillary process in the early mouse embryo. Front Genet 2023; 14:1085263. [PMID: 36891149 PMCID: PMC9986417 DOI: 10.3389/fgene.2023.1085263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/09/2023] [Indexed: 02/22/2023] Open
Abstract
The transcription factor Dlx2 plays an important role in craniomaxillofacial development. Overexpression or null mutations of Dlx2 can lead to craniomaxillofacial malformation in mice. However, the transcriptional regulatory effects of Dlx2 during craniomaxillofacial development remain to be elucidated. Using a mouse model that stably overexpresses Dlx2 in neural crest cells, we comprehensively characterized the effects of Dlx2 overexpression on the early development of maxillary processes in mice by conducting bulk RNA-Seq, scRNA-Seq and CUT&Tag analyses. Bulk RNA-Seq results showed that the overexpression of Dlx2 resulted in substantial transcriptome changes in E10.5 maxillary prominences, with genes involved in RNA metabolism and neuronal development most significantly affected. The scRNA-Seq analysis suggests that overexpression of Dlx2 did not change the differentiation trajectory of mesenchymal cells during this development process. Rather, it restricted cell proliferation and caused precocious differentiation, which may contribute to the defects in craniomaxillofacial development. Moreover, the CUT&Tag analysis using DLX2 antibody revealed enrichment of MNT and Runx2 motifs at the putative DLX2 binding sites, suggesting they may play critical roles in mediating the transcriptional regulatory effects of Dlx2. Together, these results provide important insights for understanding the transcriptional regulatory network of Dlx2 during craniofacial development.
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Affiliation(s)
- Jian Sun
- Shanghai Key Laboratory of Stomatology, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Oral and Cranio-Maxillofacial Surgery, College of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jianfei Zhang
- Shanghai Key Laboratory of Stomatology, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Oral and Cranio-Maxillofacial Surgery, College of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Bian
- Shanghai Key Laboratory of Stomatology, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Oral and Cranio-Maxillofacial Surgery, College of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Institute of Precision Medicine, Shanghai, China
| | - Xudong Wang
- Shanghai Key Laboratory of Stomatology, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Oral and Cranio-Maxillofacial Surgery, College of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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12
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Liu Q, Liang Y, Wang D, Li J. LFSC: A linear fast semi-supervised clustering algorithm that integrates reference-bulk and single-cell transcriptomes. Front Genet 2022; 13:1068075. [PMID: 36531230 PMCID: PMC9754124 DOI: 10.3389/fgene.2022.1068075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/09/2022] [Indexed: 08/29/2023] Open
Abstract
The identification of cell types in complex tissues is an important step in research into cellular heterogeneity in disease. We present a linear fast semi-supervised clustering (LFSC) algorithm that utilizes reference samples generated from bulk RNA sequencing data to identify cell types from single-cell transcriptomes. An anchor graph is constructed to depict the relationship between reference samples and cells. By applying a connectivity constraint to the learned graph, LFSC enables the preservation of the underlying cluster structure. Moreover, the overall complexity of LFSC is linear to the size of the data, which greatly improves effectiveness and efficiency. By applying LFSC to real single-cell RNA sequencing datasets, we discovered that it has superior performance over existing baseline methods in clustering accuracy and robustness. An application using infiltrating T cells in liver cancer demonstrates that LFSC can successfully find new cell types, discover differently expressed genes, and explore new cancer-associated biomarkers.
