151
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Attwaters M. A TRIP to understand gene regulation. Nat Rev Genet 2024; 25:234. [PMID: 38355835 DOI: 10.1038/s41576-024-00706-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
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152
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Rivedal M, Mikkelsen H, Marti HP, Liu L, Kiryluk K, Knoop T, Bjørneklett R, Haaskjold YL, Furriol J, Leh S, Paunas F, Bábíčková J, Scherer A, Serre C, Eikrem O, Strauss P. Glomerular transcriptomics predicts long term outcome and identifies therapeutic strategies for patients with assumed benign IgA nephropathy. Kidney Int 2024; 105:717-730. [PMID: 38154557 DOI: 10.1016/j.kint.2023.12.010] [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: 10/21/2022] [Revised: 11/17/2023] [Accepted: 12/08/2023] [Indexed: 12/30/2023]
Abstract
Some patients diagnosed with benign IgA nephropathy (IgAN) develop a progressive clinical course, not predictable by known clinical or histopathological parameters. To assess if gene expression can differentiate between progressors and non-progressors with assumed benign IgAN, we tested microdissected glomeruli from archival kidney biopsy sections from adult patients with stable clinical remission (21 non-progressors) or from 15 patients that had undergone clinical progression within a 25-year time frame. Based on 1 240 differentially expressed genes from patients with suitable sequencing results, we identified eight IgAN progressor and nine non-progressor genes using a two-component classifier. These genes, including APOL5 and ZXDC, predicted disease progression with 88% accuracy, 75% sensitivity and 100% specificity on average 21.6 years before progressive disease was clinically documented. APOL lipoproteins are associated with inflammation, autophagy and kidney disease while ZXDC is a zinc-finger transcription factor modulating adaptive immunity. Ten genes from our transcriptomics data overlapped with an external genome wide association study dataset, although the gene set enrichment test was not statistically significant. We also identified 45 drug targets in the DrugBank database, including angiotensinogen, a target of sparsentan (dual antagonist of the endothelin type A receptor and the angiotensin II type 1 receptor) currently investigated for IgAN treatment. Two validation cohorts were used for substantiating key results, one by immunohistochemistry and the other by nCounter technology. Thus, glomerular mRNA sequencing from diagnostic kidney biopsies from patients with assumed benign IgAN can differentiate between future progressors and non-progressors at the time of diagnosis.
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Affiliation(s)
- Mariell Rivedal
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Håvard Mikkelsen
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hans-Peter Marti
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Lili Liu
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Krzysztof Kiryluk
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA; Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Thomas Knoop
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Rune Bjørneklett
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
| | - Yngvar Lunde Haaskjold
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Jessica Furriol
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Sabine Leh
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Flavia Paunas
- Department of Medicine, Haugesund Hospital, Haugesund, Norway
| | - Janka Bábíčková
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Andreas Scherer
- Spheromics, Kontiolahti, Finland; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Camille Serre
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Oystein Eikrem
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Philipp Strauss
- Department of Clinical Medicine, University of Bergen, Bergen, Norway.
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153
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Yusuf N, Monahan K. Epigenetic programming of stochastic olfactory receptor choice. Genesis 2024; 62:e23593. [PMID: 38562011 PMCID: PMC11003729 DOI: 10.1002/dvg.23593] [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] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/01/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024]
Abstract
The mammalian sense of smell relies upon a vast array of receptor proteins to detect odorant compounds present in the environment. The proper deployment of these receptor proteins in olfactory sensory neurons is orchestrated by a suite of epigenetic processes that remodel the olfactory genes in differentiating neuronal progenitors. The goal of this review is to elucidate the central role of gene regulatory processes acting in neuronal progenitors of olfactory sensory neurons that lead to a singular expression of an odorant receptor in mature olfactory sensory neurons. We begin by describing the principal features of odorant receptor gene expression in mature olfactory sensory neurons. Next, we delineate our current understanding of how these features emerge from multiple gene regulatory mechanisms acting in neuronal progenitors. Finally, we close by discussing the key gaps in our understanding of how these regulatory mechanisms work and how they interact with each other over the course of differentiation.
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Affiliation(s)
- Nusrath Yusuf
- Division of Life Sciences-Molecular Biology and Biochemistry Department, Rutgers University-New Brunswick, New Brunswick, New Jersey, USA
| | - Kevin Monahan
- Division of Life Sciences-Molecular Biology and Biochemistry Department, Rutgers University-New Brunswick, New Brunswick, New Jersey, USA
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154
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Alhajlah S. The molecular mechanisms of various long non-coding RNA (lncRNA) in human lung tumors: Shedding light on the molecular mechanisms. Pathol Res Pract 2024; 256:155253. [PMID: 38513578 DOI: 10.1016/j.prp.2024.155253] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
Abstract
Although it is still mostly incomplete, unraveling the gene expression networks controlling the initiation and progression of cancer is crucial. The rapid identification and characterization of long noncoding RNAs (lncRNAs) is made possible by advancements in computational biology and RNA-seq technology. According to recent research, lncRNAs are involved in several stages in the genesis of lung cancer. These lncRNAs interact with DNA, RNA, protein molecules, and/or their combinations. They play a crucial role in transcriptional and post-transcriptional regulation, as well as chromatin architecture. Their misexpression gives cancer cells the ability to start, grow, and spread tumors. This review will focus on their abnormal expression and function in lung cancer, as well as their involvement in cancer therapy and diagnosis.
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Affiliation(s)
- Sharif Alhajlah
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, Shaqra 11961, Saudi Arabia.
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155
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Xu W, Mo W, Han D, Dai W, Xu X, Li J, Xu X. Hepatocyte-derived exosomes deliver the lncRNA CYTOR to hepatic stellate cells and promote liver fibrosis. J Cell Mol Med 2024; 28:e18234. [PMID: 38520214 PMCID: PMC10960169 DOI: 10.1111/jcmm.18234] [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] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 03/25/2024] Open
Abstract
Liver fibrosis is characterized by the activation and transformation of hepatic stellate cells (HSCs) induced by various injury factors. The degree of liver fibrosis can be significantly improved, but persistent injury factors present a significant therapeutic challenge. Hepatocytes are the most important parenchymal cell type in the liver. In this study, we explored the molecular mechanisms by which damaged liver cells activate HSCs through extracellular vesicles. We established a coculture model of LO2 and LX2 and validated its exosomal transmission activity. Subsequently, differentially expressed long noncoding RNAs (lncRNAs) were screened through RNA sequencing and their mechanisms of action as competing endogenous RNAs (ceRNAs) further confirmed using biological methods, such as FISH and luciferase assays. Damaged liver cells induced activation of LX2 and upregulation of liver fibrosis-related markers. Exosomes extracted and identified from the supernatant fraction contained differentially expressed lncRNA cytoskeleton regulator RNA (CYTOR) that competed with microRNA-125 (miR-125) for binding to glial cell line-derived neurotrophic factor (GDNF) in HSCs, in turn, promoting LX2 activation. MiR-125 could target and regulate both CYTOR and GDNF and vice versa, as verified using the luciferase assay. In an in vivo model, damaged liver extracellular vesicles induced the formation of liver fibrosis. Notably, downregulation of CYTOR within extracellular vesicles effectively inhibited liver fibrosis. The lncRNA CYTOR in exosomes of damaged liver cells is upregulated and modulates the expression of downstream GDNF through activity as a ceRNA, providing an effective mechanism for activation of HSCs.
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Affiliation(s)
- Wenqiang Xu
- Department of GastroenterologyShidong Hospital of Shanghai, School of Health Science and Engineering, University of Shanghai for Science and TechnologyShanghaiChina
| | - Wenhui Mo
- Department of GastroenterologyShidong Hospital of Shanghai, School of Health Science and Engineering, University of Shanghai for Science and TechnologyShanghaiChina
| | - Dengyu Han
- Department of GastroenterologyShidong Hospital of Shanghai, School of Health Science and Engineering, University of Shanghai for Science and TechnologyShanghaiChina
| | - Weiqi Dai
- Department of GastroenterologyShidong Hospital of Shanghai, School of Health Science and Engineering, University of Shanghai for Science and TechnologyShanghaiChina
| | - Xiaorong Xu
- Department of GastroenterologyShanghai Tenth People's Hospital, Tongji University School of MedicineShanghaiChina
| | - Jingjing Li
- Department of GastroenterologyShidong Hospital of Shanghai, School of Health Science and Engineering, University of Shanghai for Science and TechnologyShanghaiChina
| | - Xuanfu Xu
- Department of GastroenterologyShidong Hospital of Shanghai, School of Health Science and Engineering, University of Shanghai for Science and TechnologyShanghaiChina
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156
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Nath KA, Singh RD, Croatt AJ, Ackerman AW, Grande JP, O'Brien DR, Garovic VD, Adams CM, Tchkonia T, Kirkland JL. Induction of p16Ink4a Gene Expression in Heme Protein-Induced AKI and by Heme: Pathophysiologic Implications. Kidney360 2024; 5:501-514. [PMID: 38379160 DOI: 10.34067/kid.0000000000000395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/05/2024] [Indexed: 02/22/2024]
Abstract
Key Points
In heme protein–mediated AKI (HP-AKI), a senescence phenotype promptly occurs, and increased expression of p16Ink4a contributes to HP-AKI.Renal p16Ink4a expression is induced by hemoglobin, myoglobin, and heme in vivo and in renal epithelial cells exposed to heme in vitro.Impairing the binding or degradation of heme by hemopexin deficiency or heme oxygenase-1 deficiency, respectively, further upregulates p16Ink4a.
Background
Understanding the pathogenetic basis for AKI involves the study of ischemic and nephrotoxic models of AKI, the latter including heme protein–mediated AKI (HP-AKI). Recently, interest has grown regarding the role of senescence as a mechanism of kidney injury, including AKI. We examined whether senescence occurs in HP-AKI and potential inducers of and the role of a key driver of senescence, namely, p16Ink4a, in HP-AKI.
Methods
The long-established murine glycerol model of HP-AKI was used, and indices of senescence were examined. To evaluate the interaction of heme and p16Ink4a expression, murine models of genetic deficiency of hemopexin (HPX) and heme oxygenase-1 (HO-1) were used. To determine the involvement of p16Ink4a in HP-AKI, the population of p16Ink4a-expressing cells was reduced using the INK-ATTAC model.
Results
Using multiple indices, a senescence phenotype appears in the kidney within hours after the induction of HP-AKI. This phenotype includes significant upregulation of p16Ink4a. p16Ink4a is upregulated in the kidney after the individual administration of myoglobin, hemoglobin, and heme, as well as in renal epithelial cells exposed to heme in vitro. Genetic deficiencies of HPX and HO-1, which, independently, are expected to increase heme content in the kidney, exaggerate induction of p16Ink4a in the kidney and exacerbate HP-AKI, the latter shown in the present studies involving HPX
−/−
mice and in previous studies involving HO-1
−/−
mice. Finally, reduction in the population of p16Ink4a-expressing cells in the kidney improves renal function in HP-AKI even within 24 hours.
Conclusions
The pathogenesis of HP-AKI involves senescence and the induction of p16Ink4a, the latter driven, in part, by hemoglobin, myoglobin, and heme.
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Affiliation(s)
- Karl A Nath
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Raman Deep Singh
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Anthony J Croatt
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Allan W Ackerman
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Joseph P Grande
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Daniel R O'Brien
- Division of Biomedical Statistics and Informatics, Department of Health Science Research, Mayo Clinic, Rochester, Minnesota
| | - Vesna D Garovic
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Christopher M Adams
- Division of Endocrinology, Diabetes, Metabolism and Nutrition, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Tamara Tchkonia
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota
| | - James L Kirkland
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota
- Department of General Internal Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota
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157
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Jiang X, Ke X, Tian X, Chu J. An inducible CRISPRi circuit for tunable dynamic regulation of gene expression in Saccharopolyspora erythraea. Biotechnol Lett 2024; 46:161-172. [PMID: 38279045 DOI: 10.1007/s10529-023-03462-z] [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] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/14/2023] [Accepted: 12/17/2023] [Indexed: 01/28/2024]
Abstract
Actinomyces are gram-positive bacteria known for their valuable secondary metabolites. Redirecting metabolic flux towards desired products in actinomycetes requires precise and dynamic regulation of gene expression. In this study, we integrated the CRISPR interference (CRISPRi) system with a cumate-inducible promoter to develop an inducible gene downregulation method in Saccharopolyspora erythraea, a prominent erythromycin-producing actinobacterium. The functionality of the cumate-inducible promoter was validated using the gusA gene as a reporter, and the successful inducible expression of the dCas9 gene was confirmed. The developed inducible CRISPRi strategy was then employed to downregulate the expression of target genes rppA in the wild-type strain NRRL2338 and sucC in the high erythromycin-producing strain E3. Through dynamic control of sucC expression, a significant enhancement in erythromycin production was achieved in strain E3. This study demonstrated the effectiveness of an inducible gene downregulation approach using CRISPRi and a cumate-inducible promoter, providing valuable insights for optimizing natural product production in actinomyces.
