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Hervoso JL, Amoah K, Dodson J, Choudhury M, Bhattacharya A, Quinones-Valdez G, Pasaniuc B, Xiao X. Splicing-specific transcriptome-wide association uncovers genetic mechanisms for schizophrenia. Am J Hum Genet 2024; 111:1573-1587. [PMID: 38925119 DOI: 10.1016/j.ajhg.2024.06.001] [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: 10/15/2023] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Recent studies have highlighted the essential role of RNA splicing, a key mechanism of alternative RNA processing, in establishing connections between genetic variations and disease. Genetic loci influencing RNA splicing variations show considerable influence on complex traits, possibly surpassing those affecting total gene expression. Dysregulated RNA splicing has emerged as a major potential contributor to neurological and psychiatric disorders, likely due to the exceptionally high prevalence of alternatively spliced genes in the human brain. Nevertheless, establishing direct associations between genetically altered splicing and complex traits has remained an enduring challenge. We introduce Spliced-Transcriptome-Wide Associations (SpliTWAS) to integrate alternative splicing information with genome-wide association studies to pinpoint genes linked to traits through exon splicing events. We applied SpliTWAS to two schizophrenia (SCZ) RNA-sequencing datasets, BrainGVEX and CommonMind, revealing 137 and 88 trait-associated exons (in 84 and 67 genes), respectively. Enriched biological functions in the associated gene sets converged on neuronal function and development, immune cell activation, and cellular transport, which are highly relevant to SCZ. SpliTWAS variants impacted RNA-binding protein binding sites, revealing potential disruption of RNA-protein interactions affecting splicing. We extended the probabilistic fine-mapping method FOCUS to the exon level, identifying 36 genes and 48 exons as putatively causal for SCZ. We highlight VPS45 and APOPT1, where splicing of specific exons was associated with disease risk, eluding detection by conventional gene expression analysis. Collectively, this study supports the substantial role of alternative splicing in shaping the genetic basis of SCZ, providing a valuable approach for future investigations in this area.
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Affiliation(s)
- Jonatan L Hervoso
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kofi Amoah
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jack Dodson
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mudra Choudhury
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Arjun Bhattacharya
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Giovanni Quinones-Valdez
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Xinshu Xiao
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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Park D, Cenik C. Long-read RNA sequencing reveals allele-specific N 6-methyladenosine modifications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602538. [PMID: 39026828 PMCID: PMC11257478 DOI: 10.1101/2024.07.08.602538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Long-read sequencing technology enables highly accurate detection of allele-specific RNA expression, providing insights into the effects of genetic variation on splicing and RNA abundance. Furthermore, the ability to directly sequence RNA promises the detection of RNA modifications in tandem with ascertaining the allelic origin of each molecule. Here, we leverage these advantages to determine allele-biased patterns of N6-methyladenosine (m6A) modifications in native mRNA. We utilized human and mouse cells with known genetic variants to assign allelic origin of each mRNA molecule combined with a supervised machine learning model to detect read-level m6A modification ratios. Our analyses revealed the importance of sequences adjacent to the DRACH-motif in determining m6A deposition, in addition to allelic differences that directly alter the motif. Moreover, we discovered allele-specific m6A modification (ASM) events with no genetic variants in close proximity to the differentially modified nucleotide, demonstrating the unique advantage of using long reads and surpassing the capabilities of antibody-based short-read approaches. This technological advancement promises to advance our understanding of the role of genetics in determining mRNA modifications.
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Affiliation(s)
- Dayea Park
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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3
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Quinones-Valdez G, Amoah K, Xiao X. Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599101. [PMID: 38915585 PMCID: PMC11195283 DOI: 10.1101/2024.06.14.599101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Genetic regulation of alternative splicing constitutes an important link between genetic variation and disease. Nonetheless, RNA splicing is regulated by both cis-acting elements and trans-acting splicing factors. Determining splicing events that are directed primarily by the cis- or trans-acting mechanisms will greatly inform our understanding of the genetic basis of disease. Here, we show that long-read RNA-seq, combined with our new method isoLASER, enables a clear segregation of cis- and trans-directed splicing events for individual samples. The genetic linkage of splicing is largely individual-specific, in stark contrast to the tissue-specific pattern of splicing profiles. Analysis of long-read RNA-seq data from human and mouse revealed thousands of cis-directed splicing events susceptible to genetic regulation. We highlight such events in the HLA genes whose analysis was challenging with short-read data. We also highlight novel cis-directed splicing events in Alzheimer's disease-relevant genes such as MAPT and BIN1. Together, the clear demarcation of cis- and trans-directed splicing paves ways for future studies of the genetic basis of disease.