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Affiliation(s)
- Qiaoming Liu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Yingjian Liang
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Dong Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jie Li
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
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13
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Cai S, Chen Z, Tang H, Meng S, Tao L, Wang Q. Upregulated FKBP1A Suppresses Glioblastoma Cell Growth via Apoptosis Pathway. Int J Mol Sci 2022; 23. [PMID: 36499275 DOI: 10.3390/ijms232314935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022] Open
Abstract
Glioblastoma (GBM), the most deadly primary brain tumor, presents a major medical difficulty. The need for better therapeutic targets in GBM is therefore urgent. A growing body of evidence suggests that the gene FKBP1A plays an important role in tumor progression and may be therapeutically useful. However, the role of FKBP1A in glioblastoma and the underlying biologic mechanism remain unclear. The purpose of this study was to identify the role of FKBP1A in GBM and its molecular mechanism. We demonstrated that FKBP1A was the hub gene in GBM via a weighted correlation network analysis (WGCNA) and differentially expressed genes (DEGs) analysis based on the bulk RNA-seq data from TCGA and GTEx. Afterwards, we proved that the upregulated FKBP1A protein could promote GBM cell death by CCK-8 assays in U87MG and t98g GBM cell lines. We further demonstrated two key pathways of FKBP1A in GBM by bioinformatics methods: 'Apoptosis' and 'mTOR signaling pathway'. Subsequently, the key pathways were verified by flow cytometry and Western blot. We identified that upregulated FKBP1A could inhibit GBM growth via the apoptosis pathway. Together, these findings may contribute to future GBM treatment.
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14
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Okereke LC, Bello AU, Onwukwe EA. Toward Precision Radiotherapy: A Nonlinear Optimization Framework and an Accelerated Machine Learning Algorithm for the Deconvolution of Tumor-Infiltrating Immune Cells. Cells 2022; 11:cells11223604. [PMID: 36429031 PMCID: PMC9688486 DOI: 10.3390/cells11223604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Tumor-infiltrating immune cells (TIICs) form a critical part of the ecosystem surrounding a cancerous tumor. Recent advances in radiobiology have shown that, in addition to damaging cancerous cells, radiotherapy drives the upregulation of immunosuppressive and immunostimulatory TIICs, which in turn impacts treatment response. Quantifying TIICs in tumor samples could form an important predictive biomarker guiding patient stratification and the design of radiotherapy regimens and combined immune-radiation treatments. As a result of several limitations associated with experimental methods for quantifying TIICs and the availability of extensive gene sequencing data, deconvolution-based computational methods have appeared as a suitable alternative for quantifying TIICs. Accordingly, we introduce and discuss a nonlinear regression approach (remarkably different from the traditional linear modeling approach of current deconvolution-based methods) and a machine learning algorithm for approximating the solution of the resulting constrained optimization problem. This way, the deconvolution problem is treated naturally, given that the gene expression levels of pure and heterogenous samples do not have a strictly linear relationship. When applied across transcriptomics datasets, our approach, which also allows the coupling of different loss functions, yields results that closely match ground-truth values from experimental methods and exhibits superior performance over popular deconvolution-based methods.
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Affiliation(s)
- Lois Chinwendu Okereke
- Department of Pure and Applied Mathematics, Mathematics Institute (Emerging Regional Centre of Excellence (ERCE) of the European Mathematical Society (EMS)), African University of Science and Technology, Abuja 900107, Nigeria
- Correspondence:
| | - Abdulmalik Usman Bello
- Department of Pure and Applied Mathematics, Mathematics Institute (Emerging Regional Centre of Excellence (ERCE) of the European Mathematical Society (EMS)), African University of Science and Technology, Abuja 900107, Nigeria
- Department of Mathematics, Federal University Dutsin-Ma, Dutsin-Ma 821101, Nigeria
| | - Emmanuel Akwari Onwukwe
- Department of Theoretical and Applied Physics, African University of Science and Technology, Abuja 900107, Nigeria
- Inspired Innovative Sustainable (IIS) Projects & Solutions Limited, Abuja 900107, Nigeria
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15
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Wang M, Wang X, Jiang B, Zhai Y, Zheng J, Yang L, Tai X, Li Y, Fu S, Xu J, Lei X, Kuang Z, Zhang C, Bai X, Li M, Zan T, Qu S, Li Q, Zhang C. Identification of MRAP protein family as broad-spectrum GPCR modulators. Clin Transl Med 2022; 12:e1091. [PMID: 36314066 PMCID: PMC9619224 DOI: 10.1002/ctm2.1091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The melanocortin receptor accessory proteins (MRAP1 and MRAP2) are well-known endocrine regulators for the trafficking and signalling of all five melanocortin receptors (MC1R-MC5R). The observation of MRAP2 on regulating several non-melanocortin G protein-coupled receptors (GPCRs) has been sporadically reported, whereas other endogenous GPCR partners of the MRAP protein family are largely unknown. METHODS Here, we performed single-cell transcriptome analysis and drew a fine GPCR blueprint and MRAPs-associated network of two major endocrine