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Affiliation(s)
- Xing Jiang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Xiang Ke
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Xiwei Tian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
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158
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Yang L, Chen Y, He S, Yu D. The crucial role of NRF2 in erythropoiesis and anemia: Mechanisms and therapeutic opportunities. Arch Biochem Biophys 2024; 754:109948. [PMID: 38452967 DOI: 10.1016/j.abb.2024.109948] [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: 01/04/2024] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024]
Abstract
The nuclear factor erythroid 2-related factor 2 (NRF2) is a transcription factor crucial in cellular defense against oxidative and electrophilic stresses. Recent research has highlighted the significance of NRF2 in normal erythropoiesis and anemia. NRF2 regulates genes involved in vital aspects of erythroid development, including hemoglobin catabolism, inflammation, and iron homeostasis in erythrocytes. Disrupted NRF2 activity has been implicated in various pathologies involving abnormal erythropoiesis. In this review, we summarize the progress made in understanding the mechanisms of NRF2 activation in erythropoiesis and explore the roles of NRF2 in various types of anemia. This review also discusses the potential of targeting NRF2 as a new therapeutic approach to treat anemia.
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Affiliation(s)
- Lei Yang
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225009, China
| | - Yong Chen
- Department of Oncology, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, 225003, China
| | - Sheng He
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, Guangxi, 530000, China
| | - Duonan Yu
- Department of Hematology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610000, China; Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University, Yangzhou, 225009, China; Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, Guangxi, 530000, China.
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159
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Lin S, Kuang M. RNA modification-mediated mRNA translation regulation in liver cancer: mechanisms and clinical perspectives. Nat Rev Gastroenterol Hepatol 2024; 21:267-281. [PMID: 38243019 DOI: 10.1038/s41575-023-00884-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 01/21/2024]
Abstract
Malignant liver cancer is characterized by rapid tumour progression and a high mortality rate, whereas the molecular mechanisms underlying liver cancer initiation and progression are still poorly understood. The dynamic and reversible RNA modifications have crucial functions in gene expression regulation by modulating RNA processing and mRNA translation. Emerging evidence has revealed that alterations in RNA modifications facilitate the selective translation of oncogenic transcripts and promote the diverse tumorigenic processes of liver cancer. In this Review, we first highlight the current progress on the functions and mechanisms underlying RNA modifications in the regulation of mRNA translation and then summarize the exciting discoveries on aberrant RNA modification-mediated mRNA translation in the regulation of tumour initiation, metastasis, metabolism, tumour microenvironment, and drug and radiotherapy resistance in liver cancer. Finally, we discuss the diagnostic and therapeutic potentials of targeting RNA modifications and mRNA translation for the clinical management of liver cancer.
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Affiliation(s)
- Shuibin Lin
- Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China.
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Ming Kuang
- Department of Liver Surgery, Center of Hepato-Pancreato-Biliary Surgery, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China.
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, China.
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160
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Su K, Vázquez O. Enlightening epigenetics: optochemical tools illuminate the path. Trends Biochem Sci 2024; 49:290-304. [PMID: 38350805 DOI: 10.1016/j.tibs.2024.01.003] [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: 10/04/2023] [Revised: 12/20/2023] [Accepted: 01/10/2024] [Indexed: 02/15/2024]
Abstract
Optochemical tools have become potent instruments for understanding biological processes at the molecular level, and the past decade has witnessed their use in epigenetics and epitranscriptomics (also known as RNA epigenetics) for deciphering gene expression regulation. By using photoresponsive molecules such as photoswitches and photocages, researchers can achieve precise control over when and where specific events occur. Therefore, these are invaluable for studying both histone and nucleotide modifications and exploring disease-related mechanisms. We systematically report and assess current examples in the field, and identify open challenges and future directions. These outstanding proof-of-concept investigations will inspire other chemical biologists to participate in these emerging fields given the potential of photochromic molecules in research and biomedicine.
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Affiliation(s)
- Kaijun Su
- Department of Chemistry, University of Marburg, Marburg D-35043, Germany
| | - Olalla Vázquez
- Department of Chemistry, University of Marburg, Marburg D-35043, Germany; Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Marburg D-35043, Germany.
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161
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Mitra S, Malik R, Wong W, Rahman A, Hartemink AJ, Pritykin Y, Dey KK, Leslie CS. Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nat Genet 2024; 56:627-636. [PMID: 38514783 PMCID: PMC11018525 DOI: 10.1038/s41588-024-01689-8] [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] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 02/14/2024] [Indexed: 03/23/2024]
Abstract
We present a gene-level regulatory model, single-cell ATAC + RNA linking (SCARlink), which predicts single-cell gene expression and links enhancers to target genes using multi-ome (scRNA-seq and scATAC-seq co-assay) sequencing data. The approach uses regularized Poisson regression on tile-level accessibility data to jointly model all regulatory effects at a gene locus, avoiding the limitations of pairwise gene-peak correlations and dependence on peak calling. SCARlink outperformed existing gene scoring methods for imputing gene expression from chromatin accessibility across high-coverage multi-ome datasets while giving comparable to improved performance on low-coverage datasets. Shapley value analysis on trained models identified cell-type-specific gene enhancers that are validated by promoter capture Hi-C and are 11× to 15× and 5× to 12× enriched in fine-mapped eQTLs and fine-mapped genome-wide association study (GWAS) variants, respectively. We further show that SCARlink-predicted and observed gene expression vectors provide a robust way to compute a chromatin potential vector field to enable developmental trajectory analysis.
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Affiliation(s)
- Sneha Mitra
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | | | - Wilfred Wong
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York City, NY, USA
| | - Afsana Rahman
- Hunter College, City University of New York, New York City, NY, USA
| | - Alexander J Hartemink
- Department of Computer Science, Duke University, Durham, NC, USA
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Yuri Pritykin
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Kushal K Dey
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York City, NY, USA.
| | - Christina S Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York City, NY, USA.
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162
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Hart M, Kern F, Fecher-Trost C, Krammes L, Aparicio E, Engel A, Hirsch P, Wagner V, Keller V, Schmartz GP, Rheinheimer S, Diener C, Fischer U, Mayer J, Meyer MR, Flockerzi V, Keller A, Meese E. Experimental capture of miRNA targetomes: disease-specific 3'UTR library-based miRNA targetomics for Parkinson's disease. Exp Mol Med 2024; 56:935-945. [PMID: 38556547 PMCID: PMC11059366 DOI: 10.1038/s12276-024-01202-5] [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] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 04/02/2024] Open
Abstract
The identification of targetomes remains a challenge given the pleiotropic effect of miRNAs, the limited effects of miRNAs on individual targets, and the sheer number of estimated miRNA-target gene interactions (MTIs), which is around 44,571,700. Currently, targetome identification for single miRNAs relies on computational evidence and functional studies covering smaller numbers of targets. To ensure that the targetome analysis could be experimentally verified by functional assays, we employed a systematic approach and explored the targetomes of four miRNAs (miR-129-5p, miR-129-1-3p, miR-133b, and miR-873-5p) by analyzing 410 predicted target genes, both of which were previously associated with Parkinson's disease (PD). After performing 13,536 transfections, we validated 442 of the 705 putative MTIs (62,7%) through dual luciferase reporter assays. These analyses increased the number of validated MTIs by at least 2.1-fold for miR-133b and by a maximum of 24.3-fold for miR-873-5p. Our study contributes to the experimental capture of miRNA targetomes by addressing i) the ratio of experimentally verified MTIs to predicted MTIs, ii) the sizes of disease-related miRNA targetomes, and iii) the density of MTI networks. A web service to support the analyses on the MTI level is available online ( https://ccb-web.cs.uni-saarland.de/utr-seremato ), and all the data have been added to the miRATBase database ( https://ccb-web.cs.uni-saarland.de/miratbase ).
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Affiliation(s)
- Martin Hart
- Human Genetics, Saarland University, 66421, Homburg, Germany.
| | - Fabian Kern
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarland University Campus, Saarbrücken, Germany
| | - Claudia Fecher-Trost
- Department of Experimental and Clinical Pharmacology & Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421, Homburg, Germany
| | - Lena Krammes
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Ernesto Aparicio
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Annika Engel
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Pascal Hirsch
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Viktoria Wagner
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Verena Keller
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
- Department for Internal Medicine II, Saarland University Hospital, 66421, Homburg, Germany
| | | | | | - Caroline Diener
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Ulrike Fischer
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Jens Mayer
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Markus R Meyer
- Department of Experimental and Clinical Pharmacology & Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421, Homburg, Germany
| | - Veit Flockerzi
- Department of Experimental and Clinical Pharmacology & Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421, Homburg, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarland University Campus, Saarbrücken, Germany
| | - Eckart Meese
- Human Genetics, Saarland University, 66421, Homburg, Germany
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163
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de Reus AJEM, Basak O, Dykstra W, van Asperen JV, van Bodegraven EJ, Hol EM. GFAP-isoforms in the nervous system: Understanding the need for diversity. Curr Opin Cell Biol 2024; 87:102340. [PMID: 38401182 DOI: 10.1016/j.ceb.2024.102340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/30/2024] [Indexed: 02/26/2024]
Abstract
Glial fibrillary acidic protein (GFAP) is an intermediate filament (IF) protein expressed in specific types of glial cells in the nervous system. The expression of GFAP is highly regulated during brain development and in neurological diseases. The presence of distinct GFAP-isoforms in various cell types, developmental stages, and diseases indicates that GFAP (post-)transcriptional regulation has a role in glial cell physiology and pathology. GFAP-isoforms differ in sub-cellular localisation, IF-network assembly properties, and IF-dynamics which results in distinct molecular interactions and mechanical properties of the IF-network. Therefore, GFAP (post-)transcriptional regulation is likely a mechanism by which radial glia, astrocytes, and glioma cells can modulate cellular function.
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Affiliation(s)
- Alexandra J E M de Reus
- Department of Translational Neuroscience, Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Onur Basak
- Department of Translational Neuroscience, Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Werner Dykstra
- Department of Translational Neuroscience, Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jessy V van Asperen
- Institut NeuroMyoGène (INMG), Unité Physiopathologie et Génétique du Neurone et du Muscle, Unversité Claude Bernard Lyon 1 CNRS UMR 5261, INSERM U1315, Lyon, France
| | - Emma J van Bodegraven
- Department of Translational Neuroscience, Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Elly M Hol
- Department of Translational Neuroscience, Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
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164
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Munir M, Embry A, Doench JG, Heaton NS, Wilen CB, Orchard RC. Genome-wide CRISPR activation screen identifies JADE3 as an antiviral activator of NF-kB-dependent IFITM3 expression. J Biol Chem 2024; 300:107153. [PMID: 38462163 PMCID: PMC11001640 DOI: 10.1016/j.jbc.2024.107153] [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: 09/29/2023] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 03/12/2024] Open
Abstract
The innate immune system features a web of interacting pathways that require exquisite regulation. To identify novel nodes in this immune landscape, we conducted a gain-of-function, genome-wide CRISPR activation screen with influenza A virus. We identified both appreciated and novel antiviral genes, including Jade family PHD zinc finger 3 (JADE3) a protein involved in directing the histone acetyltransferase histone acetyltransferase binding to ORC1 complex to modify chromatin and regulate transcription. JADE3 is both necessary and sufficient to restrict influenza A virus infection. Our results suggest a distinct function for JADE3 as expression of the closely related paralogs JADE1 and JADE2 does not confer resistance to influenza A virus infection. JADE3 is required for both constitutive and inducible expression of the well-characterized antiviral gene interferon-induced transmembrane protein 3 (IFITM3). Furthermore, we find JADE3 activates the NF-kB signaling pathway, which is required for the promotion of IFITM3 expression by JADE3. Therefore, we propose JADE3 activates an antiviral genetic program involving NF-kB-dependent IFITM3 expression to restrict influenza A virus infection.
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Affiliation(s)
- Moiz Munir
- Departments of Immunology and Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Aaron Embry
- Departments of Immunology and Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Nicholas S Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Craig B Wilen
- Department of Laboratory Medicine and Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Robert C Orchard
- Departments of Immunology and Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
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165
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Abstract
Messenger RNA (mRNA) translation consists of initiation, elongation, termination, and ribosome recycling, carried out by the translation machinery, primarily including tRNAs, ribosomes, and translation factors (TrFs). Translational regulators transduce signals of growth and development, as well as biotic and abiotic stresses, to the translation machinery, where global or selective translational control occurs to modulate mRNA translation efficiency (TrE). As the basis of translational control, the translation machinery directly determines the quality and quantity of newly synthesized peptides and, ultimately, the cellular adaption. Thus, regulating the availability of diverse machinery components is reviewed as the central strategy of translational control. We provide classical signaling pathways (e.g., integrated stress responses) and cellular behaviors (e.g., liquid-liquid phase separation) to exemplify this strategy within different physiological contexts, particularly during host-microbe interactions. With new technologies developed, further understanding this strategy will speed up translational medicine and translational agriculture.
