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Meng X, Li C, Hei Y, Zhou X, Zhou G. Comparative alternative polyadenylation profiles in differentiated adipocytes of subcutaneous and intramuscular fat tissue in cattle. Gene 2024; 894:147949. [PMID: 37918547 DOI: 10.1016/j.gene.2023.147949] [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: 05/15/2023] [Revised: 09/16/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
Alternative polyadenylation (APA) is a key molecular mechanism involved in the post-transcriptional regulation of gene expression, which has been proven to play a critical role in cell differentiation. In the present study, we performed IVT-SAPAS sequencing to profile the dynamic changes of APA sites in bovine subcutaneous preadipocytes and intramuscular preadipocytes during adipogenesis. A total of 52621 high quality APA sites were identified in preadipocytes and adipocytes. Compared with preadipocytes, the increased usage of canonical AATAAA was observed in the cell-biased APA sites of adipocytes. Furthermore, 1933 and 2140 differentially expressed APA (DE-APA) sites, as well as 341 and 337 untranslated region-APA (UTR-APA) switching genes were identified in subcutaneous preadipocytes and intramuscular preadipocytes during adipogenesis, respectively. The UTR-APA switching genes showed divergent trends in preadipocytes, among which UTR-APA switching genes in intramuscular preadipocytes tended to use shorter 3'UTR for differentiation into mature adipocytes. APA events mediated by UTR-APA switching in intramuscular adipocytes were enriched in lipid synthesis and adipocyte differentiation. TRIB3, WWTR1, and INSIG1 played important roles in the differentiation of intramuscular preadipocytes. Briefly, our results provided new insights into understanding the mechanisms of bovine adipocyte differentiation.
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Affiliation(s)
- Xiangge Meng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chengping Li
- College of Life Science, Liaocheng University, Liaocheng, China
| | - Yu Hei
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Guoli Zhou
- College of Life Science, Liaocheng University, Liaocheng, China.
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Šimon M, Mikec Š, Morton NM, Atanur SS, Konc J, Horvat S, Kunej T. Genome-wide screening for genetic variants in polyadenylation signal (PAS) sites in mouse selection lines for fatness and leanness. Mamm Genome 2023; 34:12-31. [PMID: 36414820 PMCID: PMC9684942 DOI: 10.1007/s00335-022-09967-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
Alternative polyadenylation (APA) determines mRNA stability, localisation, translation and protein function. Several diseases, including obesity, have been linked to APA. Studies have shown that single nucleotide polymorphisms in polyadenylation signals (PAS-SNPs) can influence APA and affect phenotype and disease susceptibility. However, these studies focussed on associations between single PAS-SNP alleles with very large effects and phenotype. Therefore, we performed a genome-wide screening for PAS-SNPs in the polygenic mouse selection lines for fatness and leanness by whole-genome sequencing. The genetic variants identified in the two lines were overlapped with locations of PAS sites obtained from the PolyASite 2.0 database. Expression data for selected genes were extracted from the microarray expression experiment performed on multiple tissue samples. In total, 682 PAS-SNPs were identified within 583 genes involved in various biological processes, including transport, protein modifications and degradation, cell adhesion and immune response. Moreover, 63 of the 583 orthologous genes in human have been previously associated with human diseases, such as nervous system and physical disorders, and immune, endocrine, and metabolic diseases. In both lines, PAS-SNPs have also been identified in genes broadly involved in APA, such as Polr2c, Eif3e and Ints11. Five PAS-SNPs within 5 genes (Car, Col4a1, Itga7, Lat, Nmnat1) were prioritised as potential functional variants and could contribute to the phenotypic disparity between the two selection lines. The developed PAS-SNPs catalogue presents a key resource for planning functional studies to uncover the role of PAS-SNPs in APA, disease susceptibility and fat deposition.