organs, the hypothalamus and adrenal gland at single-cell resolution. We also integrated multiple bulk RNA-seq profiles and single-cell datasets of human and mouse tissues, and narrowed down a list of 48 GPCRs with strong endogenous co-expression correlation with MRAPs. RESULTS 36 and 46 metabolic-related GPCRs were consequently identified as novel interacting partners of MRAP1 or MRAP2, respectively. MRAPs exhibited protein-protein interactions and varying pharmacological properties on the surface translocation, constitutive activities and ligand-stimulated downstream signalling of these GPCRs. Knockdown of MRAP2 expression by hypothalamic administration of adeno-associated virus (AAV) packed shRNA stimulated body weight gain in mouse model. Co-injection of corticotropinreleasing factor (CRF), the agonist of corticotropin releasing hormone receptor 1 (CRHR1), suppressed feeding behaviour in a MRAP2-dependent manner. CONCLUSIONS Collectively, our study has comprehensively elucidated the complex GPCR networks in two major endocrine organs and redefined the MRAP protein family as broad-spectrum GPCR modulators. MRAP proteins not only serve as a vital endocrine pivot on the regulation of global GPCR activities in vivo that could explain the composite physiological phenotypes of the MRAP2 null murine model but also provide us with new insights of the phenotyping investigation of GPCR-MRAP functional complexes.
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Affiliation(s)
- Meng Wang
- Department of Plastic and Reconstructive SurgeryShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xiaozhu Wang
- Department of Plastic and Reconstructive SurgeryShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Bopei Jiang
- School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Yue Zhai
- School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Jihong Zheng
- School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Liu Yang
- Department of Endocrinology and MetabolismNational Metabolic Management CenterShanghai Tenth People's HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Xiaolu Tai
- School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Yunpeng Li
- School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Shaliu Fu
- School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Jing Xu
- School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Xiaowei Lei
- School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Zhe Kuang
- School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Cong Zhang
- Department of Plastic and Reconstructive SurgeryShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xuanxuan Bai
- School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Mingyu Li
- Fujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiamenChina
| | - Tao Zan
- Department of Plastic and Reconstructive SurgeryShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Shen Qu
- Department of Endocrinology and MetabolismNational Metabolic Management CenterShanghai Tenth People's HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Qingfeng Li
- Department of Plastic and Reconstructive SurgeryShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Chao Zhang
- Department of Plastic and Reconstructive SurgeryShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
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16
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Lai W, Li D, Kuang J, Deng L, Lu Q. Integrated analysis of single-cell RNA-seq dataset and bulk RNA-seq dataset constructs a prognostic model for predicting survival in human glioblastoma. Brain Behav 2022; 12:e2575. [PMID: 35429411 PMCID: PMC9120724 DOI: 10.1002/brb3.2575] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/20/2022] [Accepted: 03/20/2022] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Glioblastoma (GBM) is the most common primary malignant brain tumor in adults. For patients with GBM, the median overall survival (OS) is 14.6 months and the 5-year survival rate is 7.2%. It is imperative to develop a reliable model to predict the survival probability in new GBM patients. To date, most prognostic models for predicting survival in GBM were constructed based on bulk RNA-seq dataset, which failed to accurately reflect the difference between tumor cores and peripheral regions, and thus show low predictive capability. An effective prognostic model is desperately needed in clinical practice. METHODS We studied single-cell RNA-seq dataset and The Cancer Genome Atlas-glioblastoma multiforme (TCGA-GBM) dataset to identify differentially expressed genes (DEGs) that impact the OS of GBM patients. We then applied the least absolute shrinkage and selection operator (LASSO) Cox penalized regression analysis to determine the optimal genes to be included in our risk score prognostic model. Then, we used another dataset to test the accuracy of our risk score prognostic model. RESULTS We identified 2128 DEGs from the single-cell RNA-seq dataset and 6461 DEGs from the bulk RNA-seq dataset. In addition, 896 DEGs associated with the OS of GBM patients were obtained. Five of these genes (LITAF, MTHFD2, NRXN3, OSMR, and RUFY2) were selected to generate a risk score prognostic model. Using training and validation datasets, we found that patients in the low-risk group showed better OS than those in the high-risk group. We validated our risk score model with the training and validating datasets and demonstrated that it can effectively predict the OS of GBM patients. CONCLUSION We constructed a novel prognostic model to predict survival in GBM patients by integrating a scRNA-seq dataset and a bulk RNA-seq dataset. Our findings may advance the development of new therapeutic targets and improve clinical outcomes for GBM patients.