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Affiliation(s)
- Shu Yuan
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Guilong Zhou
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Guoyong Xu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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166
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Vega-Sendino M, Lüttmann FF, Olbrich T, Chen Y, Kuenne C, Stein P, Tillo D, Carey GI, Zhong J, Savy V, Radonova L, Lu T, Saykali B, Kim KP, Domingo CN, Schüler L, Günther S, Bentsen M, Bosnakovski D, Schöler H, Kyba M, Maity TK, Jenkins LM, Looso M, Williams CJ, Kim J, Ruiz S. The homeobox transcription factor DUXBL controls exit from totipotency. Nat Genet 2024; 56:697-709. [PMID: 38509386 DOI: 10.1038/s41588-024-01692-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/16/2024] [Indexed: 03/22/2024]
Abstract
In mice, exit from the totipotent two-cell (2C) stage embryo requires silencing of the 2C-associated transcriptional program. However, the molecular mechanisms involved in this process remain poorly understood. Here we demonstrate that the 2C-specific transcription factor double homeobox protein (DUX) mediates an essential negative feedback loop by inducing the expression of DUXBL to promote this silencing. We show that DUXBL gains accessibility to DUX-bound regions specifically upon DUX expression. Furthermore, we determine that DUXBL interacts with TRIM24 and TRIM33, members of the TRIM superfamily involved in gene silencing, and colocalizes with them in nuclear foci upon DUX expression. Importantly, DUXBL overexpression impairs 2C-associated transcription, whereas Duxbl inactivation in mouse embryonic stem cells increases DUX-dependent induction of the 2C-transcriptional program. Consequently, DUXBL deficiency in embryos results in sustained expression of 2C-associated transcripts leading to early developmental arrest. Our study identifies DUXBL as an essential regulator of totipotency exit enabling the first divergence of cell fates.
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Affiliation(s)
| | - Felipe F Lüttmann
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Frankfurt, Germany
| | - Teresa Olbrich
- Laboratory of Genome Integrity, CCR, NCI, NIH, Bethesda, MD, USA
| | - Yanpu Chen
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Frankfurt, Germany
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Department of Cardiology, Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Carsten Kuenne
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Paula Stein
- Reproductive and Developmental Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC, USA
| | | | - Grace I Carey
- Laboratory of Genome Integrity, CCR, NCI, NIH, Bethesda, MD, USA
| | - Jiasheng Zhong
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- German Cancer Research Center, Heidelberg, Germany
| | - Virginia Savy
- Reproductive and Developmental Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC, USA
| | - Lenka Radonova
- Reproductive and Developmental Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC, USA
| | - Tianlin Lu
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Frankfurt, Germany
| | - Bechara Saykali
- Laboratory of Genome Integrity, CCR, NCI, NIH, Bethesda, MD, USA
| | - Kee-Pyo Kim
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | | | - Leah Schüler
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Günther
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein/Main, Germany
| | - Mette Bentsen
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Darko Bosnakovski
- Lillehei Heart Institute, Department of Pediatrics, University of Minnesota, Minneapolis, USA
| | - Hans Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Michael Kyba
- Lillehei Heart Institute, Department of Pediatrics, University of Minnesota, Minneapolis, USA
| | - Tapan K Maity
- Laboratory of Cell Biology, CCR, NCI, NIH, Bethesda, MD, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, CCR, NCI, NIH, Bethesda, MD, USA
| | - Mario Looso
- Cardio-Pulmonary Institute, Frankfurt, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein/Main, Germany
| | - Carmen J Williams
- Reproductive and Developmental Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC, USA
| | - Johnny Kim
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany.
- Cardio-Pulmonary Institute, Frankfurt, Germany.
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein/Main, Germany.
- German Center for Lung Research (DZL), Partner Site Rhein/Main, Germany.
- Institute of Lung Health (ILH), Justus-Liebig-University Giessen, Giessen, Germany.
- The Center for Cardiovascular Regeneration and Immunology at TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany.
| | - Sergio Ruiz
- Laboratory of Genome Integrity, CCR, NCI, NIH, Bethesda, MD, USA.
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167
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Wang NN, Ni P, Wei YL, Hu R, Li Y, Li XB, Zheng Y. Phosphatidic acid interacts with an HD-ZIP transcription factor GhHOX4 to influence its function in fiber elongation of cotton (Gossypium hirsutum). Plant J 2024; 118:423-436. [PMID: 38184843 DOI: 10.1111/tpj.16616] [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] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/31/2023] [Accepted: 12/20/2023] [Indexed: 01/09/2024]
Abstract
Upland cotton, the mainly cultivated cotton species in the world, provides over 90% of natural raw materials (fibers) for the textile industry. The development of cotton fibers that are unicellular and highly elongated trichomes on seeds is a delicate and complex process. However, the regulatory mechanism of fiber development is still largely unclear in detail. In this study, we report that a homeodomain-leucine zipper (HD-ZIP) IV transcription factor, GhHOX4, plays an important role in fiber elongation. Overexpression of GhHOX4 in cotton resulted in longer fibers, while GhHOX4-silenced transgenic cotton displayed a "shorter fiber" phenotype compared with wild type. GhHOX4 directly activates two target genes, GhEXLB1D and GhXTH2D, for promoting fiber elongation. On the other hand, phosphatidic acid (PA), which is associated with cell signaling and metabolism, interacts with GhHOX4 to hinder fiber elongation. The basic amino acids KR-R-R in START domain of GhHOX4 protein are essential for its binding to PA that could alter the nuclear localization of GhHOX4 protein, thereby suppressing the transcriptional regulation of GhHOX4 to downstream genes in the transition from fiber elongation to secondary cell wall (SCW) thickening during fiber development. Thus, our data revealed that GhHOX4 positively regulates fiber elongation, while PA may function in the phase transition from fiber elongation to SCW formation by negatively modulating GhHOX4 in cotton.
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Affiliation(s)
- Na-Na Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Ping Ni
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Ying-Li Wei
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Rong Hu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Yang Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Xue-Bao Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Yong Zheng
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
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168
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Ciceri G, Studer L. Epigenetic control and manipulation of neuronal maturation timing. Curr Opin Genet Dev 2024; 85:102164. [PMID: 38412562 DOI: 10.1016/j.gde.2024.102164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/29/2024]
Abstract
During brain development, the sequence of developmental steps and the underlying transcriptional regulatory logic are largely conserved across species. However, the temporal unfolding of developmental programs varies dramatically across species and within a given species varies across brain regions and cell identities. The maturation of neurons in the human cerebral cortex is particularly slow and lasts for many years compared with only a few weeks for the corresponding mouse neurons. The mechanisms setting the 'schedule' of neuronal maturation remain unclear but appear to be linked to a cell-intrinsic 'clock'. Here, we discuss recent findings that highlight a role for epigenetic factors in the timing of neuronal maturation. Manipulations of those factors in stem cell-based models can override the intrinsic pace of neuronal maturation, including its protracted nature in human cortical neurons. We then contextualize the epigenetic regulation of maturation programs with findings from other model systems and propose potential interactions between epigenetic pathways and other drivers of developmental rates.
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Affiliation(s)
- Gabriele Ciceri
- The Center for Stem Cell Biology and Developmental Biology program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Lorenz Studer
- The Center for Stem Cell Biology and Developmental Biology program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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169
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Gates LA, Reis BS, Lund PJ, Paul MR, Leboeuf M, Djomo AM, Nadeem Z, Lopes M, Vitorino FN, Unlu G, Carroll TS, Birsoy K, Garcia BA, Mucida D, Allis CD. Histone butyrylation in the mouse intestine is mediated by the microbiota and associated with regulation of gene expression. Nat Metab 2024; 6:697-707. [PMID: 38413806 DOI: 10.1038/s42255-024-00992-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024]
Abstract
Post-translational modifications (PTMs) on histones are a key source of regulation on chromatin through impacting cellular processes, including gene expression1. These PTMs often arise from metabolites and are thus impacted by metabolism and environmental cues2-7. One class of metabolically regulated PTMs are histone acylations, which include histone acetylation, butyrylation, crotonylation and propionylation3,8. As these PTMs can be derived from short-chain fatty acids, which are generated by the commensal microbiota in the intestinal lumen9-11, we aimed to define how microbes impact the host intestinal chromatin landscape, mainly in female mice. Here we show that in addition to acetylation, intestinal epithelial cells from the caecum and distal mouse intestine also harbour high levels of butyrylation and propionylation on lysines 9 and 27 of histone H3. We demonstrate that these acylations are regulated by the microbiota and that histone butyrylation is additionally regulated by the metabolite tributyrin. Tributyrin-regulated gene programmes are correlated with histone butyrylation, which is associated with active gene-regulatory elements and levels of gene expression. Together, our study uncovers a regulatory layer of how the microbiota and metabolites influence the intestinal epithelium through chromatin, demonstrating a physiological setting in which histone acylations are dynamically regulated and associated with gene regulation.
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Affiliation(s)
- Leah A Gates
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, USA.
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
| | | | - Peder J Lund
- Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Matthew R Paul
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - Marylene Leboeuf
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, USA
| | - Annaelle M Djomo
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, USA
| | - Zara Nadeem
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, USA
- Hunter College of the City University of New York, Yalow Honors Scholar Program, New York, NY, USA
| | - Mariana Lopes
- Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Francisca N Vitorino
- Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Gokhan Unlu
- Laboratory of Metabolic Regulation & Genetics, The Rockefeller University, New York, NY, USA
| | - Thomas S Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - Kivanç Birsoy
- Laboratory of Metabolic Regulation & Genetics, The Rockefeller University, New York, NY, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - C David Allis
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, USA
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170
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Ahmed IA, Liu M, Gomez D. Nuclear Control of Vascular Smooth Muscle Cell Plasticity during Vascular Remodeling. The American Journal of Pathology 2024; 194:525-538. [PMID: 37820925 PMCID: PMC10988766 DOI: 10.1016/j.ajpath.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/18/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023]
Abstract
Control of vascular smooth muscle cell (SMC) gene expression is an essential process for establishing and maintaining lineage identity, contractility, and plasticity. Most mechanisms (epigenetic, transcriptional, and post-transcriptional) implicated in gene regulation occur in the nucleus. Still, intranuclear pathways are directly impacted by modifications in the extracellular environment in conditions of adaptive or maladaptive remodeling. Integration of extracellular, cellular, and genomic information into the nucleus through epigenetic and transcriptional control of genome organization plays a major role in regulating SMC functions and phenotypic transitions during vascular remodeling and diseases. This review aims to provide a comprehensive update on nuclear mechanisms, their interactions, and their integration in controlling SMC homeostasis and dysfunction. It summarizes and discusses the main nuclear mechanisms preponderant in SMCs in the context of vascular disease, such as atherosclerosis, with an emphasis on studies employing in vivo cell-specific loss-of-function and single-cell omics approaches.
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Affiliation(s)
- Ibrahim A Ahmed
- Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania; Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mingjun Liu
- Department of Pathology, New York University, New York, New York
| | - Delphine Gomez
- Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania; Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania.
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171
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Ramsey KM, Barrick D. Unraveling paralog-specific Notch signaling through thermodynamics of ternary complex formation and transcriptional activation of chimeric receptors. Protein Sci 2024; 33:e4947. [PMID: 38511488 PMCID: PMC10962485 DOI: 10.1002/pro.4947] [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] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/07/2024] [Accepted: 02/11/2024] [Indexed: 03/22/2024]
Abstract
Notch signaling in humans is mediated by four paralogous receptors that share conserved architectures and possess overlapping, yet non-redundant functions. The receptors share a canonical activation pathway wherein upon extracellular ligand binding, the Notch intracellular domain (NICD) is cleaved from the membrane and translocates to the nucleus where its N-terminal RBP-j-associated molecule (RAM) region and ankyrin repeat (ANK) domain bind transcription factor CSL and recruit co-activator Mastermind-like-1 (MAML1) to activate transcription. However, different paralogs can lead to distinct outcomes. To better understand paralog-specific differences in Notch signaling, we performed a thermodynamic analysis of the Notch transcriptional activation complexes for all four Notch paralogs using isothermal titration calorimetry. Using chimeric constructs, we find that the RAM region is the primary determinant of stability of binary RAMANK:CSL complexes, and that the ANK regions are largely the determinants of MAML1 binding to pre-formed RAMANK:CSL complexes. Free energies of these binding reactions (ΔGRA and ΔGMAML) vary among the four Notch paralogs, although variations for Notch2, 3, and 4 offset in the free energy of the ternary complex (ΔGTC, where ΔGTC = ΔGRA + ΔGMAML). To probe how these affinity differences affect Notch signaling, we performed transcriptional activation assays with the paralogous and chimeric NICDs, and analyzed the results with an independent multiplicative model that quantifies contributions of the paralogous RAM, ANK, and C-terminal regions (CTR) to activation. This analysis shows that transcription activation correlates with ΔGTC, but that activation is further modified by CTR identity in a paralog-specific way.