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Affiliation(s)
- Giovanni Quinones-Valdez
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kofi Amoah
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
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4
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Sarhadi M, Pahlavani E, Hosseini Razavi N, Ghadyani F, Abdollahi Z, Sarhadi S, Sabeti Akbar Abad M, Shahriari H, Majidpour M. IL-18 and CD14 variants in chronic HBV predisposition: a case-control study with in silico analyses focused on transcription and splicing. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-21. [PMID: 38459706 DOI: 10.1080/15257770.2024.2326132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/26/2024] [Indexed: 03/10/2024]
Abstract
Hepatitis B virus (HBV), a vaccine-avoidable infection, is a health concern worldwide, leading to liver disorders such as acute self-constraint and chronic hepatitis, liver failure, hepatic cirrhosis, and even hepatocellular carcinoma if untreated. 'Immunogeneticprofiling', genetic variations of the pro- and anti-inflammatory cytokines responsible for regulating the immune responses, cause person-to-person differences and impact the clinical manifestation of the disease. The current experimental-bioinformatics research was conducted to examine whether promoteric IL-18-rs187238 C > G and -rs1946518 T > G and intronic CD14-rs2569190 A > G variations are associated with chronic HBV. A total of 400 individuals (200 in each case and control group) participated in the study and were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. The data was also assessed bioinformatics-wise for conservation, genomic transcription and splicing, and protein interactions. Findings proposed that unlike the IL-18-rs1946518 T > G and CD14-rs2569190 A > G, the IL-18-rs187238 C > G is a protector against chronic HBV (odds ratio [OR] = 0.62, 95% confidence intervals [CI]: 0.46-0.83, and p = 0.002). The TG/CC/AA, TG/CC/AG, TT/CC/AG, and GG/CC/AA combined genotypes significantly increased chronic HBV risk (p < 0.05), while the IL-18 G/T and G/G haplotypes lessened it (p < 0.05). Moreover, IL-18-rs1946518 T > G is in the protected genomic regions across mammalian species. In contrast to the IL-18-rs1946518 T > G, IL-18-rs187238 C > G is likely to create novel binding sites for transcription factors, and the CD14-rs2569190 A > G presumably changed the ribonucleic acid splicing pattern. More research on larger populations and other ethnicities is required to authenticate these results.
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Affiliation(s)
- Mohammad Sarhadi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Elham Pahlavani
- Infectious Diseases and Tropical Medicine Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Niloufar Hosseini Razavi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Fatemeh Ghadyani
- Department of Cellular and Molecular, Faculty of Biology Sciences, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Zahra Abdollahi
- Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Kashan, Iran
| | - Somayeh Sarhadi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mahboobeh Sabeti Akbar Abad
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
- Department of Clinical Biochemistry, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Hossein Shahriari
- Clinical Immunology Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mahdi Majidpour
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
- Department of Clinical Biochemistry, Zahedan University of Medical Sciences, Zahedan, Iran
- Clinical Immunology Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
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5
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Wang R, Helbig I, Edmondson AC, Lin L, Xing Y. Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis. Brief Bioinform 2023; 24:bbad284. [PMID: 37580177 PMCID: PMC10516351 DOI: 10.1093/bib/bbad284] [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: 03/14/2023] [Revised: 07/10/2023] [Accepted: 07/20/2023] [Indexed: 08/16/2023] Open
Abstract
Genomic variants affecting pre-messenger RNA splicing and its regulation are known to underlie many rare genetic diseases. However, common workflows for genetic diagnosis and clinical variant interpretation frequently overlook splice-altering variants. To better serve patient populations and advance biomedical knowledge, it has become increasingly important to develop and refine approaches for detecting and interpreting pathogenic splicing variants. In this review, we will summarize a few recent developments and challenges in using RNA sequencing technologies for rare disease investigation. Moreover, we will discuss how recent computational splicing prediction tools have emerged as complementary approaches for revealing disease-causing variants underlying splicing defects. We speculate that continuous improvements to sequencing technologies and predictive modeling will not only expand our understanding of splicing regulation but also bring us closer to filling the diagnostic gap for rare disease patients.