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Affiliation(s)
- Wenwen Lai
- Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang, China.,Department of Biostatistics and Epidemiology, School of Public Health, Nanchang University, Nanchang, China
| | - Defu Li
- Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang, China.,Department of Biostatistics and Epidemiology, School of Public Health, Nanchang University, Nanchang, China
| | - Jie Kuang
- Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang, China
| | - Libin Deng
- Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang, China.,Department of Biostatistics and Epidemiology, School of Public Health, Nanchang University, Nanchang, China
| | - Quqin Lu
- Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang, China.,Department of Biostatistics and Epidemiology, School of Public Health, Nanchang University, Nanchang, China
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17
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Roos K, Rooda I, Keif RS, Liivrand M, Smolander OP, Salumets A, Velthut-Meikas A. Single-cell RNA-seq analysis and cell-cluster deconvolution of the human preovulatory follicular fluid cells provide insights into the pathophysiology of ovarian hyporesponse. Front Endocrinol (Lausanne) 2022; 13:945347. [PMID: 36339426 PMCID: PMC9635625 DOI: 10.3389/fendo.2022.945347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/22/2022] [Indexed: 11/13/2022] Open
Abstract
Reduction in responsiveness to gonadotropins or hyporesponsiveness may lead to the failure of in vitro fertilization (IVF), due to a low number of retrieved oocytes. The ovarian sensitivity index (OSI) is used to reflect the ovarian responsiveness to gonadotropin stimulation before IVF. Although introduced to clinical practice already years ago, its usefulness to predict clinical outcomes requires further research. Nevertheless, pathophysiological mechanisms of ovarian hyporesponse, along with advanced maternal age and in younger women, have not been fully elucidated. Follicles consist of multiple cell types responsible for a repertoire of biological processes including responding to pituitary gonadotropins necessary for follicle growth and oocyte maturation as well as ovulation. Encouraging evidence suggests that hyporesponse could be influenced by many contributing factors, therefore, investigating the variability of ovarian follicular cell types and their gene expression in hyporesponders is highly informative for increasing their prognosis for IVF live birth. Due to advancements in single-cell analysis technologies, the role of somatic cell populations in the development of infertility of ovarian etiology can be clarified. Here, somatic cells were collected from the fluid of preovulatory ovarian follicles of patients undergoing IVF, and RNA-seq was performed to study the associations between OSI and gene expression. We identified 12 molecular pathways differentially regulated between hypo- and normoresponder patient groups (FDR<0.05) from which extracellular matrix organization, post-translational protein phosphorylation, and regulation of Insulin-like Growth Factor (IGF) transport and uptake by IGF Binding Proteins were regulated age-independently. We then generated single-cell RNA-seq data from matching follicles revealing 14 distinct cell clusters. Using cell cluster-specific deconvolution from the bulk RNA-seq data of 18 IVF patients we integrated the datasets as a novel approach and discovered that the abundance of three cell clusters significantly varied between hypo- and normoresponder groups suggesting their role in contributing to the deviations from normal ovarian response to gonadotropin stimulation. Our work uncovers new information regarding the differences in the follicular gene expression between hypo- and normoresponders. In addition, the current study fills the gap in understanding the inter-patient variability of cell types in human preovulatory follicles, as revealed by single-cell analysis of follicular fluid cells.