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Affiliation(s)
- Martin Šimon
- grid.8954.00000 0001 0721 6013Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Domžale, Slovenia
| | - Špela Mikec
- grid.8954.00000 0001 0721 6013Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Domžale, Slovenia
| | - Nicholas M. Morton
- grid.511172.10000 0004 0613 128XUniversity of Edinburgh, The Queen’s Medical Research Institute, Centre for Cardiovascular Science, Edinburgh, UK
| | - Santosh S. Atanur
- grid.7445.20000 0001 2113 8111Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- grid.4305.20000 0004 1936 7988Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK
| | - Janez Konc
- grid.454324.00000 0001 0661 0844Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia
| | - Simon Horvat
- grid.8954.00000 0001 0721 6013Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Domžale, Slovenia
| | - Tanja Kunej
- grid.8954.00000 0001 0721 6013Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Domžale, Slovenia
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8
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Golden E, Rashwan R, Woodward EA, Sgro A, Wang E, Sorolla A, Waryah C, Tie WJ, Cuyàs E, Ratajska M, Kardaś I, Kozlowski P, Johnstone EKM, See HB, Duffy C, Parry J, Lagerborg KA, Czapiewski P, Menendez JA, Gorczyński A, Wasag B, Pfleger KDG, Curtis C, Lee BK, Kim J, Cursons J, Pavlos NJ, Biernat W, Jain M, Woo AJ, Redfern A, Blancafort P. The oncogene AAMDC links PI3K-AKT-mTOR signaling with metabolic reprograming in estrogen receptor-positive breast cancer. Nat Commun 2021; 12:1920. [PMID: 33772001 PMCID: PMC7998036 DOI: 10.1038/s41467-021-22101-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/25/2021] [Indexed: 12/13/2022] Open
Abstract
Adipogenesis associated Mth938 domain containing (AAMDC) represents an uncharacterized oncogene amplified in aggressive estrogen receptor-positive breast cancers. We uncover that AAMDC regulates the expression of several metabolic enzymes involved in the one-carbon folate and methionine cycles, and lipid metabolism. We show that AAMDC controls PI3K-AKT-mTOR signaling, regulating the translation of ATF4 and MYC and modulating the transcriptional activity of AAMDC-dependent promoters. High AAMDC expression is associated with sensitization to dactolisib and everolimus, and these PI3K-mTOR inhibitors exhibit synergistic interactions with anti-estrogens in IntClust2 models. Ectopic AAMDC expression is sufficient to activate AKT signaling, resulting in estrogen-independent tumor growth. Thus, AAMDC-overexpressing tumors may be sensitive to PI3K-mTORC1 blockers in combination with anti-estrogens. Lastly, we provide evidence that AAMDC can interact with the RabGTPase-activating protein RabGAP1L, and that AAMDC, RabGAP1L, and Rab7a colocalize in endolysosomes. The discovery of the RabGAP1L-AAMDC assembly platform provides insights for the design of selective blockers to target malignancies having the AAMDC amplification.
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Affiliation(s)
- Emily Golden
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, Australia
| | - Rabab Rashwan
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, Australia
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, Egypt
| | - Eleanor A Woodward
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, Australia
| | - Agustin Sgro
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, Australia
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia
| | - Edina Wang
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, Australia
| | - Anabel Sorolla
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, Australia
| | - Charlene Waryah
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, Australia
| | - Wan Jun Tie
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, Australia
| | - Elisabet Cuyàs
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA, Australia
- Girona Biomedical Research Institute, Girona, Catalonia, Spain
- ProCURE (Program Against Cancer Therapeutic Resistance), Metabolism & Cancer Group, Catalan Institute of Oncology, Girona, Catalonia, Spain
| | - Magdalena Ratajska
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
- The Centre for Cell Therapy and Regenerative Medicine, School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
- Department of Pathology, Otago University, Dunedin, New Zealand
| | - Iwona Kardaś
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
- Laboratory of Clinical Genetics, University Clinical Centre, Gdansk, Poland
| | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Elizabeth K M Johnstone
- Centre for Medical Research, The University of Western Australia, Perth, WA, Australia
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research, Nedlands, WA, Australia
- Australian Research Council Centre for Personalised Therapeutics Technologies, Melbourne and Perth, Australia
| | - Heng B See
- Centre for Medical Research, The University of Western Australia, Perth, WA, Australia
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research, Nedlands, WA, Australia
- Australian Research Council Centre for Personalised Therapeutics Technologies, Melbourne and Perth, Australia
