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Lu HL, Li L, Miao YL, Liang H, Zou JM, You JJ, Liang XF, He S. Effects and regulatory pathway of proopinmelanocortin on feeding habit domestication in mandarin fish. Gene 2023:147581. [PMID: 37336270 DOI: 10.1016/j.gene.2023.147581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/21/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023]
Abstract
Proopiomelanocortin (POMC) is a hormone precursor, and has been reported to participate in domestication. However, its effects on feeding habit domestication in fish are poorly understood. Mandarin fish (Siniperca chuatsi) feeds solely on live prey fish since first-feeding. In the present study, the high expression of pomc in mandarin fish, both the pomc siRNA and MC4R inhibitor treatments increased the success rate of domestication from live prey fish to dead prey fish and food intake of dead prey fish, suggesting the role of pomc on the special feeding habit of live prey fish in mandarin fish. In addition, one c-fos binding site was identified in the region that from -1053 bp to -931 bp upstream of the transcription start site of pomc, and this region exhibited positive promoter activity. The mandarin fish brain cells treated with c-fos siRNA displayed suppressed pomc mRNA expression, indicating that c-fos positively regulated pomc expression. Furthermore, the mRNA expression of c-fos was higher in the mandarin fish which were more difficult to domesticate. The results of ChIP assay and inhibitor treatment confirmed that the activation of c-fos gene by histone H3K4me3 was catalyzed by Setd1b in mandarin fish. Three open peaks were found at the upstream regulatory region of setd1b by ATAC-seq, and the mRNA expression of setd1b was higher in the mandarin fish which were more difficult to domesticate. These results indicated that Setd1b could methylate histone H3K4 to activate the c-fos transcription, maintaining the high expression of pomc, which might contribute to the special feeding habit of mandarin fish.
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Affiliation(s)
- Hai-Lin Lu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
| | - Ling Li
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
| | - Yun-Liang Miao
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
| | - Hui Liang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
| | - Jia-Ming Zou
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
| | - Jun-Jie You
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
| | - Xu-Fang Liang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
| | - Shan He
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China.
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Razin SV, Ulianov SV, Iarovaia OV. Enhancer Function in the 3D Genome. Genes (Basel) 2023; 14:1277. [PMID: 37372457 DOI: 10.3390/genes14061277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
In this review, we consider various aspects of enhancer functioning in the context of the 3D genome. Particular attention is paid to the mechanisms of enhancer-promoter communication and the significance of the spatial juxtaposition of enhancers and promoters in 3D nuclear space. A model of an activator chromatin compartment is substantiated, which provides the possibility of transferring activating factors from an enhancer to a promoter without establishing direct contact between these elements. The mechanisms of selective activation of individual promoters or promoter classes by enhancers are also discussed.
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Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Sergey V Ulianov
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Olga V Iarovaia
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
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Tiukacheva EA, Ulianov SV, Karpukhina A, Razin SV, Vassetzky Y. 3D genome alterations and editing in pathology. Mol Ther 2023; 31:924-933. [PMID: 36755493 PMCID: PMC10124079 DOI: 10.1016/j.ymthe.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 12/07/2022] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
The human genome is folded into a multi-level 3D structure that controls many nuclear functions including gene expression. Recently, alterations in 3D genome organization were associated with several genetic diseases and cancer. As a consequence, experimental approaches are now being developed to modify the global 3D genome organization and that of specific loci. Here, we discuss emerging experimental approaches of 3D genome editing that may prove useful in biomedicine.
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Affiliation(s)
- Eugenia A Tiukacheva
- CNRS UMR9018, Institut Gustave Roussy, 94805 Villejuif, France; Institute of Gene Biology, Moscow 119334, Russia; Moscow Institute of Physics and Technology, Moscow 141700, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; Koltzov Institute of Developmental Biology, Moscow 119334, Russia
| | - Sergey V Ulianov
- Institute of Gene Biology, Moscow 119334, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Anna Karpukhina
- CNRS UMR9018, Institut Gustave Roussy, 94805 Villejuif, France; Koltzov Institute of Developmental Biology, Moscow 119334, Russia
| | - Sergey V Razin
- Institute of Gene Biology, Moscow 119334, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Yegor Vassetzky
- CNRS UMR9018, Institut Gustave Roussy, 94805 Villejuif, France; Koltzov Institute of Developmental Biology, Moscow 119334, Russia.