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Affiliation(s)
- Kristine Roos
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
- Nova Vita Clinic AS, Tallinn, Estonia
| | - Ilmatar Rooda
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Robyn-Stefany Keif
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Maria Liivrand
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Olli-Pekka Smolander
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Andres Salumets
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Agne Velthut-Meikas
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
- *Correspondence: Agne Velthut-Meikas,
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18
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Xu S, Mei S, Lu J, Wu H, Dong X, Shi L, Zhou J, Zhang J. Transcriptome Analysis of Microglia Reveals That the TLR2/IRF7 Signaling Axis Mediates Neuroinflammation After Subarachnoid Hemorrhage. Front Aging Neurosci 2021; 13:645649. [PMID: 34276335 PMCID: PMC8278202 DOI: 10.3389/fnagi.2021.645649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/19/2021] [Indexed: 12/23/2022] Open
Abstract
Microglia-mediated neuroinflammatory response in the early brain injury after subarachnoid hemorrhage (SAH) has been reported to have an impact on progress, and the mechanism is not completely understood. Here, we performed genome-wide transcriptome analysis of microglia purified from damaged hemisphere of adult mice at 3 days after SAH or sham operation. Robust transcriptional changes were observed between SAH-induced and healthy microglia, indicating rapid activation of microglia after suffering from SAH. We identified 1576 differentially expressed genes (DEGs; 928 upregulated and 648 downregulated) in SAH-induced microglia compared with sham microglia, representing a strong alteration of the genome (6.85% of total ∼23,000 genes). Functional enrichment of these DEGs indicated that cell division, inflammatory response, cytokine production, and leukocyte chemotaxis were strongly activated in SAH-induced microglia. Moreover, we identified and proved that the TLR2/IRF7 signaling axis was involved in the regulation of this microglia-mediated inflammation in SAH mice by performing flow cytometry and immunofluorescence. Together, these results provided a perspective of microglia-mediated neuroinflammatory response in the early stage of SAH and might give a new therapeutic target for SAH.
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Affiliation(s)
- Shenbin Xu
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Shuhao Mei
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jianan Lu
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Haijian Wu
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiao Dong
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ligen Shi
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jingyi Zhou
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jianmin Zhang
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Brain Research Institute, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Brain Science, Zhejiang University, Hangzhou, China
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19
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He X, Liu L, Chen B, Wu C. Using Cell Type-Specific Genes to Identify Cell-Type Transitions Between Different in vitro Culture Conditions. Front Cell Dev Biol 2021; 9:644261. [PMID: 34249906 PMCID: PMC8267371 DOI: 10.3389/fcell.2021.644261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 04/09/2021] [Indexed: 11/13/2022] Open
Abstract
In vitro differentiation or expansion of stem and progenitor cells under chemical stimulation or genetic manipulation is used for understanding the molecular mechanisms of cell differentiation and self-renewal. However, concerns around the cell identity of in vitro-cultured cells exist. Bioinformatics methods, which rely heavily on signatures of cell types, have been developed to estimate cell types in bulk samples. The Tabula Muris Senis project provides an important basis for the comprehensive identification of signatures for different cell types. Here, we identified 46 cell type-specific (CTS) gene clusters for 83 mouse cell types. We conducted Gene Ontology term enrichment analysis on the gene clusters and revealed the specific functions of the relevant cell types. Next, we proposed a simple method, named CTSFinder, to identify different cell types between bulk RNA-Seq samples using the 46 CTS gene clusters. We applied CTSFinder on bulk RNA-Seq data from 17 organs and from developing mouse liver over different stages. We successfully identified the specific cell types between organs and captured the dynamics of different cell types during liver development. We applied CTSFinder with bulk RNA-Seq data from a growth factor-induced neural progenitor cell culture system and identified the dynamics of brain immune cells and nonimmune cells during the long-time cell culture. We also applied CTSFinder with bulk RNA-Seq data from reprogramming induced pluripotent stem cells and identified the stage when those cells were massively induced. Finally, we applied CTSFinder with bulk RNA-Seq data from in vivo and in vitro developing mouse retina and captured the dynamics of different cell types in the two development systems. The CTS gene clusters and CTSFinder method could thus serve as promising toolkits for assessing the cell identity of in vitro culture systems.