| | - Ciara Duffy
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, Australia
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia
| | - Jeremy Parry
- Department of Anatomical Pathology, Path West Laboratory, Fiona Stanley Hospital Network, Murdoch, WA, Australia
| | - Kim A Lagerborg
- Departments of Medicine and Pharmacology, University of California, San Diego, CA, USA
| | - Piotr Czapiewski
- Department of Pathomorphology, Medical University of Gdansk, Gdansk, Poland
- Institute of Pathology, Dessau Medical Centre, Dessau, Germany
| | - Javier A Menendez
- Girona Biomedical Research Institute, Girona, Catalonia, Spain
- ProCURE (Program Against Cancer Therapeutic Resistance), Metabolism & Cancer Group, Catalan Institute of Oncology, Girona, Catalonia, Spain
| | - Adam Gorczyński
- Department of Pathomorphology, Medical University of Gdansk, Gdansk, Poland
| | - Bartosz Wasag
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
- Laboratory of Clinical Genetics, University Clinical Centre, Gdansk, Poland
| | - Kevin D G Pfleger
- Centre for Medical Research, The University of Western Australia, Perth, WA, Australia
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research, Nedlands, WA, Australia
- Australian Research Council Centre for Personalised Therapeutics Technologies, Melbourne and Perth, Australia
- Dimerix Limited, Nedlands, WA, Australia
| | - Christina Curtis
- Stanford University School of Medicine (Departments of Medicine & Genetics) and Stanford Cancer Institute, Stanford, CA, USA
| | - Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University at Albany-State University of New York, Rensselaer, NY, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Joseph Cursons
- Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Nathan J Pavlos
- The Centre for Cell Therapy and Regenerative Medicine, School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
| | - Wojciech Biernat
- Department of Pathomorphology, Medical University of Gdansk, Gdansk, Poland
| | - Mohit Jain
- Departments of Medicine and Pharmacology, University of California, San Diego, CA, USA
| | - Andrew J Woo
- Centre for Medical Research, The University of Western Australia, Perth, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA, Australia
| | - Andrew Redfern
- School of Medicine, University of Western Australia, Perth, WA, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA, Australia.
- Centre for Medical Research, The University of Western Australia, Perth, WA, Australia.
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia.
- The Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
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9
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Navarro E, Mallén A, Cruzado JM, Torras J, Hueso M. Unveiling ncRNA regulatory axes in atherosclerosis progression. Clin Transl Med 2020; 9:5. [PMID: 32009226 PMCID: PMC6995802 DOI: 10.1186/s40169-020-0256-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/05/2020] [Indexed: 02/06/2023] Open
Abstract
Completion of the human genome sequencing project highlighted the richness of the cellular RNA world, and opened the door to the discovery of a plethora of short and long non-coding RNAs (the dark transcriptome) with regulatory or structural potential, which shifted the balance of pathological gene alterations from coding to non-coding RNAs. Thus, disease risk assessment currently has to also evaluate the expression of new RNAs such as small micro RNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), competing endogenous RNAs (ceRNAs), retrogressed elements, 3'UTRs of mRNAs, etc. We are interested in the pathogenic mechanisms of atherosclerosis (ATH) progression in patients suffering Chronic Kidney Disease, and in this review, we will focus in the role of the dark transcriptome (non-coding RNAs) in ATH progression. We will focus in miRNAs and in the formation of regulatory axes or networks with their mRNA targets and with the lncRNAs that function as miRNA sponges or competitive inhibitors of miRNA activity. In this sense, we will pay special attention to retrogressed genomic elements, such as processed pseudogenes and Alu repeated elements, that have been recently seen to also function as miRNA sponges, as well as to the use or miRNA derivatives in gene silencing, anti-ATH therapies. Along the review, we will discuss technical developments associated to research in lncRNAs, from sequencing technologies to databases, repositories and algorithms to predict miRNA targets, as well as new approaches to miRNA function, such as integrative or enrichment analysis and their potential to unveil RNA regulatory networks.
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Affiliation(s)
- Estanislao Navarro
- Independent Researcher, Barcelona, Spain. .,Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain.
| | - Adrian Mallén
- Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Josep M Cruzado
- Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Joan Torras
- Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Miguel Hueso
- Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain.
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