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Affiliation(s)
- Kristen M. Ramsey
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Doug Barrick
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
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172
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Bhatt B, García-Díaz P, Foight GW. Synthetic transcription factor engineering for cell and gene therapy. Trends Biotechnol 2024; 42:449-463. [PMID: 37865540 DOI: 10.1016/j.tibtech.2023.09.010] [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: 08/02/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/23/2023]
Abstract
Synthetic transcription factors (synTFs) that control beneficial transgene expression are an important method to increase the safety and efficacy of cell and gene therapy. Reliance on synTF components from non-human sources has slowed progress in the field because of concerns about immunogenicity and inducer drug properties. Recent advances in human-derived DNA-binding domains (DBDs) and transcriptional activation domains (TADs) paired with novel control modules responsive to clinically approved small molecules have poised the synTF field to overcome these hurdles. Advances include controllers inducible by autonomous signaling inputs and more complex, multi-input synTF circuits. Demonstrations of advanced control strategies with human-derived transcription factor components in clinically relevant vectors and in vivo models will facilitate progression into the clinic.
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Affiliation(s)
- Bhoomi Bhatt
- Center for Cell and Gene Therapy, Texas Children's Hospital, Houston Methodist Hospital, and Baylor College of Medicine, Houston, TX, USA
| | - Pablo García-Díaz
- Center for Cell and Gene Therapy, Texas Children's Hospital, Houston Methodist Hospital, and Baylor College of Medicine, Houston, TX, USA
| | - Glenna Wink Foight
- Center for Cell and Gene Therapy, Texas Children's Hospital, Houston Methodist Hospital, and Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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173
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Cassani M, Seydoux G. P-body-like condensates in the germline. Semin Cell Dev Biol 2024; 157:24-32. [PMID: 37407370 PMCID: PMC10761593 DOI: 10.1016/j.semcdb.2023.06.010] [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] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023]
Abstract
P-bodies are cytoplasmic condensates that accumulate low-translation mRNAs for temporary storage before translation or degradation. P-bodies have been best characterized in yeast and mammalian tissue culture cells. We describe here related condensates in the germline of animal models. Germline P-bodies have been reported at all stages of germline development from primordial germ cells to gametes. The activity of the universal germ cell fate regulator, Nanos, is linked to the mRNA decay function of P-bodies, and spatially-regulated condensation of P-body like condensates in embryos is required to localize mRNA regulators to primordial germ cells. In most cases, however, it is not known whether P-bodies represent functional compartments or non-functional condensation by-products that arise when ribonucleoprotein complexes saturate the cytoplasm. We speculate that the ubiquity of P-body-like condensates in germ cells reflects the strong reliance of the germline on cytoplasmic, rather than nuclear, mechanisms of gene regulation.
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Affiliation(s)
- Madeline Cassani
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Geraldine Seydoux
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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174
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Chan S, Wang Y, Luo Y, Zheng M, Xie F, Xue M, Yang X, Xue P, Zha C, Fang M. Differential Regulation of Male-Hormones-Related Enhancers Revealed by Chromatin Accessibility and Transcriptional Profiles in Pig Liver. Biomolecules 2024; 14:427. [PMID: 38672444 PMCID: PMC11048672 DOI: 10.3390/biom14040427] [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] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Surgical castration can effectively avoid boar taint and improve pork quality by removing the synthesis of androstenone in the testis, thereby reducing its deposition in adipose tissue. The expression of genes involved in testis-derived hormone metabolism was altered following surgical castration, but the upstream regulatory factors and underlying mechanism remain unclear. In this study, we systematically profiled chromatin accessibility and transcriptional dynamics in liver tissue of castrated and intact full-sibling Yorkshire pigs. First, we identified 897 differentially expressed genes and 6864 differential accessible regions (DARs) using RNA- and ATAC-seq. By integrating the RNA- and ATAC-seq results, 227 genes were identified, and a significant positive correlation was revealed between differential gene expression and the ATAC-seq signal. We constructed a transcription factor regulatory network after motif analysis of DARs and identified a candidate transcription factor (TF) SP1 that targeted the HSD3B1 gene, which was responsible for the metabolism of androstenone. Subsequently, we annotated DARs by incorporating H3K27ac ChIP-seq data, marking 2234 typical enhancers and 245 super enhancers involved in the regulation of all testis-derived hormones. Among these, four typical enhancers associated with HSD3B1 were identified. Furthermore, an in-depth investigation was conducted on the androstenone-related enhancers, and an androstenone-related mutation was identified in a newfound candidatetypical enhancer (andEN) with dual-luciferase assays. These findings provide further insights into how enhancers function as links between phenotypic and non-coding area variations. The discovery of upstream TF and enhancers of HSD3B1 contributes to understanding the regulatory networks of androstenone metabolism and provides an important foundation for improving pork quality.
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Affiliation(s)
- Shuheng Chan
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.C.); (Y.L.); (P.X.)
| | - Yubei Wang
- Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Yabiao Luo
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.C.); (Y.L.); (P.X.)
| | - Meili Zheng
- Beijing General Station of Animal Husbandry, Beijing 100107, China
| | - Fuyin Xie
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.C.); (Y.L.); (P.X.)
| | - Mingming Xue
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.C.); (Y.L.); (P.X.)
| | - Xiaoyang Yang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.C.); (Y.L.); (P.X.)
| | - Pengxiang Xue
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.C.); (Y.L.); (P.X.)
| | - Chengwan Zha
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.C.); (Y.L.); (P.X.)
| | - Meiying Fang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.C.); (Y.L.); (P.X.)
- Sanya Institute of China Agricultural University, Sanya 572025, China
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175
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Friedman MJ, Wagner T, Lee H, Rosenfeld MG, Oh S. Enhancer-promoter specificity in gene transcription: molecular mechanisms and disease associations. Exp Mol Med 2024; 56:772-787. [PMID: 38658702 PMCID: PMC11058250 DOI: 10.1038/s12276-024-01233-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 04/26/2024] Open
Abstract
Although often located at a distance from their target gene promoters, enhancers are the primary genomic determinants of temporal and spatial transcriptional specificity in metazoans. Since the discovery of the first enhancer element in simian virus 40, there has been substantial interest in unraveling the mechanism(s) by which enhancers communicate with their partner promoters to ensure proper gene expression. These research efforts have benefited considerably from the application of increasingly sophisticated sequencing- and imaging-based approaches in conjunction with innovative (epi)genome-editing technologies; however, despite various proposed models, the principles of enhancer-promoter interaction have still not been fully elucidated. In this review, we provide an overview of recent progress in the eukaryotic gene transcription field pertaining to enhancer-promoter specificity. A better understanding of the mechanistic basis of lineage- and context-dependent enhancer-promoter engagement, along with the continued identification of functional enhancers, will provide key insights into the spatiotemporal control of gene expression that can reveal therapeutic opportunities for a range of enhancer-related diseases.
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Affiliation(s)
- Meyer J Friedman
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tobias Wagner
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Haram Lee
- College of Pharmacy Korea University, 2511 Sejong-ro, Sejong, 30019, Republic of Korea
| | - Michael G Rosenfeld
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Soohwan Oh
- College of Pharmacy Korea University, 2511 Sejong-ro, Sejong, 30019, Republic of Korea.
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176
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Abstract
Eukaryotic transcription, a fundamental process that governs cell-specific gene expression, has long been the subject of extensive investigations in the fields of molecular biology, biochemistry, and structural biology. Recent advances in microscopy techniques have led to a fascinating concept known as "transcriptional condensates." These dynamic assemblies are the result of a phenomenon called liquid‒liquid phase separation, which is driven by multivalent interactions between the constituent proteins in cells. The essential proteins associated with transcription are concentrated in transcriptional condensates. Recent studies have shed light on the temporal dynamics of transcriptional condensates and their potential role in enhancing the efficiency of transcription. In this article, we explore the properties of transcriptional condensates, investigate how they evolve over time, and evaluate the significant impact they have on the process of transcription. Furthermore, we highlight innovative techniques that allow us to manipulate these condensates, thus demonstrating their responsiveness to cellular signals and their connection to transcriptional bursting. As our understanding of transcriptional condensates continues to grow, they are poised to revolutionize our understanding of eukaryotic gene regulation.
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Affiliation(s)
- Kwangmin Ryu
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Deahak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Gunhee Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Deahak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Won-Ki Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Deahak-ro, Yuseong-gu, Daejeon, 34141, Korea.
- KAIST Stem Cell Research Center, Korea Advanced Institute of Science and Technology (KAIST), 291 Deahak-ro, Yuseong-gu, Daejeon, 34141, Korea.
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177
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Gao L, Wang Y, Gao Q, Chen Y, Zhang Z. Transcriptional control of CCAAT/enhancer binding protein zeta gene in chicken adipose tissue. Poult Sci 2024; 103:103540. [PMID: 38417330 PMCID: PMC10907851 DOI: 10.1016/j.psj.2024.103540] [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: 10/30/2023] [Revised: 01/25/2024] [Accepted: 02/05/2024] [Indexed: 03/01/2024] Open
Abstract
CCAAT/enhancer binding protein zeta (C/EBPZ) was differentially expressed in abdominal adipose tissues of fat and lean broilers and regulated adipogenesis in chicken. The objective of this study was to elucidate the transcriptional regulation of C/EBPZ gene in chicken adipose tissue. A 2,031-base pair (bp) chicken C/EBPZ sequence (2,025 nucleotides upstream to 6 nucleotides downstream from the initiator codon, -2,025/+6) was studied. The sequence exhibited a significant promoter activity (P < 0.05) and had some cis-acting elements, notably, a core promoter was identified in nucleotides -94 to +6. Additionally, DNA pull-down assay showed that proteins interacted with chicken C/EBPZ promoter (-173/+6) in preadipocytes were implicated in transcription, post-transcriptional regulation and translation. In addition, KLF2 facilitated the activities of chicken C/EBPZ promoter (-2,025/+6, -1,409/+6, -793/+6, -485/+6, -173/+6, and -94/+6) in preadipocytes (P < 0.05). The expression levels of KLF2 and C/EBPZ in chicken abdominal adipose tissue were substantially associated (r = 0.5978278, P < 0.0001), and KLF2 increased C/EBPZ expression in vitro (P < 0.05). Additionally, chromatin immunoprecipitation (ChIP)-PCR analysis revealed that KLF2 has the ability to interact with the chicken C/EBPZ promoter regions at least at the positions -1,245/-1,048 and -571/-397. Mutation analysis showed that the CGCAGCGCCCG motif located in the chicken C/EBPZ promoter at positions -45 to -35 is involved in regulating transcription and facilitates trans activation by KLF2. These results provided some information of transcription control of C/EBPZ in chicken adipose tissue.
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Affiliation(s)
- Lingyu Gao
- Department of Histology and Embryology, Shihezi University School of Medicine, Shihezi, Xinjiang, 832000, PR China; Key Medical Laboratory of Stem Cell Transformation and Application, The First People's Hospital of Zhengzhou, Zhengzhou, Henan, 450000, PR China
| | - Yingjun Wang
- Department of Histology and Embryology, Shihezi University School of Medicine, Shihezi, Xinjiang, 832000, PR China
| | - Qin Gao
- Department of Histology and Embryology, Shihezi University School of Medicine, Shihezi, Xinjiang, 832000, PR China
| | - Yuechan Chen
- Department of Reproductive Medicine, The First Affiliated Hospital of Shihezi University, Shihezi, Xinjiang, 832000, PR China
| | - Zhiwei Zhang
- Department of Histology and Embryology, Shihezi University School of Medicine, Shihezi, Xinjiang, 832000, PR China.
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178
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Xia YQ, Yang Y, Liu YY, Cheng JX, Liu Y, Li CH, Liu PF. DNA Methylation Analysis Reveals Potential Mechanism in Takifugu rubripes Against Cryptocaryon irritans Infection. Mar Biotechnol (NY) 2024; 26:288-305. [PMID: 38446292 DOI: 10.1007/s10126-024-10296-x] [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] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/02/2024] [Indexed: 03/07/2024]
Abstract
Takifugu rubripes (T. rubripes) is a valuable commercial fish, and Cryptocaryon irritans (C. irritans) has a significant impact on its aquaculture productivity. DNA methylation is one of the earliest discovered ways of gene epigenetic modification and also an important form of modification, as well as an essential type of alteration that regulates gene expression, including immune response. To further explore the anti-infection mechanism of T. rubripes in inhibiting this disease, we determined genome-wide DNA methylation profiles in the gill of T. rubripes using whole-genome bisulfite sequencing (WGBS) and combined with RNA sequence (RNA-seq). A total of 4659 differentially methylated genes (DMGs) in the gene body and 1546 DMGs in the promoter between the infection and control group were identified. And we identified 2501 differentially expressed genes (DEGs), including 1100 upregulated and 1401 downregulated genes. After enrichment analysis, we identified DMGs and DEGs of immune-related pathways including MAPK, Wnt, ErbB, and VEGF signaling pathways, as well as node genes prkcb, myca, tp53, and map2k2a. Based on the RNA-Seq results, we plotted a network graph to demonstrate the relationship between immune pathways and functional related genes, in addition to gene methylation and expression levels. At the same time, we predicted the CpG island and transcription factor of four immune-related key genes prkcb and mapped the gene structure. These unique discoveries could be helpful in the understanding of C. irritans pathogenesis, and the candidate genes screened may serve as optimum methylation-based biomarkers that can be utilized for the correct diagnosis and therapy T. rubripes in the development of the ability to resist C. irritans infection.
