1
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Li P, Ma X, Gu X. LncRNA MAFG-AS1 is involved in human cancer progression. Eur J Med Res 2023; 28:497. [PMID: 37941063 PMCID: PMC10631199 DOI: 10.1186/s40001-023-01486-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) refer to a type of non-protein-coding transcript of more than 200 nucleotides. LncRNAs play fundamental roles in disease development and progression, and lncRNAs are dysregulated in many pathophysiological processes. Thus, lncRNAs may have potential value in clinical applications. The lncRNA, MAF BZIP Transcription Factor G (MAFG)-AS1, is dysregulated in several cancer, including breast cancer, lung cancer, liver cancer, bladder cancer, colorectal cancer, gastric cancer, esophagus cancer, prostate cancer, pancreatic cancer, ovarian cancer, and glioma. Altered MAFG-AS1 levels are also associated with diverse clinical characteristics and patient outcomes. Mechanistically, MAFG-AS1 mediates a variety of cellular processes via the regulation of target gene expression. Therefore, the diagnostic, prognostic, and therapeutic aspects of MAFG-AS1 have been widely explored. In this review, we discuss the expression, major roles, and molecular mechanisms of MAFG-AS1, the relationship between MAFG-AS1 and clinical features of diseases, and the clinical applications of MAFG-AS1.
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Affiliation(s)
- Penghui Li
- Department of Oncology, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471000, Henan, China
| | - Xiao Ma
- Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Xinyu Gu
- Department of Oncology, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471000, Henan, China.
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2
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Richer S, Tian Y, Schoenfelder S, Hurst L, Murrell A, Pisignano G. Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters. Genome Biol 2023; 24:40. [PMID: 36869353 PMCID: PMC9983196 DOI: 10.1186/s13059-023-02876-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 02/13/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND There is widespread interest in the three-dimensional chromatin conformation of the genome and its impact on gene expression. However, these studies frequently do not consider parent-of-origin differences, such as genomic imprinting, which result in monoallelic expression. In addition, genome-wide allele-specific chromatin conformation associations have not been extensively explored. There are few accessible bioinformatic workflows for investigating allelic conformation differences and these require pre-phased haplotypes which are not widely available. RESULTS We developed a bioinformatic pipeline, "HiCFlow," that performs haplotype assembly and visualization of parental chromatin architecture. We benchmarked the pipeline using prototype haplotype phased Hi-C data from GM12878 cells at three disease-associated imprinted gene clusters. Using Region Capture Hi-C and Hi-C data from human cell lines (1-7HB2, IMR-90, and H1-hESCs), we can robustly identify the known stable allele-specific interactions at the IGF2-H19 locus. Other imprinted loci (DLK1 and SNRPN) are more variable and there is no "canonical imprinted 3D structure," but we could detect allele-specific differences in A/B compartmentalization. Genome-wide, when topologically associating domains (TADs) are unbiasedly ranked according to their allele-specific contact frequencies, a set of allele-specific TADs could be defined. These occur in genomic regions of high sequence variation. In addition to imprinted genes, allele-specific TADs are also enriched for allele-specific expressed genes. We find loci that have not previously been identified as allele-specific expressed genes such as the bitter taste receptors (TAS2Rs). CONCLUSIONS This study highlights the widespread differences in chromatin conformation between heterozygous loci and provides a new framework for understanding allele-specific expressed genes.
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Affiliation(s)
- Stephen Richer
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Yuan Tian
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
- UCL Cancer Institute, University College London, Paul O'Gorman Building, London, UK
| | | | - Laurence Hurst
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Adele Murrell
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
| | - Giuseppina Pisignano
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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3
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Bruscadin JJ, Cardoso TF, da Silva Diniz WJ, de Souza MM, Afonso J, Vieira D, Malheiros J, Andrade BGN, Petrini J, Ferraz JBS, Zerlotini A, Mourão GB, Coutinho LL, de Almeida Regitano LC. Differential Allele-Specific Expression Revealed Functional Variants and Candidate Genes Related to Meat Quality Traits in B. indicus Muscle. Genes (Basel) 2022; 13:genes13122336. [PMID: 36553605 PMCID: PMC9777870 DOI: 10.3390/genes13122336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Traditional transcriptomics approaches have been used to identify candidate genes affecting economically important livestock traits. Regulatory variants affecting these traits, however, remain under covered. Genomic regions showing allele-specific expression (ASE) are under the effect of cis-regulatory variants, being useful for improving the accuracy of genomic selection models. Taking advantage of the better of these two methods, we investigated single nucleotide polymorphisms (SNPs) in regions showing differential ASE (DASE SNPs) between contrasting groups for beef quality traits. For these analyses, we used RNA sequencing data, imputed genotypes and genomic estimated breeding values of muscle-related traits from 190 Nelore (Bos indicus) steers. We selected 40 contrasting unrelated samples for the analysis (N = 20 animals per contrasting group) and used a beta-binomial model to identify ASE SNPs in only one group (i.e., DASE SNPs). We found 1479 DASE SNPs (FDR ≤ 0.05) associated with 55 beef-quality traits. Most DASE genes were involved with tenderness and muscle homeostasis, presenting a co-expression module enriched for the protein ubiquitination process. The results overlapped with epigenetics and phenotype-associated data, suggesting that DASE SNPs are potentially linked to cis-regulatory variants affecting simultaneously the transcription and phenotype through chromatin state modulation.
