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Yin H, Duo H, Li S, Qin D, Xie L, Xiao Y, Sun J, Tao J, Zhang X, Li Y, Zou Y, Yang Q, Yang X, Hao Y, Li B. Unlocking biological insights from differentially expressed genes: Concepts, methods, and future perspectives. J Adv Res 2024:S2090-1232(24)00560-5. [PMID: 39647635 DOI: 10.1016/j.jare.2024.12.004] [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: 07/28/2024] [Revised: 10/12/2024] [Accepted: 12/03/2024] [Indexed: 12/10/2024] Open
Abstract
BACKGROUND Identifying differentially expressed genes (DEGs) is a core task of transcriptome analysis, as DEGs can reveal the molecular mechanisms underlying biological processes. However, interpreting the biological significance of large DEG lists is challenging. Currently, gene ontology, pathway enrichment and protein-protein interaction analysis are common strategies employed by biologists. Additionally, emerging analytical strategies/approaches (such as network module analysis, knowledge graph, drug repurposing, cell marker discovery, trajectory analysis, and cell communication analysis) have been proposed. Despite these advances, comprehensive guidelines for systematically and thoroughly mining the biological information within DEGs remain lacking. AIM OF REVIEW This review aims to provide an overview of essential concepts and methodologies for the biological interpretation of DEGs, enhancing the contextual understanding. It also addresses the current limitations and future perspectives of these approaches, highlighting their broad applications in deciphering the molecular mechanism of complex diseases and phenotypes. To assist users in extracting insights from extensive datasets, especially various DEG lists, we developed DEGMiner (https://www.ciblab.net/DEGMiner/), which integrates over 300 easily accessible databases and tools. KEY SCIENTIFIC CONCEPTS OF REVIEW This review offers strong support and guidance for exploring DEGs, and also will accelerate the discovery of hidden biological insights within genomes.
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Affiliation(s)
- Huachun Yin
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China; Department of Neurosurgery, Xinqiao Hospital, The Army Medical University, Chongqing 400037, PR China; Department of Neurobiology, Chongqing Key Laboratory of Neurobiology, The Army Medical University, Chongqing 400038, PR China
| | - Hongrui Duo
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Song Li
- Department of Neurosurgery, Xinqiao Hospital, The Army Medical University, Chongqing 400037, PR China
| | - Dan Qin
- Department of Biology, College of Science, Northeastern University, Boston, MA 02115, USA
| | - Lingling Xie
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Yingxue Xiao
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Jing Sun
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Jingxin Tao
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Xiaoxi Zhang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Yinghong Li
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, PR China
| | - Yue Zou
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Qingxia Yang
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, PR China
| | - Xian Yang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Youjin Hao
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China.
| | - Bo Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China.
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Thakur BL, Baris AM, Fu H, Redon CE, Pongor L, Mosavarpour S, Gross J, Jang SM, Sebastian R, Utani K, Jenkins L, Indig F, Aladjem M. Convergence of SIRT1 and ATR signaling to modulate replication origin dormancy. Nucleic Acids Res 2022; 50:5111-5128. [PMID: 35524559 PMCID: PMC9122590 DOI: 10.1093/nar/gkac299] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 04/08/2022] [Accepted: 04/13/2022] [Indexed: 11/15/2023] Open
Abstract
During routine genome duplication, many potential replication origins remain inactive or 'dormant'. Such origin dormancy is achieved, in part, by an interaction with the metabolic sensor SIRT1 deacetylase. We report here that dormant origins are a group of consistent, pre-determined genomic sequences that are distinguished from baseline (i.e. ordinarily active) origins by their preferential association with two phospho-isoforms of the helicase component MCM2. During normal unperturbed cell growth, baseline origins, but not dormant origins, associate with a form of MCM2 that is phosphorylated by DBF4-dependent kinase (DDK) on serine 139 (pS139-MCM2). This association facilitates the initiation of DNA replication from baseline origins. Concomitantly, SIRT1 inhibits Ataxia Telangiectasia and Rad3-related (ATR)-kinase-mediated phosphorylation of MCM2 on serine 108 (pS108-MCM2) by deacetylating the ATR-interacting protein DNA topoisomerase II binding protein 1 (TOPBP1), thereby preventing ATR recruitment to chromatin. In cells devoid of SIRT1 activity, or challenged by replication stress, this inhibition is circumvented, enabling ATR-mediated S108-MCM2 phosphorylation. In turn, pS108-MCM2 enables DDK-mediated phosphorylation on S139-MCM2 and facilitates replication initiation at dormant origins. These observations suggest that replication origin dormancy and activation are regulated by distinct post-translational MCM modifications that reflect a balance between SIRT1 activity and ATR signaling.