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Affiliation(s)
- Xuelin He
- Department of Nephrology, Beilun People's Hospital, Ningbo, China.,Kidney Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Hangzhou, China
| | - Li Liu
- Department of Library, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Baode Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chao Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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20
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Aliee H, Theis FJ. AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution. Cell Syst 2021; 12:706-715.e4. [PMID: 34293324 DOI: 10.1016/j.cels.2021.05.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 07/31/2020] [Accepted: 05/07/2021] [Indexed: 12/25/2022]
Abstract
Knowing cell-type proportions in a tissue is very important to identify which cells or cell types are targeted by a disease or perturbation. Hence, several deconvolution methods have been proposed to infer cell-type proportions from bulk RNA samples. Their performance with noisy reference profiles and closely correlated cell types highly depends on the set of genes undergoing deconvolution. In this work, we introduce AutoGeneS, a platform that automatically extracts discriminative genes and reveals the cellular heterogeneity of bulk RNA samples. AutoGeneS requires no prior knowledge about marker genes and selects genes by simultaneously optimizing multiple criteria: minimizing the correlation and maximizing the distance between cell types. AutoGeneS can be applied to reference profiles from various sources like single-cell experiments or sorted cell populations. Ground truth cell proportions analyzed by flow cytometry confirmed the accuracy of AutoGeneS in identifying cell-type proportions. AutoGeneS is available for use via a standalone Python package (https://github.com/theislab/AutoGeneS).
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Affiliation(s)
- Hananeh Aliee
- Institute of Computational Biology, Helmholtz Centre, Munich, Bayern 85764, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Centre, Munich, Bayern 85764, Germany; Department of Mathematics, Technical University of Munich, Munich, Bayern 85748, Germany; TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.
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21
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Khalyfa A, Warren W, Andrade J, Bottoms CA, Rice ES, Cortese R, Kheirandish-Gozal L, Gozal D. Transcriptomic Changes of Murine Visceral Fat Exposed to Intermittent Hypoxia at Single Cell Resolution. Int J Mol Sci 2020; 22:E261. [PMID: 33383883 DOI: 10.3390/ijms22010261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/22/2020] [Accepted: 12/24/2020] [Indexed: 12/12/2022] Open
Abstract
Intermittent hypoxia (IH) is a hallmark of obstructive sleep apnea (OSA) and induces metabolic dysfunction manifesting as inflammation, increased lipolysis and insulin resistance in visceral white adipose tissues (vWAT). However, the cell types and their corresponding transcriptional pathways underlying these functional perturbations are unknown. Here, we applied single nucleus RNA sequencing (snRNA-seq) coupled with aggregate RNA-seq methods to evaluate the cellular heterogeneity in vWAT following IH exposures mimicking OSA. C57BL/6 male mice were exposed to IH and room air (RA) for 6 weeks, and nuclei from vWAT were isolated and processed for snRNA-seq followed by differential expressed gene (DEGs) analyses by cell type, along with gene ontology and canonical pathways enrichment tests of significance. IH induced significant transcriptional changes compared to RA across 14 different cell types identified in vWAT. We identified cell-specific signature markers, transcriptional networks, metabolic signaling pathways, and cellular subpopulation enrichment in vWAT. Globally, we also identify 298 common regulated genes across multiple cellular types that are associated with metabolic pathways. Deconvolution of cell types in vWAT using global RNA-seq revealed that distinct adipocytes appear to be differentially implicated in key aspects of metabolic dysfunction. Thus, the heterogeneity of vWAT and its response to IH at the cellular level provides important insights into the metabolic morbidity of OSA and may possibly translate into therapeutic targets.
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Affiliation(s)
- Koji Kadota
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.,Interfaculty Initiative in Information Studies, The University of Tokyo, Tokyo, Japan
| | - Kentaro Shimizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.,Interfaculty Initiative in Information Studies, The University of Tokyo, Tokyo, Japan
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