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Michaelis V, Kasper S, Naperkowski L, Pusse J, Thiel A, Ebert F, Aschner M, Schwerdtle T, Haase H, Bornhorst J. The Impact of Zinc on Manganese Bioavailability and Cytotoxicity in HepG2 Cells. Mol Nutr Food Res 2023; 67:e2200283. [PMID: 36683243 DOI: 10.1002/mnfr.202200283] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
SCOPE Despite their essentiality, several studies have shown that either manganese (Mn) or zinc (Zn) overexposure may lead to detrimental health effects. Although Mn is transported by some of the SLC family transporters that translocate Zn, the role of Zn in hepatocellular Mn transport and Mn-induced toxicity have yet to be fully characterized. METHODS AND RESULTS The human hepatoma cell line, HepG2, is utilized. Total cellular Mn and Zn amounts are determined after cells are treated with Zn 2 or 24 h prior to Mn incubation for additional 24 h with inductively coupled plasma-based spectrometry and labile Zn is assessed with the fluorescent probe FluoZin-3. Furthermore, mRNA expression of genes involved in metal homeostasis, and mechanistic endpoints associated with Mn-induced cytotoxicity are addressed. These results suggest that Zn protects against Mn-induced cytotoxicity and impacts Mn bioavailability to a great extent when cells are preincubated with higher Zn concentrations for longer duration as characterized by decreased activation of caspase-3 as well as lactate dehydrogenase (LDH) release. CONCLUSIONS Zn protects against Mn-induced cytotoxicity in HepG2 cells possibly due to decreased Mn bioavailability. Additionally, mRNA expression of metal homeostasis-related genes indicates possible underlying pathways that should to be addressed in future studies.
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Affiliation(s)
- Vivien Michaelis
- Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstraße 20, 42119, Wuppertal, Germany
| | - Silja Kasper
- Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstraße 20, 42119, Wuppertal, Germany
| | - Lisa Naperkowski
- Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstraße 20, 42119, Wuppertal, Germany
| | - Jan Pusse
- Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstraße 20, 42119, Wuppertal, Germany
| | - Alicia Thiel
- Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstraße 20, 42119, Wuppertal, Germany
| | - Franziska Ebert
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany
| | - Michael Aschner
- Department of Molecular Pharmacology, Neuroscience, and Pediatrics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Tanja Schwerdtle
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, 14558, Nuthetal, Germany
- German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589, Berlin, Germany
| | - Hajo Haase
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, 14558, Nuthetal, Germany
- Department of Food Chemistry and Toxicology, Berlin Institute of Technology, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Julia Bornhorst
- Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstraße 20, 42119, Wuppertal, Germany
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, 14558, Nuthetal, Germany
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Wang J, Wei B, Thakur K, Wang CY, Li KX, Wei ZJ. Transcriptome Analysis Reveals the Anti-cancerous Mechanism of Licochalcone A on Human Hepatoma Cell HepG2. Front Nutr 2022; 8:807574. [PMID: 34988109 PMCID: PMC8720858 DOI: 10.3389/fnut.2021.807574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/30/2021] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma is a malignancy with a low survival rate globally, and there is imperative to unearth novel natural phytochemicals as effective therapeutic strategies. Licochalcone A is a chalcone from Glycyrrhiza that displayed various pharmacological efficacy. A globally transcriptome analysis was carried out to reveal the gene expression profiling to explore Licochalcone A's function as an anti-cancer phytochemical on HepG2 cells and investigate its potential mechanisms. Altogether, 6,061 dysregulated genes were detected (3,414 up-regulated and 2,647 down-regulated). SP1 was expected as the transcription factor that regulates the functions of most screened genes. GO and KEGG analysis was conducted, and the MAPK signaling pathway and the FoxO signaling pathway were two critical signal pathways. Protein-protein interaction (PPI) network analysis based on STRING platform to discover the hub genes (MAPK1, ATF4, BDNF, CASP3, etc.) in the MAPK signaling pathway and (AKT3, GADD45A, IL6, CDK2, CDKN1A, etc.) the FoxO signaling pathway. The protein level of essential genes that participated in significant pathways was consistent with the transcriptome data. This study will provide an inclusive understanding of the potential anti-cancer mechanism of Licochalcone A on hepatocellular, signifying Licochalcone A as a promising candidate for cancer therapy.
