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Liu D, Dong Y, Gao J, Wu Z, Zhang L, Wang B. Role of the circular RNA regulatory network in the pathogenesis of biliary atresia. Exp Ther Med 2024; 27:95. [PMID: 38313582 PMCID: PMC10831818 DOI: 10.3892/etm.2024.12383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 11/13/2023] [Indexed: 02/06/2024] Open
Abstract
Circular RNAs (circRNAs) serve an essential role in the occurrence and development of cholangiocarcinoma, but the expression and function of circRNA in biliary atresia (BA) is not clear. In the present study, circRNA expression profiles were investigated in the liver tissues of patients with BA as well as in the choledochal cyst (CC) tissues of control patients using RNA sequencing. A total of 78 differentially expressed circRNAs (DECs) were identified between the BA and CC tissues. The expression levels of eight circRNAs (hsa_circ_0006137, hsa_circ_0079422, hsa_circ_0007375, hsa_circ_0005597, hsa_circ_0006961, hsa_circ_0081171, hsa_circ_0084665 and hsa_circ_0075828) in the liver tissues of the BA group and control group were measured using reverse transcription-quantitative polymerase chain reaction. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis demonstrated that the identified DECs are involved in a variety of biological processes, including apoptosis and metabolism. In addition, based on the GO and KEGG pathway enrichment analyses, it was revealed that target genes that can be affected by circRNAs regulatory network were enriched in the TGF-β signaling pathway, EGFR tyrosine kinase inhibitor resistance pathway and transcription factor regulation pathway as well as other pathways that may be associated with the pathogenesis of BA. The present study revealed that circRNAs are potentially implicated in the pathogenesis of BA and could help to find promising targets and biomarkers for BA.
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Affiliation(s)
- Dong Liu
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen, Guangdong 518000, P.R. China
| | - Yinghui Dong
- Department of Ultrasound, Shenzhen People's Hospital, Shenzhen, Guangdong 518000, P.R. China
| | - Jiahui Gao
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen, Guangdong 518000, P.R. China
| | - Zhouguang Wu
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen, Guangdong 518000, P.R. China
| | - Lihui Zhang
- Department of Traditional Chinese Medicine, Shenzhen Children's Hospital, Shenzhen, Guangdong 518000, P.R. China
| | - Bin Wang
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen, Guangdong 518000, P.R. China
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Zhang Q, Pan J, Zhu Y, Liu J, Pang Y, Li J, Han P, Gou M, Li J, Su P, Li Q, Chi Y. The metabolic adaptation of bile acids and cholesterol after biliary atresia in lamprey via transcriptome-based analysis. Heliyon 2023; 9:e19107. [PMID: 37636398 PMCID: PMC10450982 DOI: 10.1016/j.heliyon.2023.e19107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 08/29/2023] Open
Abstract
Lamprey underwent biliary atresia (BA) at its metamorphosis stage. In contrast to patients with BA who develop progressive disease, lamprey can grow and develop normally, suggesting that lamprey has several adaptations for BA. Here we show that adaptive changes in bile acid and cholesterol metabolism are produced after lamprey BA. Among 1102 differentially expressed genes (DGEs) after BA in lamprey, many are enriched in gene ontology (GO) terms and pathways related to steroid metabolism. We find that among the DGEs related to bile acids and cholesterol metabolism, the expression of cytochrome P450 family 7 subfamily A member 1 (CYP7A1), sodium-dependent taurine cotransport polypeptide (NTCP) are significantly downregulated, whereas nuclear receptor farnesoid X receptor (FXR), multidrug resistance-associated protein 3 (MRP3), 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR), sterol O-acyltransferase 1 (SOAT1), and ATP binding cassette subfamily A member 1 (ABCA1) are remarkably upregulated. The changes in expression level are also validated by RT-qPCR. Furthermore, the level of high-density lipoprotein-cholesterol (HDL-C) and low-density lipoprotein-cholesterol (LDL-C) in juvenile serum is higher compared to larvae. Taken together, the findings collectively indicate that after BA, lamprey may maintain bile acids and cholesterol homeostasis in liver tissue by inhibiting bile acids synthesis and uptake, promoting its efflux back to circulation, and enhancing cholesterol esterification for storage as lipid droplets and its egress to form nascent HDL (nHDL). Understanding the possible molecular mechanisms of lamprey metabolic adaptation sheds new light on the understanding of the development and treatment of diseases caused by abnormal bile acid and cholesterol metabolism in humans.