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Affiliation(s)
- Yu-Qing Xia
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, People's Republic of China
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
| | - Yi Yang
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
- College of Marine Technology and Environment, Dalian Ocean University, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
| | - Yan-Yun Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
- College of Marine Technology and Environment, Dalian Ocean University, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
| | - Jian-Xin Cheng
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
- College of Life Science, Liaoning Normal University, Dalian, 116081, People's Republic of China
| | - Ying Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, People's Republic of China
| | - Cheng-Hua Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, People's Republic of China.
| | - Peng-Fei Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian, 116023, People's Republic of China.
- College of Marine Technology and Environment, Dalian Ocean University, 52 Heishijiao Street, Dalian, 116023, People's Republic of China.
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179
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Bugaj AM, Kunath N, Saasen VL, Fernandez-Berrocal MS, Vankova A, Sætrom P, Bjørås M, Ye J. Dissecting gene expression networks in the developing hippocampus through the lens of NEIL3 depletion. Prog Neurobiol 2024; 235:102599. [PMID: 38522610 DOI: 10.1016/j.pneurobio.2024.102599] [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: 01/04/2024] [Revised: 03/09/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024]
Abstract
Gene regulation in the hippocampus is fundamental for its development, synaptic plasticity, memory formation, and adaptability. Comparisons of gene expression among different developmental stages, distinct cell types, and specific experimental conditions have identified differentially expressed genes contributing to the organization and functionality of hippocampal circuits. The NEIL3 DNA glycosylase, one of the DNA repair enzymes, plays an important role in hippocampal maturation and neuron functionality by shaping transcription. While differential gene expression (DGE) analysis has identified key genes involved, broader gene expression patterns crucial for high-order hippocampal functions remain uncharted. By utilizing the weighted gene co-expression network analysis (WGCNA), we mapped gene expression networks in immature (p8-neonatal) and mature (3 m-adult) hippocampal circuits in wild-type and NEIL3-deficient mice. Our study unveiled intricate gene network structures underlying hippocampal maturation, delineated modules of co-expressed genes, and pinpointed highly interconnected hub genes specific to the maturity of hippocampal subregions. We investigated variations within distinct gene network modules following NEIL3 depletion, uncovering NEIL3-targeted hub genes that influence module connectivity and specificity. By integrating WGCNA with DGE, we delve deeper into the NEIL3-dependent molecular intricacies of hippocampal maturation. This study provides a comprehensive systems-level analysis for assessing the potential correlation between gene connectivity and functional connectivity within the hippocampal network, thus shaping hippocampal function throughout development.
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Affiliation(s)
- Anna M Bugaj
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway
| | - Nicolas Kunath
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway; Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway; Department of Neurology, University Hospital of Trondheim, Trondheim 7491, Norway
| | - Vidar Langseth Saasen
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway
| | - Marion S Fernandez-Berrocal
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway
| | - Ana Vankova
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway; Department of Microbiology, Oslo University Hospital, University of Oslo, Oslo 0424, Norway; Centre for Embryology and Healthy Development, University of Oslo, Oslo 0373, Norway.
| | - Jing Ye
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway.
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180
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Tchatchouang A, Brunette I, Rochette PJ, Proulx S. Expression and Impact of Fibronectin, Tenascin-C, Osteopontin, and Type XIV Collagen in Fuchs Endothelial Corneal Dystrophy. Invest Ophthalmol Vis Sci 2024; 65:38. [PMID: 38656280 PMCID: PMC11044831 DOI: 10.1167/iovs.65.4.38] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 04/02/2024] [Indexed: 04/26/2024] Open
Abstract
Purpose Fuchs endothelial corneal dystrophy (FECD) is characterized by Descemet's membrane (DM) abnormalities, namely an increased thickness and a progressive appearance of guttae and fibrillar membranes. The goal of this study was to identify abnormal extracellular matrix (ECM) proteins expressed in FECD DMs and to evaluate their impact on cell adhesion and migration. Methods Gene expression profiles from in vitro (GSE112039) and ex vivo (GSE74123) healthy and FECD corneal endothelial cells were analyzed to identify deregulated matrisome genes. Healthy and end-stage FECD DMs were fixed and analyzed for guttae size and height. Immunostaining of fibronectin, tenascin-C, osteopontin, and type XIV collagen was performed on ex vivo specimens, as well as on tissue-engineered corneal endothelium reconstructed using healthy and FECD cells. An analysis of ECM protein expression according to guttae and fibrillar membrane was performed using immunofluorescent staining and phase contrast microscopy. Finally, cell adhesion was evaluated on fibronectin, tenascin-C, and osteopontin, and cell migration was studied on fibronectin and tenascin-C. Results SPP1 (osteopontin), FN1 (fibronectin), and TNC (tenascin-C) genes were upregulated in FECD ex vivo cells, and SSP1 was upregulated in both in vitro and ex vivo FECD conditions. Osteopontin, fibronectin, tenascin-C, and type XIV collagen were expressed in FECD specimens, with differences in their location. Corneal endothelial cell adhesion was not significantly affected by fibronectin or tenascin-C but was decreased by osteopontin. The combination of fibronectin and tenascin-C significantly increased cell migration. Conclusions This study highlights new abnormal ECM components in FECD, suggests a certain chronology in their deposition, and demonstrates their impact on cell behavior.
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Affiliation(s)
- Ange Tchatchouang
- Centre de recherche du CHU de Québec–Université Laval, axe médecine régénératrice, Québec, Québec, Canada
- Département d'ophtalmologie et d'ORL–CCF, Faculté de médecine, Université Laval, Québec, Québec, Canada
- Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Québec, Québec, Canada
| | - Isabelle Brunette
- Centre de recherche de l'hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
| | - Patrick J. Rochette
- Centre de recherche du CHU de Québec–Université Laval, axe médecine régénératrice, Québec, Québec, Canada
- Département d'ophtalmologie et d'ORL–CCF, Faculté de médecine, Université Laval, Québec, Québec, Canada
- Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Québec, Québec, Canada
| | - Stéphanie Proulx
- Centre de recherche du CHU de Québec–Université Laval, axe médecine régénératrice, Québec, Québec, Canada
- Département d'ophtalmologie et d'ORL–CCF, Faculté de médecine, Université Laval, Québec, Québec, Canada
- Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Québec, Québec, Canada
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181
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Zhao F, Deng Y, Yang F, Yan Y, Feng F, Peng B, Gao J, Bedford MT, Li H. Molecular Basis for SPINDOC-Spindlin1 Engagement and Its Role in Transcriptional Attenuation. J Mol Biol 2024; 436:168371. [PMID: 37977297 DOI: 10.1016/j.jmb.2023.168371] [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: 09/19/2023] [Revised: 11/11/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Spindlin1 is a histone reader with three Tudor-like domains and its transcriptional co-activator activity could be attenuated by SPINDOC. The first two Tudors are involved in histone methylation readout, while the function of Tudor 3 is largely unknown. Here our structural and binding studies revealed an engagement mode of SPINDOC-Spindlin1, in which a hydrophobic motif of SPINDOC, DOCpep3, stably interacts with Spindlin1 Tudor 3, and two neighboring K/R-rich motifs, DOCpep1 and DOCpep2, bind to the acidic surface of Spindlin1 Tudor 2. Although DOCpep3-Spindlin1 engagement is compatible with histone readout, an extended SPINDOC fragment containing the K/R-rich region attenuates histone or TCF4 binding by Spindlin1 due to introduced competition. This inhibitory effect is more pronounced for weaker binding targets but not for strong ones such as H3 "K4me3-K9me3" bivalent mark. Further ChIP-seq and RT-qPCR indicated that SPINDOC could promote genomic relocation of Spindlin1, thus modulate downstream gene transcription. Collectively, we revealed multivalent engagement between SPINDOC and Spindlin1, in which a hydrophobic motif acts as the primary binding site for stable SPINDOC-Spindlin1 association, while K/R-rich region modulates the target selectivity of Spindlin1 via competitive inhibition, therefore attenuating the transcriptional co-activator activity of Spindlin1.
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Affiliation(s)
- Fan Zhao
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yafang Deng
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Fen Yang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, China
| | - Yan Yan
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China
| | - Fan Feng
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Bo Peng
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Juntao Gao
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China.
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.
| | - Haitao Li
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China; SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, MOE Key Laboratory of Coal Environmental Pathogenesis and Prevention, Shanxi Medical University, Taiyuan, Shanxi Province 030001, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
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182
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Tang H, Kang R, Liu J, Tang D. ATF4 in cellular stress, ferroptosis, and cancer. Arch Toxicol 2024; 98:1025-1041. [PMID: 38383612 DOI: 10.1007/s00204-024-03681-x] [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: 08/23/2023] [Accepted: 01/15/2024] [Indexed: 02/23/2024]
Abstract
Activating transcription factor 4 (ATF4), a member of the ATF/cAMP response element-binding (CREB) family, plays a critical role as a stress-induced transcription factor. It orchestrates cellular responses, particularly in the management of endoplasmic reticulum stress, amino acid deprivation, and oxidative challenges. ATF4's primary function lies in regulating gene expression to ensure cell survival during stressful conditions. However, when considering its involvement in ferroptosis, characterized by severe lipid peroxidation and pronounced endoplasmic reticulum stress, the ATF4 pathway can either inhibit or promote ferroptosis. This intricate relationship underscores the complexity of cellular responses to varying stress levels. Understanding the connections between ATF4, ferroptosis, and endoplasmic reticulum stress holds promise for innovative cancer therapies, especially in addressing apoptosis-resistant cells. In this review, we provide an overview of ATF4, including its structure, modifications, and functions, and delve into its dual role in both ferroptosis and cancer.
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Affiliation(s)
- Hu Tang
- DAMP Laboratory, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, China
| | - Rui Kang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jiao Liu
- DAMP Laboratory, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, China.
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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183
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Li Q, Kang J, Liu N, Huang J, Zhang X, Pang K, Zhang S, Wang M, Zhao Y, Dong S, Li H, Zhao D, Lu F, Zhang W. Hydrogen sulfide improves endothelial barrier function by modulating the ubiquitination degradation of KLF4 through TRAF7 S-sulfhydration in diabetic aorta. Free Radic Biol Med 2024; 216:118-138. [PMID: 38479633 DOI: 10.1016/j.freeradbiomed.2024.02.024] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/29/2024] [Accepted: 02/27/2024] [Indexed: 04/05/2024]
Abstract
Anomalous vascular endothelium significantly contributes to various cardiovascular diseases. VE-cadherin plays a vital role in governing the endothelial barrier. Krüppel-like factor 4(KLF4), as a transcription factor, which binds the VE-cadherin promoter and enhances its transcription. Tumor necrosis factor receptor-associated factor 7 (TRAF7) is an E3 ubiquitin ligase that has been shown to modulate the degradation of KLF4. H2S can covalently modify cysteine residues on proteins through S-sulfhydration, thereby influencing the structure and functionality of the target protein. However, the role of S-sulfhydration on endothelial barrier integrity remains to be comprehensively elucidated. This study aims to investigate whether protein S-sulfhydration in the endothelium regulates endothelial integrity and its underlying mechanism. In this study, we observed that protein S-sulfhydration was reduced in the endothelium during diabetes and TRAF7 was the main target. Overexpression of TRAF7-Cys327 mutant could mitigate the endothelial barrier damage by weakening TRAF7 interaction with KLF4 and reducing ubiquitination degradation of KLF4. In conclusion, our research demonstrates that H2S plays a pivotal role in regulating S-sulfhydration of TRAF7 at Cys327. This regulation effectively inhibits the ubiquitin-mediated degradation of KLF4, resulting in an upregulation of VE-cadherin levels. This molecular mechanism contributes to the prevention of endothelial barrier damage.
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Affiliation(s)
- Qianzhu Li
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Jiaxin Kang
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Ning Liu
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Jiayi Huang
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Xueya Zhang
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Kemiao Pang
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Shiwu Zhang
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Mengyi Wang
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Yajun Zhao
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Shiyun Dong
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Hongxia Li
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Dechao Zhao
- Department of Cardiology, First Affiliated Hospital of Harbin Medical University, Harbin 150001, China.
| | - Fanghao Lu
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China.
| | - Weihua Zhang
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China.
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184
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Berggren KA, Schwartz RE, Kleiner RE, Ploss A. The impact of epitranscriptomic modifications on liver disease. Trends Endocrinol Metab 2024; 35:331-346. [PMID: 38212234 DOI: 10.1016/j.tem.2023.12.007] [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: 10/27/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/13/2024]
Abstract
RNA modifications have emerged as important mechanisms of gene regulation. Developmental, metabolic, and cell cycle regulatory processes are all affected by epitranscriptomic modifications, which control gene expression in a dynamic manner. The hepatic tissue is highly metabolically active and has an impressive ability to regenerate after injury. Cell proliferation, differentiation, and metabolism, which are all essential to the liver response to injury and regeneration, are regulated via RNA modification. Two such modifications, N6-methyladenosine (m6A)and 5-methylcytosine (m5C), have been identified as prognostic disease markers and potential therapeutic targets for liver diseases. Here, we describe progress in understanding the role of RNA modifications in liver biology and disease and discuss specific areas where unexpected results could lead to improved future understanding.
