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Yu J, Leng J, Hou Z, Sun D, Wu LY. Incorporating network diffusion and peak location information for better single-cell ATAC-seq data analysis. Brief Bioinform 2024; 25:bbae093. [PMID: 38493346 PMCID: PMC10944575 DOI: 10.1093/bib/bbae093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/22/2023] [Accepted: 02/20/2024] [Indexed: 03/18/2024] Open
Abstract
Single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) data provided new insights into the understanding of epigenetic heterogeneity and transcriptional regulation. With the increasing abundance of dataset resources, there is an urgent need to extract more useful information through high-quality data analysis methods specifically designed for scATAC-seq. However, analyzing scATAC-seq data poses challenges due to its near binarization, high sparsity and ultra-high dimensionality properties. Here, we proposed a novel network diffusion-based computational method to comprehensively analyze scATAC-seq data, named Single-Cell ATAC-seq Analysis via Network Refinement with Peaks Location Information (SCARP). SCARP formulates the Network Refinement diffusion method under the graph theory framework to aggregate information from different network orders, effectively compensating for missing signals in the scATAC-seq data. By incorporating distance information between adjacent peaks on the genome, SCARP also contributes to depicting the co-accessibility of peaks. These two innovations empower SCARP to obtain lower-dimensional representations for both cells and peaks more effectively. We have demonstrated through sufficient experiments that SCARP facilitated superior analyses of scATAC-seq data. Specifically, SCARP exhibited outstanding cell clustering performance, enabling better elucidation of cell heterogeneity and the discovery of new biologically significant cell subpopulations. Additionally, SCARP was also instrumental in portraying co-accessibility relationships of accessible regions and providing new insight into transcriptional regulation. Consequently, SCARP identified genes that were involved in key Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to diseases and predicted reliable cis-regulatory interactions. To sum up, our studies suggested that SCARP is a promising tool to comprehensively analyze the scATAC-seq data.
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Affiliation(s)
- Jiating Yu
- School of Mathematics and Statistics, Nanjing University of Information Science & Technology, Nanjing 210044, China
- IAM, MADIS, NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiacheng Leng
- IAM, MADIS, NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Zhejiang Lab, Hangzhou 311121, China
| | - Zhichao Hou
- IAM, MADIS, NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Duanchen Sun
- School of Mathematics, Shandong University, Jinan 250100, China
| | - Ling-Yun Wu
- IAM, MADIS, NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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Wang EJY, Chen IH, Kuo BYT, Yu CC, Lai MT, Lin JT, Lin LYT, Chen CM, Hwang T, Sheu JJC. Alterations of Cytoskeleton Networks in Cell Fate Determination and Cancer Development. Biomolecules 2022; 12:biom12121862. [PMID: 36551290 PMCID: PMC9775460 DOI: 10.3390/biom12121862] [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: 11/03/2022] [Revised: 12/03/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022] Open
Abstract
Cytoskeleton proteins have been long recognized as structural proteins that provide the necessary mechanical architecture for cell development and tissue homeostasis. With the completion of the cancer genome project, scientists were surprised to learn that huge numbers of mutated genes are annotated as cytoskeletal or associated proteins. Although most of these mutations are considered as passenger mutations during cancer development and evolution, some genes show high mutation rates that can even determine clinical outcomes. In addition, (phospho)proteomics study confirms that many cytoskeleton-associated proteins, e.g., β-catenin, PIK3CA, and MB21D2, are important signaling mediators, further suggesting their biofunctional roles in cancer development. With emerging evidence to indicate the involvement of mechanotransduction in stemness formation and cell differentiation, mutations in these key cytoskeleton components may change the physical/mechanical properties of the cells and determine the cell fate during cancer development. In particular, tumor microenvironment remodeling triggered by such alterations has been known to play important roles in autophagy, metabolism, cancer dormancy, and immune evasion. In this review paper, we will highlight the current understanding of how aberrant cytoskeleton networks affect cancer behaviors and cellular functions through mechanotransduction.
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Affiliation(s)
- Evan Ja-Yang Wang
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - I-Hsuan Chen
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813405, Taiwan
- Department of Pharmacy, College of Pharmacy and Health Care, Tajen University, Pingtung County 907391, Taiwan
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Brian Yu-Ting Kuo
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - Chia-Cheng Yu
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813405, Taiwan
- Department of Pharmacy, College of Pharmacy and Health Care, Tajen University, Pingtung County 907391, Taiwan
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 114202, Taiwan
| | - Ming-Tsung Lai
- Department of Pathology, Taichung Hospital, Ministry of Health and Welfare, Taichung 403301, Taiwan
| | - Jen-Tai Lin
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813405, Taiwan
| | - Leo Yen-Ting Lin
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - Chih-Mei Chen
- Human Genetic Center, China Medical University Hospital, Taichung 404327, Taiwan
| | - Tritium Hwang
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - Jim Jinn-Chyuan Sheu
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Institute of Biopharmaceutical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
- Institute of Precision Medicine, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
- Correspondence: ; Tel.: +886-7-5252000 (ext. 7102)
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Zhou R, Lu G, Yan Z, Jiang R, Sun Y, Zhang P. Epigenetic mechanisms of DNA methylation in the transgenerational effect of ethylhexyl salicylate on zebrafish. CHEMOSPHERE 2022; 295:133926. [PMID: 35150701 DOI: 10.1016/j.chemosphere.2022.133926] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/24/2022] [Accepted: 02/06/2022] [Indexed: 06/14/2023]
Abstract
In this study, a 120-day whole-life cycle exposure and oviposition experiment on zebrafish with maternal and paternal mixed mating strategy was conducted to investigate the epigenetic mechanism of DNA methylation in ethylhexyl salicylate (EHS, 1, 10, 100 μg/L)-induced transgenerational effects. Results showed that EHS could induce the decrease of DNA methyltransferase 1 (DNMT1) activity and average global DNA methylation level in maternal parents and the increase of the above indexes in paternal parents, while the change of glycine N-methyltransferase activity was opposite to DNMT1. The average global DNA methylation levels were significantly increased in the offsprings of both parents exposed and father-only exposed to EHS, suggesting that EHS-induced epigenetic modifications may be stable and heritable. Hierarchical clustering analysis of promoter at different methylation sites showed that the DNA methylation pattern of offsprings were similar to that of the paternal parents, meaning that the offsprings may have inherited paternal DNA methylation pattern with eya2, pcdh2g5 and pcdh2g1 as key genes and lead to high locomotor activity in offsprings. KEGG pathway analysis showed that parental exposure to EHS may interfere with the central nervous system, insulin function system, melanogenesis system and the normal development of somatic axis of offsprings.
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Affiliation(s)
- Ranran Zhou
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China; School of Environmental Science & Engineering, Nanjing Tech University, 30 Puzhu Southern Road, Nanjing, 211816, China
| | - Guanghua Lu
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Zhenhua Yan
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Runren Jiang
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yu Sun
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Peng Zhang
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
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