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Affiliation(s)
- Qipeng Zhang
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China
- Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Jilong Pan
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China
- Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Yingying Zhu
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China
- Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Jindi Liu
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China
- Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Yue Pang
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China
- Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Jiarui Li
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China
- Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Pengju Han
- College of Life Sciences, Sichuan University, Sichuan, China
| | - Meng Gou
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China
- Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Jun Li
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China
- Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Peng Su
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China
- Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Qingwei Li
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China
- Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Yan Chi
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China
- Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
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Guo H, Zhu Y, Li J, Zhang Q, Chi Y. LIMP2 gene, evolutionarily conserved regulation by TFE3, relieves lysosomal stress induced by cholesterol. Life Sci 2022; 307:120888. [PMID: 35987341 DOI: 10.1016/j.lfs.2022.120888] [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: 05/27/2022] [Revised: 08/11/2022] [Accepted: 08/14/2022] [Indexed: 11/30/2022]
Abstract
AIM Excess cholesterol deposition in lysosomes may result in lysosomal stress and dysfunction. Here, we focus on the role of lysosome membrane protein 2 (LIMP2) in relieving the lysosomal stress caused by excess cholesterol and the mechanism that regulate its expression. MATERIAL AND METHODS Cholesterol enrichment in lamprey liver tissue was evaluated by RNA transcriptome data analysis, RT-qPCR, H&E, and Oil Red O staining. Gene markers of autophagy and cholesterol synthesis were determined by western blot or RT-qPCR. Lysosomal morphology and pH value was measured by confocal observation or flow cytometry. Dual-Luciferase reporter assay was performed to test the expression regulation relationship. KEY FINDINGS We report that lamprey limp2 (L-limp2) is evolutionarily highly conserved with human LIMP2 (H-LIMP2). The biological function of L-limp2, consistent with H-LIMP2, includes maintaining lysosomal morphology, modulating autophagy, and aiding cholesterol efflux from lysosomes. Furthermore, we find that both L-limp2 and H-limp2 can restore cholesterol-induced elevation of lysosomal pH and impaired autophagic flux. We demonstrate that lamprey transcription factor binding to IGHM enhancer 3 (L-TFE3) can bind with coordinated lysosomal expression and regulation (CLEAR) elements on the L-limp2 promoter and regulate its expression. Moreover, this regulatory relationship is also available in humans. Taken together, the present study demonstrates that the evolutionarily conserved TFE3-LIMP2 axis may have a protective role against the impaired lysosomal function caused by excess cholesterol. SIGNIFICANCE The protective effect of TFE3-LIMP2 axis against cholesterol-triggered lysosomal stress may provide a new target for the treatment of diseases caused by excessive cholesterol accumulation in lysosomes.
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Affiliation(s)
- Hanze Guo
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China; College of Life Science and Technology, Dalian University, Dalian 116622, China
| | - Yingying Zhu
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Jiarui Li
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Qipeng Zhang
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Yan Chi
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China.
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Dornburg A, Wang Z, Wang J, Mo ES, López-Giráldez F, Townsend JP. Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification. Genome Biol Evol 2020; 13:5983394. [PMID: 33196781 PMCID: PMC7851593 DOI: 10.1093/gbe/evaa228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2020] [Indexed: 12/14/2022] Open
Abstract
Comparative genomic analyses have enormous potential for identifying key genes central to human health phenotypes, including those that promote cancers. In particular, the successful development of novel therapeutics using model species requires phylogenetic analyses to determine molecular homology. Accordingly, we investigate the evolutionary histories of anaplastic lymphoma kinase (ALK)—which can underlie tumorigenesis in neuroblastoma, nonsmall cell lung cancer, and anaplastic large-cell lymphoma—its close relative leukocyte tyrosine kinase (LTK) and their candidate ligands. Homology of ligands identified in model organisms to those functioning in humans remains unclear. Therefore, we searched for homologs of the human genes across metazoan genomes, finding that the candidate ligands Jeb and Hen-1 were restricted to nonvertebrate species. In contrast, the ligand augmentor (AUG) was only identified in vertebrates. We found two ALK-like and four AUG-like protein-coding genes in lamprey. Of these six genes, only one ALK-like and two AUG-like genes exhibited early embryonic expression that parallels model mammal systems. Two copies of AUG are present in nearly all jawed vertebrates. Our phylogenetic analysis strongly supports the presence of previously unrecognized functional convergences of ALK and LTK between actinopterygians and sarcopterygians—despite contemporaneous, highly conserved synteny of ALK and LTK. These findings provide critical guidance regarding the propriety of fish and mammal models with regard to model organism-based investigation of these medically important genes. In sum, our results provide the phylogenetic context necessary for effective investigations of the functional roles and biology of these critically important receptors.
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Affiliation(s)
- Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina Charlotte
| | - Zheng Wang
- Department of Ecology and Evolutionary Biology, Yale University, New Haven.,Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut
| | - Junrui Wang
- Department of Ecology and Evolutionary Biology, Yale University, New Haven.,Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Elizabeth S Mo
- Yale Combined Program in the Biological and Biomedical Sciences, Yale School of Medicine, Yale University, New Haven
| | | | - Jeffrey P Townsend
- Department of Ecology and Evolutionary Biology, Yale University, New Haven.,Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut.,Program in Microbiology, Yale University, New Haven
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