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Affiliation(s)
- Keith A Berggren
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ralph E Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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185
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Lee EH, Lee JH, Kim DY, Lee YS, Jo Y, Dao T, Kim KE, Song DK, Seo JH, Seo YK, Seong JK, Moon C, Han E, Kim MK, Ryu S, Shin M, Roh GS, Jung HR, Osborne TF, Ryu D, Jeon TI, Im SS. Loss of SREBP-1c ameliorates iron-induced liver fibrosis by decreasing lipocalin-2. Exp Mol Med 2024; 56:1001-1012. [PMID: 38622198 PMCID: PMC11058876 DOI: 10.1038/s12276-024-01213-2] [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] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/10/2024] [Accepted: 02/01/2024] [Indexed: 04/17/2024] Open
Abstract
Sterol regulatory element-binding protein (SREBP)-1c is involved in cellular lipid homeostasis and cholesterol biosynthesis and is highly increased in nonalcoholic steatohepatitis (NASH). However, the molecular mechanism by which SREBP-1c regulates hepatic stellate cells (HSCs) activation in NASH animal models and patients have not been fully elucidated. In this study, we examined the role of SREBP-1c in NASH and the regulation of LCN2 gene expression. Wild-type and SREBP-1c knockout (1cKO) mice were fed a high-fat/high-sucrose diet, treated with carbon tetrachloride (CCl4), and subjected to lipocalin-2 (LCN2) overexpression. The role of LCN2 in NASH progression was assessed using mouse primary hepatocytes, Kupffer cells, and HSCs. LCN2 expression was examined in samples from normal patients and those with NASH. LCN2 gene expression and secretion increased in CCl4-induced liver fibrosis mice model, and SREBP-1c regulated LCN2 gene transcription. Moreover, treatment with holo-LCN2 stimulated intracellular iron accumulation and fibrosis-related gene expression in mouse primary HSCs, but these effects were not observed in 1cKO HSCs, indicating that SREBP-1c-induced LCN2 expression and secretion could stimulate HSCs activation through iron accumulation. Furthermore, LCN2 expression was strongly correlated with inflammation and fibrosis in patients with NASH. Our findings indicate that SREBP-1c regulates Lcn2 gene expression, contributing to diet-induced NASH. Reduced Lcn2 expression in 1cKO mice protects against NASH development. Therefore, the activation of Lcn2 by SREBP-1c establishes a new connection between iron and lipid metabolism, affecting inflammation and HSCs activation. These findings may lead to new therapeutic strategies for NASH.
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Affiliation(s)
- Eun-Ho Lee
- Department of Physiology, Keimyung University School of Medicine, Daegu, 42601, Republic of Korea
| | - Jae-Ho Lee
- Department of Physiology, Keimyung University School of Medicine, Daegu, 42601, Republic of Korea
| | - Do-Young Kim
- Department of Physiology, Keimyung University School of Medicine, Daegu, 42601, Republic of Korea
| | - Young-Seung Lee
- Department of Animal Science, College of Agriculture and Life Science, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Yunju Jo
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Tam Dao
- Department of Molecular Cell Biology, Sungkyunkwan University (SKKU) School of Medicine, Suwon, 16419, Republic of Korea
| | - Kyung Eun Kim
- Department of Anatomy, College of Medicine, Institute of Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Dae-Kyu Song
- Department of Physiology, Keimyung University School of Medicine, Daegu, 42601, Republic of Korea
| | - Ji Hae Seo
- Department of Biochemistry, School of Medicine, Keimyung University, Daegu, 42601, Republic of Korea
| | - Young-Kyo Seo
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, BK21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Changjong Moon
- Department of Veterinary Anatomy and Animal Behavior, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Eugene Han
- Department of Internal Medicine, Keimyung University School of Medicine, Daegu, 42601, Republic of Korea
| | - Mi Kyung Kim
- Department of Internal Medicine, Keimyung University School of Medicine, Daegu, 42601, Republic of Korea
| | - Seungwan Ryu
- Department of Surgery, Keimyung University School of Medicine, Daegu, 42601, Republic of Korea
| | - Minsang Shin
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, 42601, Republic of Korea
| | - Gu Seob Roh
- Department of Anatomy, College of Medicine, Institute of Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Hye Ra Jung
- Department of Pathology, Keimyung University School of Medicine, Daegu, 42601, Republic of Korea
| | - Timothy F Osborne
- Institute for Fundamental Biomedical Research, Department of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, St. Petersburg, FL, 33701, USA
| | - Dongryeol Ryu
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Tae-Il Jeon
- Department of Animal Science, College of Agriculture and Life Science, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Seung-Soon Im
- Department of Physiology, Keimyung University School of Medicine, Daegu, 42601, Republic of Korea.
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186
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Truong TTT, Liu ZSJ, Panizzutti B, Dean OM, Berk M, Kim JH, Walder K. Use of gene regulatory network analysis to repurpose drugs to treat bipolar disorder. J Affect Disord 2024; 350:230-239. [PMID: 38190860 DOI: 10.1016/j.jad.2024.01.034] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/03/2023] [Accepted: 01/03/2024] [Indexed: 01/10/2024]
Abstract
BACKGROUND Bipolar disorder (BD) presents significant challenges in drug discovery, necessitating alternative approaches. Drug repurposing, leveraging computational techniques and expanding biomedical data, holds promise for identifying novel treatment strategies. METHODS This study utilized gene regulatory networks (GRNs) to identify significant regulatory changes in BD, using network-based signatures for drug repurposing. Employing the PANDA algorithm, we investigated the variations in transcription factor-GRNs between individuals with BD and unaffected individuals, incorporating binding motifs, protein interactions, and gene co-expression data. The differences in edge weights between BD and controls were then used as differential network signatures to identify drugs potentially targeting the disease-associated gene signature, employing the CLUEreg tool in the GRAND database. RESULTS Using a large RNA-seq dataset of 216 post-mortem brain samples from the CommonMind consortium, we constructed GRNs based on co-expression for individuals with BD and unaffected controls, involving 15,271 genes and 405 TFs. Our analysis highlighted significant influences of these TFs on immune response, energy metabolism, cell signalling, and cell adhesion pathways in the disorder. By employing drug repurposing, we identified 10 promising candidates potentially repurposed as BD treatments. LIMITATIONS Non-drug-naïve transcriptomics data, bulk analysis of BD samples, potential bias of GRNs towards well-studied genes. CONCLUSIONS Further investigation into repurposing candidates, especially those with preclinical evidence supporting their efficacy, like kaempferol and pramocaine, is warranted to understand their mechanisms of action and effectiveness in treating BD. Additionally, novel targets such as PARP1 and A2b offer opportunities for future research on their relevance to the disorder.
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Affiliation(s)
- Trang T T Truong
- Deakin University, IMPACT, The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, Australia
| | - Zoe S J Liu
- Deakin University, IMPACT, The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, Australia
| | - Bruna Panizzutti
- Deakin University, IMPACT, The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, Australia
| | - Olivia M Dean
- Deakin University, IMPACT, The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, Australia; Florey Institute of Neuroscience and Mental Health, Parkville, Australia
| | - Michael Berk
- Deakin University, IMPACT, The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, Australia; Florey Institute of Neuroscience and Mental Health, Parkville, Australia; Orygen, The National Centre of Excellence in Youth Mental Health, Centre for Youth Mental Health, The Florey Institute for Neuroscience and Mental Health and the Department of Psychiatry, University of Melbourne, Parkville 3010, Australia
| | - Jee Hyun Kim
- Deakin University, IMPACT, The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, Australia; Florey Institute of Neuroscience and Mental Health, Parkville, Australia
| | - Ken Walder
- Deakin University, IMPACT, The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, Australia.
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187
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Zhu L, Xin YJ, He M, Bian J, Cheng XL, Li R, Li JJ, Wang J, Liu JY, Yang L. Downregulation of miR-337-3p in hypoxia/reoxygenation neuroblastoma cells increases KCTD11 expression. J Biochem Mol Toxicol 2024; 38:e23685. [PMID: 38495002 DOI: 10.1002/jbt.23685] [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] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 12/18/2023] [Accepted: 03/07/2024] [Indexed: 03/19/2024]
Abstract
Neurodegeneration is linked to the progressive loss of neural function and is associated with several diseases. Hypoxia is a hallmark in many of these diseases, and several therapies have been developed to treat this disease, including gene expression therapies that should be tightly controlled to avoid side effects. Cells experiencing hypoxia undergo a series of physiological responses that are induced by the activation of various transcription factors. Modulation of microRNA (miRNA) expression to alter transcriptional regulation has been demonstrated to be beneficial in treating multiple diseases, and in this study, we therefore explored potential miRNA candidates that could influence hypoxia-induced nerve cell death. Our data suggest that in mouse neuroblasts Neuro-2a cells with hypoxia/reoxygenation (H/R), miR-337-3p is downregulated to increase the expression of Potassium channel tetramerization domain containing 11 (KCTD11) and subsequently promote apoptosis. Here, we demonstrate for the first time that KCTD11 plays a role in the cellular response to hypoxia, and we also provide a possible regulatory mechanism by identifying the axis of miR-337-3p/KCTD11 as a promising candidate modulator of nerve cell survival after H/R exposure.
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Affiliation(s)
- Lin Zhu
- Department of Clinical Laboratory, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Yi-Juan Xin
- Department of Clinical Laboratory, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Mu He
- Department of Clinical Laboratory, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Jun Bian
- Department of General Surgery, Xi'an Jiaotong University Affiliated Children's Hospital, Xi'an, Shaanxi, China
| | - Xiao-Li Cheng
- Department of Clinical Laboratory, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Rui Li
- Department of Clinical Laboratory, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Jin-Jie Li
- Department of Clinical Laboratory, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Juan Wang
- Department of Clinical Laboratory, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Jia-Yun Liu
- Department of Clinical Laboratory, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Liu Yang
- Department of Clinical Laboratory, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi, China
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188
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Van HT, Xie G, Dong P, Liu Z, Ge K. KMT2 Family of H3K4 Methyltransferases: Enzymatic Activity-dependent and -independent Functions. J Mol Biol 2024; 436:168453. [PMID: 38266981 PMCID: PMC10957308 DOI: 10.1016/j.jmb.2024.168453] [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] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 01/26/2024]
Abstract
Histone-lysine N-methyltransferase 2 (KMT2) methyltransferases are critical for gene regulation, cell differentiation, animal development, and human diseases. KMT2 biological roles are often attributed to their methyltransferase activities on lysine 4 of histone H3 (H3K4). However, recent data indicate that KMT2 proteins also possess non-enzymatic functions. In this review, we discuss the current understanding of KMT2 family, with a focus on their enzymatic activity-dependent and -independent functions. Six mammalian KMT2 proteins of three subgroups, KMT2A/B (MLL1/2), KMT2C/D (MLL3/4), and KMT2F/G (SETD1A/B or SET1A/B), have shared and distinct protein domains, catalytic substrates, genomic localizations, and associated complex subunits. Recent studies have revealed the importance of KMT2C/D in enhancer regulation, differentiation, development, tumor suppression and highlighted KMT2C/D enzymatic activity-dependent and -independent roles in mouse embryonic development and cell differentiation. Catalytic dependent and independent functions for KMT2A/B and KMT2F/G in gene regulation, differentiation, and development are less understood. Finally, we provide our perspectives and lay out future research directions that may help advance the investigation on enzymatic activity-dependent and -independent biological roles and working mechanisms of KMT2 methyltransferases.
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Affiliation(s)
- Hieu T Van
- Adipocyte Biology and Gene Regulation Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 50, Room 4149, 50 South Dr, Bethesda, MD 20892, USA.
| | - Guojia Xie
- Adipocyte Biology and Gene Regulation Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 50, Room 4149, 50 South Dr, Bethesda, MD 20892, USA.
| | - Peng Dong
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
| | - Kai Ge
- Adipocyte Biology and Gene Regulation Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 50, Room 4149, 50 South Dr, Bethesda, MD 20892, USA.
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189
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Recktenwald M, Hutt E, Davis L, MacAulay J, Daringer NM, Galie PA, Staehle MM, Vega SL. Engineering transcriptional regulation for cell-based therapies. SLAS Technol 2024; 29:100121. [PMID: 38340892 DOI: 10.1016/j.slast.2024.100121] [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: 11/30/2023] [Revised: 01/10/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
A major aim in the field of synthetic biology is developing tools capable of responding to user-defined inputs by activating therapeutically relevant cellular functions. Gene transcription and regulation in response to external stimuli are some of the most powerful and versatile of these cellular functions being explored. Motivated by the success of chimeric antigen receptor (CAR) T-cell therapies, transmembrane receptor-based platforms have been embraced for their ability to sense extracellular ligands and to subsequently activate intracellular signal transduction. The integration of transmembrane receptors with transcriptional activation platforms has not yet achieved its full potential. Transient expression of plasmid DNA is often used to explore gene regulation platforms in vitro. However, applications capable of targeting therapeutically relevant endogenous or stably integrated genes are more clinically relevant. Gene regulation may allow for engineered cells to traffic into tissues of interest and secrete functional proteins into the extracellular space or to differentiate into functional cells. Transmembrane receptors that regulate transcription have the potential to revolutionize cell therapies in a myriad of applications, including cancer treatment and regenerative medicine. In this review, we will examine current engineering approaches to control transcription in mammalian cells with an emphasis on systems that can be selectively activated in response to extracellular signals. We will also speculate on the potential therapeutic applications of these technologies and examine promising approaches to expand their capabilities and tighten the control of gene regulation in cellular therapies.