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Affiliation(s)
- Robert Wang
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ingo Helbig
- The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew C Edmondson
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lan Lin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yi Xing
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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6
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Pu T, Peddle A, Zhu J, Tejpar S, Verbandt S. Neoantigen identification: Technological advances and challenges. Methods Cell Biol 2023; 183:265-302. [PMID: 38548414 DOI: 10.1016/bs.mcb.2023.06.005] [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] [Indexed: 04/02/2024]
Abstract
Neoantigens have emerged as promising targets for cutting-edge immunotherapies, such as cancer vaccines and adoptive cell therapy. These neoantigens are unique to tumors and arise exclusively from somatic mutations or non-genomic aberrations in tumor proteins. They encompass a wide range of alterations, including genomic mutations, post-transcriptomic variants, and viral oncoproteins. With the advancements in technology, the identification of immunogenic neoantigens has seen rapid progress, raising new opportunities for enhancing their clinical significance. Prediction of neoantigens necessitates the acquisition of high-quality samples and sequencing data, followed by mutation calling. Subsequently, the pipeline involves integrating various tools that can predict the expression, processing, binding, and recognition potential of neoantigens. However, the continuous improvement of computational tools is constrained by the availability of datasets which contain validated immunogenic neoantigens. This review article aims to provide a comprehensive summary of the current knowledge as well as limitations in neoantigen prediction and validation. Additionally, it delves into the origin and biological role of neoantigens, offering a deeper understanding of their significance in the field of cancer immunotherapy. This article thus seeks to contribute to the ongoing efforts to harness neoantigens as powerful weapons in the fight against cancer.
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Affiliation(s)
- Ting Pu
- Digestive Oncology Unit, KULeuven, Leuven, Belgium
| | | | - Jingjing Zhu
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
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7
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Cao S, Zhu H, Cui J, Liu S, Li Y, Shi J, Mo J, Wang Z, Wang H, Hu J, Chen L, Li Y, Xia L, Xiao S. Allele-specific RNA N 6-methyladenosine modifications reveal functional genetic variants in human tissues. Genome Res 2023; 33:1369-1380. [PMID: 37714712 PMCID: PMC10547253 DOI: 10.1101/gr.277704.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 06/13/2023] [Indexed: 09/17/2023]
Abstract
An intricate network of cis- and trans-elements acts on RNA N 6-methyladenosine (m6A), which in turn may affect gene expression and, ultimately, human health. A complete understanding of this network requires new approaches to accurately measure the subtle m6A differences arising from genetic variants, many of which have been associated with common diseases. To address this gap, we developed a method to accurately and sensitively detect transcriptome-wide allele-specific m6A (ASm6A) from MeRIP-seq data and applied it to uncover 12,056 high-confidence ASm6A modifications from 25 human tissues. We also identified 1184 putative functional variants for ASm6A regulation, a subset of which we experimentally validated. Importantly, we found that many of these ASm6A-associated genetic variants were enriched for common disease-associated and complex trait-associated risk loci, and verified that two disease risk variants can change m6A modification status. Together, this work provides a tool to detangle the dynamic network of RNA modifications at the allelic level and highlights the interplay of m6A and genetics in human health and disease.
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Affiliation(s)
- Shuo Cao
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Haoran Zhu
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jinru Cui
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Sun Liu
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yuhe Li
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Junfang Shi
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Junyuan Mo
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Zihan Wang
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Hailan Wang
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiaxin Hu
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Lizhi Chen
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yuan Li
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Laixin Xia
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China;
| | - Shan Xiao
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China;
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangzhou 510515, China
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8
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Collins JM, Lester H, Shabnaz S, Wang D. A frequent CYP2D6 variant promotes skipping of exon 3 and reduces CYP2D6 protein expression in human liver samples. Front Pharmacol 2023; 14:1186540. [PMID: 37576811 PMCID: PMC10412816 DOI: 10.3389/fphar.2023.1186540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023] Open
Abstract
CYP2D6 is one of the most polymorphic drug-metabolizing enzymes in the liver. While genetic CYP2D6 variants serve as clinical biomarkers to predict CYP2D6 activity, large inter-person variability in CYP2D6 expression remains unaccounted for. Previous results suggest that there is variable expression of a CYP2D6 splice isoform with an in-frame deletion of exon 3 (CYP2D6ΔE3) encoding a protein lacking numerous active site residues. Here, using fragment analysis and RT-qPCR, we revealed that rs1058164 G (MAF = 27%-43%) is associated with increased formation of CYP2D6∆E3 in human liver samples (1.4-2.5-fold) and transfected cells. Furthermore, western blots showed that rs1058164 G was associated with a 50% decrease in full-length hepatic CYP2D6 protein expression. In addition, by studying a larger liver cohort, we confirmed our previous results that rs16947 (CYP2D6*2) reduces full-length CYP2D6 mRNA by increasing the production of an unstable splice isoform lacking exon 6 (CYP2D6ΔE6) and that the impact of CYP2D6ΔE6 is offset in carriers of the downstream enhancer variant rs5758550. The three frequent SNPs (rs1058164, rs16947, and rs5758550) form various 3-SNP-haplotypes, each with distinct CYP2D6 expression characteristics. Using an expression score (ES) system, we tested the impact of the 3-SNP-haplotype on improving the standard model to predict hepatic CYP2D6 protein expression based on genotype. A model that incorporates the 3-SNP-haplotype provided the best fit for CYP2D6 expression and also accounted for more variability in CYP2D6 protein levels (59%) than a model based on the accepted standard (36%) or one that only adds rs16947 and rs5758550 (42%). Clinical studies are needed to determine whether including the 3-SNP-haplotype alongside current standard CYP2D6 models improves the predictive value of CYP2D6 panels.