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Affiliation(s)
- Jun Wang
- School of Biological Food and Environment, Hefei University, Hefei, China
| | - Bo Wei
- School of Biological Food and Environment, Hefei University, Hefei, China
| | - Kiran Thakur
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China.,School of Biological Science and Engineering, North Minzu University, Yinchuan, China
| | - Chu-Yan Wang
- School of Biological Food and Environment, Hefei University, Hefei, China
| | - Ke-Xin Li
- School of Biological Food and Environment, Hefei University, Hefei, China
| | - Zhao-Jun Wei
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China.,School of Biological Science and Engineering, North Minzu University, Yinchuan, China
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Zhang F, Guo S, Zhong W, Huang K, Liu Y. Integrative Analysis of Metallothioneins Identifies MT1H as Candidate Prognostic Biomarker in Hepatocellular Carcinoma. Front Mol Biosci 2021; 8:672416. [PMID: 34676244 PMCID: PMC8523949 DOI: 10.3389/fmolb.2021.672416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 08/16/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Metallothioneins (MTs) play crucial roles in the modulation of zinc/copper homeostasis, regulation of neoplastic growth and proliferation, and protection against apoptosis. The present study attempted to visualize the prognostic landscape of MT functional isoforms and identify potential prognostic biomarkers in hepatocellular carcinoma (HCC). Methods: The transcriptional expression, comprehensive prognostic performances, and gene-gene interaction network of MT isoforms in HCC were evaluated via Oncomine, GEPIA, Kaplan-Meier plotter, and GeneMANIA databases. Characterized by good prognostic value in three external cohorts, MT1H was specifically selected as a potential prognostic biomarker in HCC with various clinicopathological features. Functional and pathway enrichment analyses of MT1H status were performed using cBioPortal, the Database for Annotation, Visualization, and Integrated Discovery (DAVID), and ssGSVA method. Results: MT1E/1F/1G/1H/1M/1X/2A was greatly downregulated in HCC. Prognostic analyses elucidated the essential correlations between MT1A/1B/1H/1X/2A/4 attenuation and poor overall survival, between MT1B/1H/4 downregulation and worse relapse-free survival, and between MT1A/1B/1E/1H/1M/2A/4 downregulation and diminished progression-free survival in HCC. Taken together, these results indicated the powerful prognostic value of MT1H among MTs in HCC. In-depth analyses suggested that MT1H may be more applicable to alcohol-derived HCC and involved in the downregulation of the inflammatory pathway, Jak-STAT pathway, TNF pathway, and Wnt signaling pathway. Conclusion: MT-specific isoforms displayed aberrant expression and varying prognostic value in HCC. MT1H repression in HCC was multi-dimensionally detrimental to patient outcomes. Therefore, MT1H was possibly associated with carcinogenesis and exploited as a novel prognostic biomarker and candidate therapeutic target for HCC.
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Affiliation(s)
- Feng Zhang
- Department of General Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Shantou University Medical College, Shantou, China
| | - Shuijiao Guo
- Department of Operating Room, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Wenhui Zhong
- Department of General Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Shantou University Medical College, Shantou, China
| | - Kaijun Huang
- Department of General Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- *Correspondence: Yubin Liu, ; Kaijun Huang,
| | - Yubin Liu
- Department of General Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- *Correspondence: Yubin Liu, ; Kaijun Huang,
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7
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Hu Y, Zhao H, Zhao Y, Zheng J, Guo Y, Ma J. Characterization of chromosome organization in the differentiation of acute myeloid leukemia cells by all-trans retinoic acid. Life Sci 2020; 249:117479. [PMID: 32119959 DOI: 10.1016/j.lfs.2020.117479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/16/2020] [Accepted: 02/26/2020] [Indexed: 12/16/2022]
Abstract
A concomitant change of nucleus shape and chromosome conformation often happens in all-trans retinoic acid (ATRA)-induced differentiation of acute myeloid leukemia cells. However, the relation between the 3D chromosome architecture and the genome-wide epigenetic pattern for transcriptional regulation is poorly understood. In this study, high-throughput chromosome conformation capture (Hi-C) and chromosome immunoprecipitation (ChIP-seq) were employed to investigate the landscape of chromosome distal interaction and H3K4/27me3 in HL-60 cells treated with ATRA. We observed a general loss of topological associated domains (TADs) at PTPN11 during the differentiation of HL-60 cells. Furthermore, the significantly reduced enrichment of CCCTC binding factor (CTCF) near the boundary where PTPN11 located, as well as the decreased H3K4me3 and increased H3K27me3 enrichment at PTPN11 upon ATRA treatment was observed. Taken together, our study indicated a regulatory mechanism behind the silenced PTPN11 in HL-60 cells differentiation.
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Affiliation(s)
- Yanping Hu
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, PR China; Henan Key Laboratory of Molecular Pathology, Zhengzhou, Henan 450008, PR China
| | - Hongchao Zhao
- Department of gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450008, PR China
| | - Yixun Zhao
- Endoscopic Center, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, PR China
| | - Jiawen Zheng
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, PR China
| | - Yongjun Guo
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, PR China; Henan Key Laboratory of Molecular Pathology, Zhengzhou, Henan 450008, PR China.
| | - Jie Ma
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, PR China; Henan Key Laboratory of Molecular Pathology, Zhengzhou, Henan 450008, PR China.
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