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Affiliation(s)
- Matthias Recktenwald
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Evan Hutt
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Leah Davis
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - James MacAulay
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Nichole M Daringer
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Peter A Galie
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Mary M Staehle
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Sebastián L Vega
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA; Department of Orthopaedic Surgery, Cooper Medical School of Rowan University, Camden, NJ 08103, USA.
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190
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Wang Y, Tang X, Lu J. Convergent and divergent evolution of microRNA-mediated regulation in metazoans. Biol Rev Camb Philos Soc 2024; 99:525-545. [PMID: 37987240 DOI: 10.1111/brv.13033] [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] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
The evolution of microRNAs (miRNAs) has been studied extensively to understand their roles in gene regulation and evolutionary processes. This review focuses on how miRNA-mediated regulation has evolved in bilaterian animals, highlighting both convergent and divergent evolution. Since animals and plants display significant differences in miRNA biogenesis and target recognition, the 'independent origin' hypothesis proposes that miRNA pathways in these groups independently evolved from the RNA interference (RNAi) pathway, leading to modern miRNA repertoires through convergent evolution. However, recent evidence raises the alternative possibility that the miRNA pathway might have already existed in the last common ancestor of eukaryotes, and that the differences in miRNA pathway and miRNA repertoires among animal and plant lineages arise from lineage-specific innovations and losses of miRNA pathways, miRNA acquisition, and loss of miRNAs after eukaryotic divergence. The repertoire of miRNAs has considerably expanded during bilaterian evolution, primarily through de novo creation and duplication processes, generating new miRNAs. Although ancient functionally established miRNAs are rarely lost, many newly emerged miRNAs are transient and lineage specific, following a birth-death evolutionary pattern aligning with the 'out-of-the-testis' and 'transcriptional control' hypotheses. Our focus then shifts to the convergent molecular evolution of miRNAs. We summarize how miRNA clustering and seed mimicry contribute to this phenomenon, and we review how miRNAs from different sources converge to degrade maternal messenger RNAs (mRNAs) during animal development. Additionally, we describe how miRNAs evolve across species due to changes in sequence, seed shifting, arm switching, and spatiotemporal expression patterns, which can result in variations in target sites among orthologous miRNAs across distant strains or species. We also provide a summary of the current understanding regarding how the target sites of orthologous miRNAs can vary across strains or distantly related species. Although many paralogous miRNAs retain their seed or mature sequences after duplication, alterations can occur in the seed or mature sequences or expression patterns of paralogous miRNAs, leading to functional diversification. We discuss our current understanding of the functional divergence between duplicated miRNAs, and illustrate how the functional diversification of duplicated miRNAs impacts target site evolution. By investigating these topics, we aim to enhance our current understanding of the functions and evolutionary dynamics of miRNAs. Additionally, we shed light on the existing challenges in miRNA evolutionary studies, particularly the complexity of deciphering the role of miRNA-mediated regulatory network evolution in shaping gene expression divergence and phenotypic differences among species.
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Affiliation(s)
- Yirong Wang
- Bioinformatics Center, College of Biology, Hunan University, Changsha, 410082, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
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191
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Swiatlowska P, Iskratsch T. Cardiovascular Mechano-Epigenetics: Force-Dependent Regulation of Histone Modifications and Gene Regulation. Cardiovasc Drugs Ther 2024; 38:215-222. [PMID: 36653625 PMCID: PMC10959834 DOI: 10.1007/s10557-022-07422-z] [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] [Accepted: 12/28/2022] [Indexed: 01/19/2023]
Abstract
The local mechanical microenvironment impacts on the cell behavior. In the cardiovascular system, cells in both the heart and the vessels are exposed to continuous blood flow, blood pressure, stretching forces, and changing extracellular matrix stiffness. The force-induced signals travel all the way to the nucleus regulating epigenetic changes such as chromatin dynamics and gene expression. Mechanical cues are needed at the very early stage for a faultless embryological development, while later in life, aberrant mechanical signaling can lead to a range of pathologies, including diverse cardiovascular diseases. Hence, an investigation of force-generated epigenetic alteration at different time scales is needed to understand fully the phenotypic changes in disease onset and progression. That being so, cardiovascular mechano-epigenetics emerges as an attractive field of study. Given the rapid advances in this emergent field of research, this short review aims to provide an analysis of the state of knowledge of force-induced epigenetic changes in the cardiovascular field.
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Affiliation(s)
- Pamela Swiatlowska
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
| | - Thomas Iskratsch
- School of Engineering and Materials Science, Queen Mary University of London, London, UK.
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192
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Pourquoi A, Miller MR, Koch SR, Boyle K, Surratt V, Nguyen H, Panja S, Cartailler JP, Shrestha S, Stark RJ. DIFFERENTIAL SIGNALING EFFECTS OF ESCHERICHIA COLI AND STAPHYLOCOCCUS AUREUS IN HUMAN WHOLE BLOOD INDICATE DISTINCT REGULATION OF THE NRF2 PATHWAY. Shock 2024; 61:557-563. [PMID: 38604133 PMCID: PMC11018340 DOI: 10.1097/shk.0000000000002305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
ABSTRACT Escherichia coli and Staphylococcus aureus are two of the most common bacterial species responsible for sepsis. While it is observed that they have disparate clinical phenotypes, the signaling differences elicited by each bacteria that drive this variance remain unclear. Therefore, we used human whole blood exposed to heat-killed E. coli or S. aureus and measured the transcriptomic signatures. Relative to unstimulated control blood, heat-killed bacteria exposure led to significant dysregulation (upregulated and downregulated) of >5,000 genes for each experimental condition, with a slight increase in gene alterations by S. aureus. While there was significant overlap regarding proinflammatory pathways, Gene Ontology overrepresentation analysis of the most altered genes suggested biological processes like macrophage differentiation and ubiquinone biosynthesis were more unique to heat-killed S. aureus, compared with heat-killed E. coli exposure. Using Ingenuity Pathway Analysis, it was demonstrated that nuclear factor erythroid 2-related factor 2 signaling, a main transcription factor in antioxidant responses, was predominately upregulated in S. aureus exposed blood relative to E. coli. Furthermore, the use of pharmacologics that preferentially targeted the nuclear factor erythroid 2-related factor 2 pathway led to differential cytokine profiles depending on the type of bacterial exposure. These findings reveal significant inflammatory dysregulation between E. coli and S. aureus and provide insight into the targeting of unique pathways to curb bacteria-specific responses.
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Affiliation(s)
| | | | - Stephen R Koch
- Vanderbilt University Medical Center, Nashville, Tennessee
| | | | | | - Hong Nguyen
- Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sourav Panja
- Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Shristi Shrestha
- Vanderbilt University, Creative Data Solutions, Nashville, Tennessee
| | - Ryan J Stark
- Vanderbilt University Medical Center, Nashville, Tennessee
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193
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Jiménez-Moreno N, Lane JD. ATG8 proteins are co-factors for human dopaminergic neuronal transcriptional control: implications for neuronal resilience in Parkinson disease. Autophagy 2024; 20:955-957. [PMID: 37312406 PMCID: PMC11062359 DOI: 10.1080/15548627.2023.2221958] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 06/01/2023] [Indexed: 06/15/2023] Open
Abstract
Parkinson disease (PD) is caused by the loss of ventral midbrain dopaminergic neurons (mDANs) in the substantia nigra pars compacta (SNpc). These cells are especially vulnerable to stress but can be protected by autophagy enhancement strategies in vitro and in vivo. In our recent study, we focused on the LIM (Lin11, Isl-1, and Mec-3)-domain homeobox transcription factors LMX1A (LIM homeobox transcription factor 1 alpha) and LMX1B (LIM homeobox transcription factor 1 beta), crucial drivers of mDAN differentiation with roles in autophagy gene expression for stress protection in the developed brain. Using human induced pluripotent stem cell (hiPSC)-derived mDANs and transformed human cell lines, we found that these autophagy gene transcription factors are themselves regulated by autophagy-mediated turnover. LMX1B possesses a non-canonical LC3-interacting region (LIR) in its C-terminus through which it interacts with ATG8 family members. The LMX1B LIR-like domain enables binding to ATG8 proteins in the nucleus, where ATG8 proteins act as co-factors for robust transcription of LMX1B target genes. Thus, we propose a novel role for ATG8 proteins as autophagy gene transcriptional co-factors for mDAN stress protection in PD.
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Affiliation(s)
- Natalia Jiménez-Moreno
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland, UK
| | - Jon D. Lane
- Cell Biology Laboratories, School of Biochemistry, University of Bristol, Bristol, England, UK
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Khamit A, Chakraborty P, Zahorán S, Villányi Z, Orvos H, Hermesz E. Stress-Induced Changes in Nucleocytoplasmic Localization of Crucial Factors in Gene Expression Regulation. Int J Mol Sci 2024; 25:3895. [PMID: 38612704 PMCID: PMC11012061 DOI: 10.3390/ijms25073895] [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: 02/16/2024] [Revised: 03/29/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
This study investigates the toxic effect of harmful materials, unfiltered by the placenta, on neonatal umbilical cord (UC) vessels, focusing on stress-induced adaptations in transcriptional and translational processes. It aims to analyze changes in pathways related to mRNA condensate formation, transcriptional regulation, and DNA damage response under maternal smoking-induced stress. UC vessels from neonates born to smoking (Sm) and nonsmoking mothers (Ctr) were examined. Immunofluorescence staining and confocal microscopy assessed the localization of key markers, including Transcription Complex Subunit 1 (CNOT1) and the largest subunit of RNA polymerase II enzyme (RPB1). Additionally, markers of DNA damage response, such as Poly(ADP-ribose) polymerase-1, were evaluated. In Sm samples, dissolution of CNOT1 granules in UC vessels was observed, potentially aiding stalled translation and enhancing transcription via RPB1 assembly and translocation. Control vessels showed predominant cytoplasmic RPB1 localization. Despite adaptive responses, Sm endothelial cells exhibited significant damage, indicated by markers like Poly(ADP-ribose) polymerase-1. Ex vivo metal treatment on control vessels mirrored Sm sample alterations, emphasizing marker roles in cell survival under toxic exposure. Maternal smoking induces specific molecular adaptations in UC vessels, affecting mRNA condensate formation, transcriptional regulation, and DNA damage response pathways. Understanding these intricate molecular mechanisms could inform interventions to improve neonatal health outcomes and mitigate adverse effects of toxic exposure during pregnancy.
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Affiliation(s)
- Ali Khamit
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, H-6701 Szeged, Hungary; (A.K.); (P.C.); (S.Z.); (Z.V.)
| | - Payal Chakraborty
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, H-6701 Szeged, Hungary; (A.K.); (P.C.); (S.Z.); (Z.V.)
| | - Szabolcs Zahorán
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, H-6701 Szeged, Hungary; (A.K.); (P.C.); (S.Z.); (Z.V.)
| | - Zoltán Villányi
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, H-6701 Szeged, Hungary; (A.K.); (P.C.); (S.Z.); (Z.V.)
| | - Hajnalka Orvos
- Department of Obstetrics and Gynecology, Albert Szent-Györgyi Medical School, University of Szeged, H-6701 Szeged, Hungary;
| | - Edit Hermesz
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, H-6701 Szeged, Hungary; (A.K.); (P.C.); (S.Z.); (Z.V.)
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195
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Chen Z, Long L, Wan M, Huang M, Wu H, Huang Q. Identification of osteogenic differentiation-related miRNA-mRNA regulatory network of human periodontal ligament stem cells. Cell Mol Biol (Noisy-le-grand) 2024; 70:83-88. [PMID: 38650150 DOI: 10.14715/cmb/2024.70.3.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Indexed: 04/25/2024]
Abstract
This study aimed to investigate the hub genes and miRNA-mRNA regulatory network around periodontal ligament stem cells (PDLSC) for osteogenic differentiation through bioinformatic analysis. The dataset with osteogenic differentiation of human PDLSC was downloaded from the GEO database. The Weighted gene coexpression network analysis (WGCNA) was performed to identify key modules and hub genes. In addition, differentially expressed genes (DEGs) analysis was conducted with limma. The functional enrichment of differentially expressed hub genes was implemented with KEGG and GSEA analysis. The targeted genes of differentially expressed miRNA were predicted based on miRWalk database. The miRNA-mRNA interaction network of osteogenic differentiation of PDLSC was constructed and visualized. The WGNCA results showed that the light-cyan module was positively correlated with osteogenic differentiation (r=0.98, P<0.05). A total of 3125 hub genes and 1426 differentially expressed hub genes were detected in OG group. Innate immune-related signaling pathways and metabolic pathways were involved in the osteogenic differentiation. In addition, total of 2 upregulated miRNAs with 63 targeted DEGs and 6 downregulated miRNAs with 214 targeted DEGs were detected, which contributed to osteogenic differentiation by regulating amino acid metabolism signaling pathway. We identified hub genes and miRNA-mRNA regulatory network contributing to osteogenic differentiation of human PDLSC, which will provide novel strategy for periodontal disease therapy.