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Affiliation(s)
- Jennifer Jessica Bruscadin
- Center of Biological Sciences and Health, Federal University of São Carlos, São Carlos 13560-000, SP, Brazil
- Embrapa Pecuária Sudeste, São Carlos 13560-000, SP, Brazil
| | | | | | | | - Juliana Afonso
- Embrapa Pecuária Sudeste, São Carlos 13560-000, SP, Brazil
| | - Dielson Vieira
- Embrapa Pecuária Sudeste, São Carlos 13560-000, SP, Brazil
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jessica Malheiros
- Federal University of Latin American Integration-UNILA, Foz do Iguaçu 85851-000, PR, Brazil
| | | | - Juliana Petrini
- Center for Functional Genomics, Department of Animal Science, 13400-000, University of São Paulo (ESALQ—USP), Piracicaba 13400-000, SP, Brazil
| | - José Bento Sterman Ferraz
- Department of Veterinary Medicine, University of São Paulo (FMVZ—USP), Pirassununga 13630-000, SP, Brazil
| | | | - Gerson Barreto Mourão
- Center for Functional Genomics, Department of Animal Science, 13400-000, University of São Paulo (ESALQ—USP), Piracicaba 13400-000, SP, Brazil
| | - Luiz Lehmann Coutinho
- Center for Functional Genomics, Department of Animal Science, 13400-000, University of São Paulo (ESALQ—USP), Piracicaba 13400-000, SP, Brazil
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4
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Castro-Mondragon JA, Aure M, Lingjærde O, Langerød A, Martens JWM, Børresen-Dale AL, Kristensen V, Mathelier A. Cis-regulatory mutations associate with transcriptional and post-transcriptional deregulation of gene regulatory programs in cancers. Nucleic Acids Res 2022; 50:12131-12148. [PMID: 36477895 PMCID: PMC9757053 DOI: 10.1093/nar/gkac1143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 11/03/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
Most cancer alterations occur in the noncoding portion of the human genome, where regulatory regions control gene expression. The discovery of noncoding mutations altering the cells' regulatory programs has been limited to few examples with high recurrence or high functional impact. Here, we show that transcription factor binding sites (TFBSs) have similar mutation loads to those in protein-coding exons. By combining cancer somatic mutations in TFBSs and expression data for protein-coding and miRNA genes, we evaluate the combined effects of transcriptional and post-transcriptional alterations on the regulatory programs in cancers. The analysis of seven TCGA cohorts culminates with the identification of protein-coding and miRNA genes linked to mutations at TFBSs that are associated with a cascading trans-effect deregulation on the cells' regulatory programs. Our analyses of cis-regulatory mutations associated with miRNAs recurrently predict 12 mature miRNAs (derived from 7 precursors) associated with the deregulation of their target gene networks. The predictions are enriched for cancer-associated protein-coding and miRNA genes and highlight cis-regulatory mutations associated with the dysregulation of key pathways associated with carcinogenesis. By combining transcriptional and post-transcriptional regulation of gene expression, our method predicts cis-regulatory mutations related to the dysregulation of key gene regulatory networks in cancer patients.
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Affiliation(s)
- Jaime A Castro-Mondragon
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Miriam Ragle Aure
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway,Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Ole Christian Lingjærde
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway,Centre for Bioinformatics, Department of Informatics, University of Oslo, Gaustadalléen 23 B, N-0373 Oslo, Norway,KG Jebsen Centre for B-cell malignancies, Institute for Clinical Medicine, University of Oslo, Ullernchausseen 70, N-0372 Oslo, Norway
| | - Anita Langerød
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway
| | - John W M Martens
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, The Netherlands
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway
| | - Vessela N Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway,Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
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5
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Bruscadin JJ, Cardoso TF, da Silva Diniz WJ, Afonso J, de Souza MM, Petrini J, Nascimento Andrade BG, da Silva VH, Ferraz JBS, Zerlotini A, Mourão GB, Coutinho LL, de Almeida Regitano LC. Allele-specific expression reveals functional SNPs affecting muscle-related genes in bovine. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - GENE REGULATORY MECHANISMS 2022; 1865:194886. [DOI: 10.1016/j.bbagrm.2022.194886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/27/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022]
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6
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Sen A, Huo Y, Elster J, Zage PE, McVicker G. Allele-specific expression reveals genes with recurrent cis-regulatory alterations in high-risk neuroblastoma. Genome Biol 2022; 23:71. [PMID: 35246212 PMCID: PMC8896304 DOI: 10.1186/s13059-022-02640-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Neuroblastoma is a pediatric malignancy with a high frequency of metastatic disease at initial diagnosis. Neuroblastoma tumors have few recurrent protein-coding mutations but contain extensive somatic copy number alterations (SCNAs) suggesting that mutations that alter gene dosage are important drivers of tumorigenesis. Here, we analyze allele-specific expression in 96 high-risk neuroblastoma tumors to discover genes impacted by cis-acting mutations that alter dosage. RESULTS We identify 1043 genes with recurrent, neuroblastoma-specific allele-specific expression. While most of these genes lie within common SCNA regions, many of them exhibit allele-specific expression in copy neutral samples and these samples are enriched for mutations that are predicted to cause nonsense-mediated decay. Thus, both SCNA and non-SCNA mutations frequently alter gene expression in neuroblastoma. We focus on genes with neuroblastoma-specific allele-specific expression in the absence of SCNAs and find 26 such genes that have reduced expression in stage 4 disease. At least two of these genes have evidence for tumor suppressor activity including the transcription factor TFAP2B and the protein tyrosine phosphatase PTPRH. CONCLUSIONS In summary, our allele-specific expression analysis discovers genes that are recurrently dysregulated by both large SCNAs and other cis-acting mutations in high-risk neuroblastoma.