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Affiliation(s)
| | | | | | - Danxin Wang
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, FL, United States
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9
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Chan AP, Choi Y, Rangan A, Zhang G, Podder A, Berens M, Sharma S, Pirrotte P, Byron S, Duggan D, Schork NJ. Interrogating the Human Diplome: Computational Methods, Emerging Applications, and Challenges. Methods Mol Biol 2023; 2590:1-30. [PMID: 36335489 DOI: 10.1007/978-1-0716-2819-5_1] [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] [Indexed: 05/17/2023]
Abstract
Human DNA sequencing protocols have revolutionized human biology, biomedical science, and clinical practice, but still have very important limitations. One limitation is that most protocols do not separate or assemble (i.e., "phase") the nucleotide content of each of the maternally and paternally derived chromosomal homologs making up the 22 autosomal pairs and the chromosomal pair making up the pseudo-autosomal region of the sex chromosomes. This has led to a dearth of studies and a consequent underappreciation of many phenomena of fundamental importance to basic and clinical genomic science. We discuss a few protocols for obtaining phase information as well as their limitations, including those that could be used in tumor phasing settings. We then describe a number of biological and clinical phenomena that require phase information. These include phenomena that require precise knowledge of the nucleotide sequence in a chromosomal segment from germline or somatic cells, such as DNA binding events, and insight into unique cis vs. trans-acting functionally impactful variant combinations-for example, variants implicated in a phenotype governed by compound heterozygosity. In addition, we also comment on the need for reliable and consensus-based diploid-context computational workflows for variant identification as well as the need for laboratory-based functional verification strategies for validating cis vs. trans effects of variant combinations. We also briefly describe available resources, example studies, as well as areas of further research, and ultimately argue that the science behind the study of human diploidy, referred to as "diplomics," which will be enabled by nucleotide-level resolution of phased genomes, is a logical next step in the analysis of human genome biology.
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Affiliation(s)
- Agnes P Chan
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
| | - Yongwook Choi
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
| | - Aditya Rangan
- Courant Institute of Mathematical Sciences at New York University, New York, NY, USA
| | - Guangfa Zhang
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
| | - Avijit Podder
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
| | - Michael Berens
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
- The City of Hope National Medical Center, Duarte, CA, USA
| | - Sunil Sharma
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
- The City of Hope National Medical Center, Duarte, CA, USA
| | - Patrick Pirrotte
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
- The City of Hope National Medical Center, Duarte, CA, USA
| | - Sara Byron
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
- The City of Hope National Medical Center, Duarte, CA, USA
| | - Dave Duggan
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
- The City of Hope National Medical Center, Duarte, CA, USA
| | - Nicholas J Schork
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA.
- The City of Hope National Medical Center, Duarte, CA, USA.