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Affiliation(s)
- Bhushan L Thakur
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892-4255, USA
| | - Adrian M Baris
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892-4255, USA
| | - Haiqing Fu
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892-4255, USA
| | - Christophe E Redon
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892-4255, USA
| | - Lorinc S Pongor
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892-4255, USA
| | - Sara Mosavarpour
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892-4255, USA
| | - Jacob M Gross
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892-4255, USA
| | - Sang-Min Jang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892-4255, USA
| | - Robin Sebastian
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892-4255, USA
| | - Koichi Utani
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892-4255, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892-4255, USA
| | - Fred E Indig
- Confocal Imaging Facility, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892-4255, USA
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Yang Y, Liu Y, Wang Y, Chao Y, Zhang J, Jia Y, Tie J, Hu D. Regulation of SIRT1 and Its Roles in Inflammation. Front Immunol 2022; 13:831168. [PMID: 35359990 PMCID: PMC8962665 DOI: 10.3389/fimmu.2022.831168] [Citation(s) in RCA: 177] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/15/2022] [Indexed: 12/28/2022] Open
Abstract
The silent information regulator sirtuin 1 (SIRT1) protein, a highly conserved NAD+-dependent deacetylase belonging to the sirtuin family, is a post-translational regulator that plays a role in modulating inflammation. SIRT1 affects multiple biological processes by deacetylating a variety of proteins including histones and non-histone proteins. Recent studies have revealed intimate links between SIRT1 and inflammation, while alterations to SIRT1 expression and activity have been linked to inflammatory diseases. In this review, we summarize the mechanisms that regulate SIRT1 expression, including upstream activators and suppressors that operate on the transcriptional and post-transcriptional levels. We also summarize factors that influence SIRT1 activity including the NAD+/NADH ratio, SIRT1 binding partners, and post-translational modifications. Furthermore, we underscore the role of SIRT1 in the development of inflammation by commenting on the proteins that are targeted for deacetylation by SIRT1. Finally, we highlight the potential for SIRT1-based therapeutics for inflammatory diseases.
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Affiliation(s)
- Yunshu Yang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Yang Liu
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Yunwei Wang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Yongyi Chao
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Jinxin Zhang
- Department of Emergency, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Yanhui Jia
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Jun Tie
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi’an, China
- *Correspondence: Dahai Hu, ; Jun Tie,
| | - Dahai Hu
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
- *Correspondence: Dahai Hu, ; Jun Tie,
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Regulation of histone deacetylase activities and functions by phosphorylation and its physiological relevance. Cell Mol Life Sci 2020; 78:427-445. [PMID: 32683534 DOI: 10.1007/s00018-020-03599-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/02/2020] [Accepted: 07/09/2020] [Indexed: 12/31/2022]
Abstract
Histone deacetylases (HDACs) are conserved enzymes that regulate many cellular processes by catalyzing the removal of acetyl groups from lysine residues on histones and non-histone proteins. As appropriate for proteins that occupy such an essential biological role, HDAC activities and functions are in turn highly regulated. Overwhelming evidence suggests that the dysregulation of HDACs plays a major role in many human diseases. The regulation of HDACs is achieved by multiple different mechanisms, including posttranslational modifications. One of the most common posttranslational modifications on HDACs is reversible phosphorylation. Many HDAC phosphorylations are context-dependent, occurring in specific tissues or as a consequence of certain stimuli. Additionally, whereas phosphorylation can regulate some HDACs in a non-specific manner, many HDAC phosphorylations result in specific consequences. Although some of these modifications support normal HDAC function, aberrations can contribute to disease development. Here we review and critically evaluate how reversible phosphorylation activates or deactivates HDACs and, thereby, regulates their many functions under various cellular and physiological contexts.
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Kino T. GR-regulating Serine/Threonine Kinases: New Physiologic and Pathologic Implications. Trends Endocrinol Metab 2018; 29:260-270. [PMID: 29501228 DOI: 10.1016/j.tem.2018.01.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 12/17/2022]
Abstract
Glucocorticoid hormones, end products of the hypothalamic-pituitary-adrenal axis, virtually influence all human functions both in a basal homeostatic condition and under stress. The glucocorticoid receptor (GR), a nuclear hormone receptor superfamily protein, mediates these actions of glucocorticoids by acting as a ligand-dependent transcription factor. Because glucocorticoid actions are diverse and strong, many biological pathways adjust them in local tissues by targeting the GR signaling pathway as part of the regulatory loop coordinating complex human functions. Phosphorylation of GR protein by serine/threonine kinases is one of the major regulatory mechanisms for this communication. In this review, recent progress in research investigating GR phosphorylation by these kinases is discussed, along with the possible physiologic and pathophysiologic implications.
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Affiliation(s)
- Tomoshige Kino
- Department of Human Genetics, Division of Translational Medicine, Sidra Medical and Research Center, Doha 26999, Qatar.