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Affiliation(s)
- Zhenrong Chen
- Department of Stomatology, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.
| | - Lulu Long
- Department of Gynecology, Guangdong Women and Children Hospital Guangzhou, Guangdong, China.
| | - Mianjia Wan
- Department of Stomatology, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.
| | - Min Huang
- Department of Gynecology, Guangdong Women and Children Hospital Guangzhou, Guangdong, China.
| | - Haijuan Wu
- Department of Stomatology, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.
| | - Qun Huang
- Department of Stomatology, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.
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196
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Cheng H, Wang Y, Xuan J. Identification of hub genes and key pathways in spinal cord injury via bioinformatics analysis. Cell Mol Biol (Noisy-le-grand) 2024; 70:61-66. [PMID: 38650155 DOI: 10.14715/cmb/2024.70.3.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Indexed: 04/25/2024]
Abstract
This study aimed to explore the hub genes and related key pathways in Spinal Cord Injury (SCI) based on the bioinformatics analysis. Two microarray datasets (GSE45006, GSE45550) were obtained from the GEO database and were merged and batch-corrected. The differentially expressed genes (DEGs) in SCI were explored with the Limma, and the weighted gene co-expression network analysis (WGCNA) was conducted to explore the module genes. Functional enrichment analysis and Gene set variation analysis (GSVA) were used to investigate the biological functions and key pathways of the key genes related to SCI. Then the protein-protein interaction (PPI) network was generated using the STING online tool, and the hub genes in SCI were identified. Receiver operating characteristic (ROC) curves were applied to assess the diagnostic value of the selected hub genes. We identified 554 DEGs in SCI, and 1236 key genes in SCI were selected via WGCNA. Totally 111 key genes related to SCI were discovered. Furthermore, the functional enrichment analysis showed that these key mRNAs were primarily enriched in the extracellular matrix (ECM)-related pathways and processes associated with wound healing and cell growth. The PPI network further filtered six hub genes (Cd44, Timp1, Loxl1, Col6a1, Col3a1, Col5a1) ranked by the degree, and the diagnostic value of the six hub genes was confirmed by the ROC curves. Six hub genes including Cd44, Timp1, Loxl1, Col6a1, Col3a1, and Col5a1 were identified in SCI, with differential expression and excellent diagnostic value, which might provide insight into the targeted therapy of SCI.
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Affiliation(s)
- Hao Cheng
- Department of Spine Surgery, Jinhua Municipal Central Hospital, Jinhua, Zhejiang 321000, China.
| | - Yanben Wang
- Department of Spine Surgery, Jinhua Municipal Central Hospital, Jinhua, Zhejiang 321000, China.
| | - Jun Xuan
- Department of Spine Surgery, Jinhua Municipal Central Hospital, Jinhua, Zhejiang 321000, China.
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197
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Zhou X. Identification of important genes for human periodontal ligament cells in response to mechanical force based on WGCNA. Cell Mol Biol (Noisy-le-grand) 2024; 70:192-196. [PMID: 38650134 DOI: 10.14715/cmb/2024.70.3.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Indexed: 04/25/2024]
Abstract
To identify the differentially important genes of human periodontal ligament cells (PDLC) in response to different types of force, the dataset with regard to human PDLC in response to force was retrieved from the GEO. Differentially expressed genes (DEG) analysis between mechanical force (MF) and the control group was conducted. The gene set enrichment analysis (GSEA) was applied to identify the functional enrichment in different MF groups. Weighted gene co-expression network analysis (WGCNA) of transcriptomic data was performed to identify the highly correlated genes in human PDLC in response to MF. The Lasso regression model was applied to screen the key genes. Results showed A total of 2861 DEGs were identified between the MF group and control group, including 1470 up-regulated DEGs and 1391 down-regulated DEGs. Different biological processes were enriched between the static group and the intermittent group. The Myc targets, TGF-β signaling pathway and PI3K/AKT/MTOR signaling pathway were enriched in intermittent-MF and static-MF groups. The turquoise module (including 386 hub genes) in WGCNA was highly correlated with intermittent traits and the black module (including 33 hub genes) was positively correlated with static traits. The lasso analysis result showed that the CLIC4, NPLOC4 and PRDX6 had the greatest impact on the human PDLC with mechanic stimuli with good predictive efficiency. In conclusion, we developed important genes for human PDLC in response to MF, which might be potential markers for orthodontic tooth movement.
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Affiliation(s)
- Xiaofeng Zhou
- Yichang Central People's Hospital, The First Clinical Medical of China Three Gorges University, Yichang, Hubei, China.
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198
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Gao Y, Yu T. Identification of DLEU2 as biomarker based on lncRNA-Mediated ceRNA network in rupture of intracranial aneurysm. Cell Mol Biol (Noisy-le-grand) 2024; 70:148-154. [PMID: 38650140 DOI: 10.14715/cmb/2024.70.3.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Indexed: 04/25/2024]
Abstract
Intracranial aneurysms (IA) is a potentially devastating clinical problem that may cause lethal subarachnoid hemorrhage upon rupture, but the molecular mechanisms remain further elucidated. Our goal in this work was to build the lncRNA-mediated ceRNA network in IS and explore the associated pathways and functions. The deep transcriptome sequencing dataset profile of rupture of IA and normal tissues (SRP150595) was obtained from NCBI database. To determine which genes were differently expressed, weighted gene co-expression network analysis and other integrated bioinformatics techniques were used (DEGs). The action mechanism and associated pathways of DEGs in IA were investigated using GO annotations and KEGG analysis. The Starbase database was used to build the ceRNA network. Vascular smooth muscle cells (VSMC) were used for the transwell assay and CCK-8. A total of 248 common differentially expressed-protein coding RNA and 76 DE-lncRNAs were obtained. Functional enrichment analysis indicated that the DEGs of IA are involved in pathways of inflammation and immune response. A lncRNAs-mediated ceRNA network including lncRNAs BASP1-AS1, DLEU2, LINC02035, LINC02363, MMP25-AS1, AC008771.1 was constructed. The biological behavior of VSMC was suppressed when DLEU2 was knocked down. In conclusion, a lncRNAs-mediated ceRNA network was constructed in IA based on the integrated bioinformatics analyses, in which DLEU2 was identified to be a novel and potential biomarker of IA.
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Affiliation(s)
- Yanlei Gao
- Emergency Department, Affiliated Yantai Yuhuangding Hospital of Qingdao University. No. 20, Yudong Road, Zhifu District, Yantai City, Shandong Province, 264000, China.
| | - Tao Yu
- Emergency Department, Affiliated Yantai Yuhuangding Hospital of Qingdao University. No. 20, Yudong Road, Zhifu District, Yantai City, Shandong Province, 264000, China.
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199
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Wirthlin ME, Schmid TA, Elie JE, Zhang X, Kowalczyk A, Redlich R, Shvareva VA, Rakuljic A, Ji MB, Bhat NS, Kaplow IM, Schäffer DE, Lawler AJ, Wang AZ, Phan BN, Annaldasula S, Brown AR, Lu T, Lim BK, Azim E, Clark NL, Meyer WK, Pond SLK, Chikina M, Yartsev MM, Pfenning AR, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements. Science 2024; 383:eabn3263. [PMID: 38422184 DOI: 10.1126/science.abn3263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/20/2024] [Indexed: 03/02/2024]
Abstract
Vocal production learning ("vocal learning") is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from the Egyptian fruit bat (Rousettus aegyptiacus) with analyses of the genomes of 215 placental mammals. First, we identified a set of proteins evolving more slowly in vocal learners. Then, we discovered a vocal motor cortical region in the Egyptian fruit bat, an emergent vocal learner, and leveraged that knowledge to identify active cis-regulatory elements in the motor cortex of vocal learners. Machine learning methods applied to motor cortex open chromatin revealed 50 enhancers robustly associated with vocal learning whose activity tended to be lower in vocal learners. Our research implicates convergent losses of motor cortex regulatory elements in mammalian vocal learning evolution.
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Affiliation(s)
- Morgan E Wirthlin
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Tobias A Schmid
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Julie E Elie
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94708, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Xiaomeng Zhang
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Amanda Kowalczyk
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Ruby Redlich
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Varvara A Shvareva
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Ashley Rakuljic
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Maria B Ji
- Department of Psychology, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Ninad S Bhat
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Irene M Kaplow
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Daniel E Schäffer
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Alyssa J Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Andrew Z Wang
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - BaDoi N Phan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Siddharth Annaldasula
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Ashley R Brown
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Tianyu Lu
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Byung Kook Lim
- Neurobiology section, Division of Biological Science, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eiman Azim
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Nathan L Clark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | | | - Maria Chikina
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Michael M Yartsev
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94708, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Andreas R Pfenning
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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Raheem A, Lu D, Khalid AK, Zhao G, Fu Y, Chen Y, Chen X, Hu C, Chen J, Chen H, Guo A. The Identification of a Novel Nucleomodulin MbovP467 of Mycoplasmopsis bovis and Its Potential Contribution in Pathogenesis. Cells 2024; 13:604. [PMID: 38607043 PMCID: PMC11011252 DOI: 10.3390/cells13070604] [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] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024] Open
Abstract
Mycoplasmopsis bovis is a causative agent of crucial diseases in both dairy and beef cattle leading to substantial economic losses. However, limited control measures for M. bovis-related diseases exist due to a lack of understanding about the virulence factors of this pathogen, a common challenge in mycoplasma research. Consequently, this study aimed to characterize a novel nucleomodulin as a virulence-related factor of M. bovis. Employing bioinformatic tools, we initially predicted MbovP467 to be a secreted protein with a nuclear localization signal based on SignalP scores and the cNLS (Nuclear Localization Signal) Mapper, respectively. Subsequently, the MbovP467 gene was synthesized and cloned into a pEGFP plasmid with EGFP labeling to obtain a recombinant plasmid (rpEGFP-MbovP467) and then was also cloned in pET-30a with a consideration for an Escherichia coli codon bias and expressed and purified for the production of polyclonal antibodies against the recombinant MbovP467 protein. Confocal microscopy and a Western blotting assay confirmed the nuclear location of MbovP467 in bovine macrophages (BoMacs). RNA-seq data revealed 220 up-regulated and 20 down-regulated genes in the rpEGFP-MbovP467-treated BoMac group compared to the control group (pEGFP). A GO- and KEGG-enrichment analysis identified associations with inflammatory responses, G protein-coupled receptor signaling pathways, nuclear receptor activity, sequence-specific DNA binding, the regulation of cell proliferation, IL-8, apoptotic processes, cell growth and death, the TNF signaling pathway, the NF-κB signaling pathway, pathways in cancer, and protein families of signaling and cellular processes among the differentially expressed up-regulated mRNAs. Further experiments, investigating cell viability and the inflammatory response, demonstrated that MbovP467 reduces BoMac cell viability and induces the mRNA expression of IL-1β, IL-6, IL-8, TNF-α, and apoptosis in BoMac cells. Further, MbovP467 increased the promoter activity of TNF-α. In conclusion, this study identified a new nucleomodulin, MbovP467, for M. bovis, which might have an important role in M. bovis pathogenesis.
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Affiliation(s)
- Abdul Raheem
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.R.); (D.L.); (A.K.K.); (Y.F.); (Y.C.); (X.C.); (C.H.); (J.C.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Doukun Lu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.R.); (D.L.); (A.K.K.); (Y.F.); (Y.C.); (X.C.); (C.H.); (J.C.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Abdul Karim Khalid
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.R.); (D.L.); (A.K.K.); (Y.F.); (Y.C.); (X.C.); (C.H.); (J.C.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Gang Zhao
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western China, School of Life Sciences, Ningxia University, Yinchuan 750021, China;
| | - Yingjie Fu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.R.); (D.L.); (A.K.K.); (Y.F.); (Y.C.); (X.C.); (C.H.); (J.C.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingyu Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.R.); (D.L.); (A.K.K.); (Y.F.); (Y.C.); (X.C.); (C.H.); (J.C.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.R.); (D.L.); (A.K.K.); (Y.F.); (Y.C.); (X.C.); (C.H.); (J.C.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Changmin Hu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.R.); (D.L.); (A.K.K.); (Y.F.); (Y.C.); (X.C.); (C.H.); (J.C.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianguo Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.R.); (D.L.); (A.K.K.); (Y.F.); (Y.C.); (X.C.); (C.H.); (J.C.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Huanchun Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.R.); (D.L.); (A.K.K.); (Y.F.); (Y.C.); (X.C.); (C.H.); (J.C.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Aizhen Guo
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.R.); (D.L.); (A.K.K.); (Y.F.); (Y.C.); (X.C.); (C.H.); (J.C.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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