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10
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Chu YD, Fan TC, Lai MW, Yeh CT. GALNT14-mediated O-glycosylation on PHB2 serine-161 enhances cell growth, migration and drug resistance by activating IGF1R cascade in hepatoma cells. Cell Death Dis 2022; 13:956. [PMID: 36376274 PMCID: PMC9663550 DOI: 10.1038/s41419-022-05419-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022]
Abstract
The single nucleotide polymorphism (SNP) rs9679162 located on GALNT14 gene predicts therapeutic outcomes in patients with intermediate and advanced hepatocellular carcinoma (HCC), but the molecular mechanism remains unclear. Here, the associations between SNP genotypes, GALNT14 expression, and downstream molecular events were determined. A higher GALNT14 cancerous/noncancerous ratio was associated with the rs9679162-GG genotype, leading to an unfavorable postoperative prognosis. A novel exon-6-skipped GALNT14 mRNA variant was identified in patients carrying the rs9679162-TT genotype, which was associated with lower GALNT14 expression and favorable prognosis. Cell-based experiments showed that elevated levels of GALNT14 promoted HCC growth, migration, and resistance to anticancer drugs. Using a comparative lectin-capture glycoproteomic approach, PHB2 was identified as a substrate for GALNT14-mediated O-glycosylation. Site-directed mutagenesis experiments revealed that serine-161 (Ser161) was the O-glycosylation site. Further analysis showed that O-glycosylation of PHB2-Ser161 was required for the GALNT14-mediated growth-promoting phenotype. O-glycosylation of PHB2 was positively correlated with GALNT14 expression in HCC, resulting in increased interaction between PHB2 and IGFBP6, which in turn led to the activation of IGF1R-mediated signaling. In conclusion, the GALNT14-rs9679162 genotype was associated with differential expression levels of GALNT14 and the generation of a novel exon-6-skipped GALNT14 mRNA variant, which was associated with a favorable prognosis in HCC. The GALNT14/PHB2/IGF1R cascade modulated the growth, migration, and anticancer drug resistance of HCC cells, thereby opening the possibility of identifying new therapeutic targets against HCC.
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Affiliation(s)
- Yu-De Chu
- grid.413801.f0000 0001 0711 0593Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Tan-Chi Fan
- grid.454210.60000 0004 1756 1461Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Ming-Wei Lai
- grid.413801.f0000 0001 0711 0593Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan ,grid.454211.70000 0004 1756 999XDivision of Pediatric Gastroenterology Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chau-Ting Yeh
- grid.413801.f0000 0001 0711 0593Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan ,grid.145695.a0000 0004 1798 0922Molecular Medicine Research Center, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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11
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Castaldi PJ, Abood A, Farber CR, Sheynkman GM. Bridging the splicing gap in human genetics with long-read RNA sequencing: finding the protein isoform drivers of disease. Hum Mol Genet 2022; 31:R123-R136. [PMID: 35960994 PMCID: PMC9585682 DOI: 10.1093/hmg/ddac196] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 02/04/2023] Open
Abstract
Aberrant splicing underlies many human diseases, including cancer, cardiovascular diseases and neurological disorders. Genome-wide mapping of splicing quantitative trait loci (sQTLs) has shown that genetic regulation of alternative splicing is widespread. However, identification of the corresponding isoform or protein products associated with disease-associated sQTLs is challenging with short-read RNA-seq, which cannot precisely characterize full-length transcript isoforms. Furthermore, contemporary sQTL interpretation often relies on reference transcript annotations, which are incomplete. Solutions to these issues may be found through integration of newly emerging long-read sequencing technologies. Long-read sequencing offers the capability to sequence full-length mRNA transcripts and, in some cases, to link sQTLs to transcript isoforms containing disease-relevant protein alterations. Here, we provide an overview of sQTL mapping approaches, the use of long-read sequencing to characterize sQTL effects on isoforms, the linkage of RNA isoforms to protein-level functions and comment on future directions in the field. Based on recent progress, long-read RNA sequencing promises to be part of the human disease genetics toolkit to discover and treat protein isoforms causing rare and complex diseases.