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Candidate Gene Identification of Feed Efficiency and Coat Color Traits in a C57BL/6J × Kunming F2 Mice Population Using Genome-Wide Association Study. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7132941. [PMID: 28828387 PMCID: PMC5554547 DOI: 10.1155/2017/7132941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 06/21/2017] [Indexed: 11/18/2022]
Abstract
Feed efficiency (FE) is a very important trait in livestock industry. Identification of the candidate genes could be of benefit for the improvement of FE trait. Mouse is used as the model for many studies in mammals. In this study, the candidate genes related to FE and coat color were identified using C57BL/6J (C57) × Kunming (KM) F2 mouse population. GWAS results showed that 61 and 2 SNPs were genome-wise suggestive significantly associated with feed conversion ratio (FCR) and feed intake (FI) traits, respectively. Moreover, the Erbin, Msrb2, Ptf1a, and Fgf10 were considered as the candidate genes of FE. The Lpl was considered as the candidate gene of FI. Further, the coat color trait was studied. KM mice are white and C57 ones are black. The GWAS results showed that the most significant SNP was located at chromosome 7, and the closely linked gene was Tyr. Therefore, our study offered useful target genes related to FE in mice; these genes may play similar roles in FE of livestock. Also, we identified the major gene of coat color in mice, which would be useful for better understanding of natural mutation of the coat color in mice.
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Obesity-Linked Phosphorylation of SIRT1 by Casein Kinase 2 Inhibits Its Nuclear Localization and Promotes Fatty Liver. Mol Cell Biol 2017; 37:MCB.00006-17. [PMID: 28533219 DOI: 10.1128/mcb.00006-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/05/2017] [Indexed: 12/15/2022] Open
Abstract
Sirtuin1 (SIRT1) deacetylase delays and improves many obesity-related diseases, including nonalcoholic fatty liver disease (NAFLD) and diabetes, and has received great attention as a drug target. SIRT1 function is aberrantly low in obesity, so understanding the underlying mechanisms is important for drug development. Here, we show that obesity-linked phosphorylation of SIRT1 inhibits its function and promotes pathological symptoms of NAFLD. In proteomic analysis, Ser-164 was identified as a major serine phosphorylation site in SIRT1 in obese, but not lean, mice, and this phosphorylation was catalyzed by casein kinase 2 (CK2), the levels of which were dramatically elevated in obesity. Mechanistically, phosphorylation of SIRT1 at Ser-164 substantially inhibited its nuclear localization and modestly affected its deacetylase activity. Adenovirus-mediated liver-specific expression of SIRT1 or a phosphor-defective S164A-SIRT1 mutant promoted fatty acid oxidation and ameliorated liver steatosis and glucose intolerance in diet-induced obese mice, but these beneficial effects were not observed in mice expressing a phosphor-mimic S164D-SIRT1 mutant. Remarkably, phosphorylated S164-SIRT1 and CK2 levels were also highly elevated in liver samples of NAFLD patients and correlated with disease severity. Thus, inhibition of phosphorylation of SIRT1 by CK2 may serve as a new therapeutic approach for treatment of NAFLD and other obesity-related diseases.
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Lu J, Xu Q, Ji M, Guo X, Xu X, Fargo DC, Li X. The phosphorylation status of T522 modulates tissue-specific functions of SIRT1 in energy metabolism in mice. EMBO Rep 2017; 18:841-857. [PMID: 28364022 PMCID: PMC5412809 DOI: 10.15252/embr.201643803] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/21/2017] [Accepted: 02/22/2017] [Indexed: 12/31/2022] Open
Abstract
SIRT1, the most conserved mammalian NAD+-dependent protein deacetylase, is an important metabolic regulator. However, the mechanisms by which SIRT1 is regulated in vivo remain unclear. Here, we report that phosphorylation modification of T522 on SIRT1 is crucial for tissue-specific regulation of SIRT1 activity in mice. Dephosphorylation of T522 is critical for repression of its activity during adipogenesis. The phospho-T522 level is reduced during adipogenesis. Knocking-in a constitutive T522 phosphorylation mimic activates the β-catenin/GATA3 pathway, repressing PPARγ signaling, impairing differentiation of white adipocytes, and ameliorating high-fat diet-induced dyslipidemia in mice. In contrast, phosphorylation of T522 is crucial for activation of hepatic SIRT1 in response to over-nutrition. Hepatic SIRT1 is hyperphosphorylated at T522 upon high-fat diet feeding. Knocking-in a SIRT1 mutant defective in T522 phosphorylation disrupts hepatic fatty acid oxidation, resulting in hepatic steatosis after high-fat diet feeding. In addition, the T522 dephosphorylation mimic impairs systemic energy metabolism. Our findings unveil an important link between environmental cues, SIRT1 phosphorylation, and energy homeostasis and demonstrate that the phosphorylation of T522 is a critical element in tissue-specific regulation of SIRT1 activity in vivo.
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Affiliation(s)
- Jing Lu
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Qing Xu
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Ming Ji
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Xiumei Guo
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Xiaojiang Xu
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - David C Fargo
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Xiaoling Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
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