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Affiliation(s)
- Arko Sen
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Yuchen Huo
- Department of Pediatrics, Division of Hematology-Oncology, University of California San Diego, La Jolla, California, USA
| | - Jennifer Elster
- Department of Pediatrics, Division of Hematology-Oncology, University of California San Diego, La Jolla, California, USA.,Peckham Center for Cancer and Blood Disorders, Rady Children's Hospital-San Diego, San Diego, California, USA
| | - Peter E Zage
- Department of Pediatrics, Division of Hematology-Oncology, University of California San Diego, La Jolla, California, USA.,Peckham Center for Cancer and Blood Disorders, Rady Children's Hospital-San Diego, San Diego, California, USA
| | - Graham McVicker
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA.
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Valentini S, Marchioretti C, Bisio A, Rossi A, Zaccara S, Romanel A, Inga A. TranSNPs: A class of functional SNPs affecting mRNA translation potential revealed by fraction-based allelic imbalance. iScience 2021; 24:103531. [PMID: 34917903 PMCID: PMC8666669 DOI: 10.1016/j.isci.2021.103531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/27/2021] [Accepted: 11/23/2021] [Indexed: 12/23/2022] Open
Abstract
Few studies have explored the association between SNPs and alterations in mRNA translation potential. We developed an approach to identify SNPs that can mark allele-specific protein expression levels and could represent sources of inter-individual variation in disease risk. Using MCF7 cells under different treatments, we performed polysomal profiling followed by RNA sequencing of total or polysome-associated mRNA fractions and designed a computational approach to identify SNPs showing a significant change in the allelic balance between total and polysomal mRNA fractions. We identified 147 SNPs, 39 of which located in UTRs. Allele-specific differences at the translation level were confirmed in transfected MCF7 cells by reporter assays. Exploiting breast cancer data from TCGA we identified UTR SNPs demonstrating distinct prognosis features and altering binding sites of RNA-binding proteins. Our approach produced a catalog of tranSNPs, a class of functional SNPs associated with allele-specific translation and potentially endowed with prognostic value for disease risk.
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Affiliation(s)
- Samuel Valentini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Caterina Marchioretti
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
- Department of Biomedical Sciences (DBS), University of Padova, 35131 Padova, Italy
| | - Alessandra Bisio
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Annalisa Rossi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Sara Zaccara
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
- Weill Medical College, Cornell University, New York 10065, NY, USA
| | - Alessandro Romanel
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Alberto Inga
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
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8
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Robles-Espinoza CD, Mohammadi P, Bonilla X, Gutierrez-Arcelus M. Allele-specific expression: applications in cancer and technical considerations. Curr Opin Genet Dev 2021; 66:10-19. [PMID: 33383480 PMCID: PMC7985293 DOI: 10.1016/j.gde.2020.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/26/2020] [Accepted: 10/31/2020] [Indexed: 11/18/2022]
Abstract
Allele-specific gene expression can influence disease traits. Non-coding germline genetic variants that alter regulatory elements can cause allele-specific gene expression and contribute to cancer susceptibility. In tumors, both somatic copy number alterations and somatic single nucleotide variants have been shown to lead to allele-specific expression of genes, many of which are considered drivers of tumor growth. Here, we review recent studies revealing the pervasive presence of this phenomenon in cancer susceptibility and progression. Furthermore, we underscore the importance of careful experimental design and computational analysis for accurate allelic expression quantification and avoidance of false positives. Finally, we discuss additional methodological challenges encountered in cancer studies and in the burgeoning field of single-cell transcriptomics.
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Affiliation(s)
- Carla Daniela Robles-Espinoza
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Boulevard Juriquilla 3001, Santiago de Querétaro 76230, Mexico; Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Pejman Mohammadi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA; Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA, USA
| | - Ximena Bonilla
- Department of Computer Science, ETH Zurich, Universitätsstr. 6, 8092 Zürich, Switzerland; Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, Lausanne 1015, Switzerland; University Hospital Zurich, Rämistrasse 100, 8091 Zürich, Switzerland
| | - Maria Gutierrez-Arcelus
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Division of Immunology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
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