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Affiliation(s)
- Peter J Castaldi
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Division of General Medicine and Primary Care, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Abdullah Abood
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Charles R Farber
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Public Health Sciences, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Gloria M Sheynkman
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22903, USA
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12
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Gress A, Srikakulam SK, Keller S, Ramensky V, Kalinina OV. d-StructMAn: Containerized structural annotation on the scale from genetic variants to whole proteomes. Gigascience 2022; 11:6706670. [PMID: 36130085 PMCID: PMC9487898 DOI: 10.1093/gigascience/giac086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/06/2022] [Accepted: 08/18/2022] [Indexed: 11/30/2022] Open
Abstract
Background Structural annotation of genetic variants in the context of intermolecular interactions and protein stability can shed light onto mechanisms of disease-related phenotypes. Three-dimensional structures of related proteins in complexes with other proteins, nucleic acids, or ligands enrich such functional interpretation, since intermolecular interactions are well conserved in evolution. Results We present d-StructMAn, a novel computational method that enables structural annotation of local genetic variants, such as single-nucleotide variants and in-frame indels, and implements it in a highly efficient and user-friendly tool provided as a Docker container. Using d-StructMAn, we annotated several very large sets of human genetic variants, including all variants from ClinVar and all amino acid positions in the human proteome. We were able to provide annotation for more than 46% of positions in the human proteome representing over 60% proteins. Conclusions d-StructMAn is the first of its kind and a highly efficient tool for structural annotation of protein-coding genetic variation in the context of observed and potential intermolecular interactions. d-StructMAn is readily applicable to proteome-scale datasets and can be an instrumental building machine-learning tool for predicting genotype-to-phenotype relationships.
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Affiliation(s)
- Alexander Gress
- Correspondence address. Alexander Gress, Campus Saarland University 66123 Saarbrücken Building E2.1 Room 101; E-mail:
| | - Sanjay K Srikakulam
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)/Helmholtz Centre for Infection Research (HZI), Saarbrücken 8: 66123, Germany
- Graduate School of Computer Science, Saarland University, Saarbrücken 5: 101990, Germany
- Interdisciplinary Graduate School of Natural Product Research, Saarland University, Saarbrücken 6: 119991, Germany
| | - Sebastian Keller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)/Helmholtz Centre for Infection Research (HZI), Saarbrücken 8: 66123, Germany
- Graduate School of Computer Science, Saarland University, Saarbrücken 5: 101990, Germany
- Research Group Computational Biology, Max Planck Institute for Informatics, Saarbrücken 7: 66421, Germany
| | - Vasily Ramensky
- National Medical Research Center for Therapy and Preventive Medicine of the Ministry of Healthcare of Russian Federation, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Olga V Kalinina
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)/Helmholtz Centre for Infection Research (HZI), Saarbrücken 8: 66123, Germany
- Medical Faculty, Saarland University, Homburg, Germany
- Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
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13
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Quinones-Valdez G, Fu T, Chan TW, Xiao X. scAllele: A versatile tool for the detection and analysis of variants in scRNA-seq. SCIENCE ADVANCES 2022; 8:eabn6398. [PMID: 36054357 DOI: 10.1126/sciadv.abn6398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) data contain rich information at the gene, transcript, and nucleotide levels. Most analyses of scRNA-seq have focused on gene expression profiles, and it remains challenging to extract nucleotide variants and isoform-specific information. Here, we present scAllele, an integrative approach that detects single-nucleotide variants, insertions, deletions, and their allelic linkage with splicing patterns in scRNA-seq. We demonstrate that scAllele achieves better performance in identifying nucleotide variants than other commonly used tools. In addition, the read-specific variant calls by scAllele enables allele-specific splicing analysis, a unique feature not afforded by other methods. Applied to a lung cancer scRNA-seq dataset, scAllele identified variants with strong allelic linkage to alternative splicing, some of which are cancer specific and enriched in cancer-relevant pathways. scAllele represents a versatile tool to uncover multilayer information and previously unidentified biological insights from scRNA-seq data.
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Affiliation(s)
| | - Ting Fu
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tracey W Chan
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xinshu Xiao
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA 90095, USA
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14
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Zou X, Schaefke B, Li Y, Jia F, Sun W, Li G, Liang W, Reif T, Heyd F, Gao Q, Tian S, Li Y, Tang Y, Fang L, Hu Y, Chen W. Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law. Life Sci Alliance 2022; 5:5/4/e202101333. [PMID: 34969779 PMCID: PMC8739531 DOI: 10.26508/lsa.202101333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 11/24/2022] Open
Abstract
This study globally investigates the allelic splicing pattern in multiple tissues of an F1 hybrid mouse and reveals the underlying driving forces shaping such tissue-dependent splicing divergence. Alternative splicing is ubiquitous, but the mechanisms underlying its pattern of evolutionary divergence across mammalian tissues are still underexplored. Here, we investigated the cis-regulatory divergences and their relationship with tissue-dependent trans-regulation in multiple tissues of an F1 hybrid between two mouse species. Large splicing changes between tissues are highly conserved and likely reflect functional tissue-dependent regulation. In particular, micro-exons frequently exhibit this pattern with high inclusion levels in the brain. Cis-divergence of splicing appears to be largely non-adaptive. Although divergence is in general associated with higher densities of sequence variants in regulatory regions, events with high usage of the dominant isoform apparently tolerate more mutations, explaining why their exon sequences are highly conserved but their intronic splicing site flanking regions are not. Moreover, we demonstrate that non-adaptive mutations are often masked in tissues where accurate splicing likely is more important, and experimentally attribute such buffering effect to trans-regulatory splicing efficiency.
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Affiliation(s)
- Xudong Zou
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Bernhard Schaefke
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Yisheng Li
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Fujian Jia
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wei Sun
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Guipeng Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Weizheng Liang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Tristan Reif
- Institute for Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Florian Heyd
- Institute for Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Qingsong Gao
- Laboratory for Systems Biology and Functional Genomics, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Shuye Tian
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yanping Li
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yisen Tang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Liang Fang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Yuhui Hu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wei Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China .,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
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15
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Keane JT, Afrasiabi A, Schibeci SD, Swaminathan S, Parnell GP, Booth DR. The interaction of Epstein-Barr virus encoded transcription factor EBNA2 with multiple sclerosis risk loci is dependent on the risk genotype. EBioMedicine 2021; 71:103572. [PMID: 34488019 PMCID: PMC8426200 DOI: 10.1016/j.ebiom.2021.103572] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 12/12/2022] Open
Abstract
Background Epstein-Barr virus (EBV) infection may be necessary for the development of Multiple sclerosis (MS). Earlier we had identified six MS risk loci that are co-located with binding sites for the EBV transcription factor Epstein-Barr Nuclear Antigen 2 (EBNA2) in EBV-infected B cells (lymphoblastoid cell lines – LCLs). Methods We used an allele-specific chromatin immunoprecipitation PCR assay to assess EBNA2 allelic preference. We treated LCLs with a peptide inhibitor of EBNA2 (EBNA2-TAT), reasoning that inhibiting EBNA2 function would alter gene expression at these loci if it was mediated by EBNA2. Findings We found that EBNA2 binding was dependent on the risk allele for five of these six MS risk loci (p < 0·05). Treatment with EBNA2-TAT significantly altered the expression of TRAF3 (p < 0·05), CD40 (p < 0·001), CLECL1 (p <0·0001), TNFAIP8 (p < 0·001) and TNFRSF1A (p < 0·001). Interpretation These data suggest that EBNA2 can enhance or reduce expression of the gene depending on the risk allele, likely promoting EBV infection. This is consistent with the concept that these MS risk loci affect MS risk through altering the response to EBNA2. Together with the extensive data indicating a pathogenic role for EBV in MS, this study supports targeting EBV and EBNA2 to reduce their effect on MS pathogenesis. Funding Funding was provided by grants from MS Research Australia, National Health and Medical Research Council of Australia, Australian Government Research Training Program, Multiple Sclerosis International Federation, Trish Multiple Sclerosis Research Foundation.
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Affiliation(s)
- Jeremy Thomas Keane
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Ali Afrasiabi
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia; BioMedical Machine Learning Lab, The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Stephen Donald Schibeci
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Sanjay Swaminathan
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia; Department of Medicine, Western Sydney University, Sydney, NSW 2560, Australia
| | - Grant Peter Parnell
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia.
| | - David Richmond Booth
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia.
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16
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Abstract
Diploidy has profound implications for population genetics and susceptibility to genetic diseases. Although two copies are present for most genes in the human genome, they are not necessarily both active or active at the same level in a given individual. Genomic imprinting, resulting in exclusive or biased expression in favor of the allele of paternal or maternal origin, is now believed to affect hundreds of human genes. A far greater number of genes display unequal expression of gene copies due to cis-acting genetic variants that perturb gene expression. The availability of data generated by RNA sequencing applied to large numbers of individuals and tissue types has generated unprecedented opportunities to assess the contribution of genetic variation to allelic imbalance in gene expression. Here we review the insights gained through the analysis of these data about the extent of the genetic contribution to allelic expression imbalance, the tools and statistical models for gene expression imbalance, and what the results obtained reveal about the contribution of genetic variants that alter gene expression to complex human diseases and phenotypes.
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Affiliation(s)
- Siobhan Cleary
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway H91 H3CY, Ireland;
| | - Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway H91 H3CY, Ireland;
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