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Hughes AEO, Montgomery MC, Liu C, Weimer ET. Allele-specific quantification of human leukocyte antigen transcript isoforms by nanopore sequencing. Front Immunol 2023; 14:1199618. [PMID: 37662944 PMCID: PMC10471969 DOI: 10.3389/fimmu.2023.1199618] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/05/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction While tens of thousands of HLA alleles have been identified by DNA sequencing, the contribution of alternative splicing to HLA diversity is not well characterized. In this study, we sought to determine if long-read sequencing could be used to accurately quantify allele-specific HLA transcripts in primary human lymphocytes. Methods cDNA libraries were prepared from peripheral blood lymphocytes from 12 donors and sequenced by nanopore long-read sequencing. HLA reads were aligned to donor-specific reference sequences based on the known type of each donor. Allele-specific exon utilization was calculated as the proportion of reads aligning to each allele containing known exons, and transcript isoforms were quantified based on patterns of exon utilization within individual reads. Results Splice variants were rare among class I HLA genes (median exon retention rate 99%-100%), except for several HLA-C alleles with exon 5 spliced out of up to 15% of reads. Splice variants were also rare among class II HLA genes (median exon retention rate 98%-100%), except for HLA-DQB1. Consistent with previous work, exon 5 of HLA-DQB1 was spliced out in alleles with a mutated splice acceptor site at rs28688207. Surprisingly, a 28% loss of exon 5 was also observed in HLA-DQB1 alleles with an intact splice acceptor site at rs28688207. Discussion We describe a simple bioinformatic workflow to quantify allele-specific expression of HLA transcript isoforms. Further studies are warranted to characterize the repertoire of HLA transcripts expressed in different cell types and tissues across diverse populations.
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Affiliation(s)
- Andrew E. O. Hughes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Maureen C. Montgomery
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, University of North Carolina Hospitals, Chapel Hill, NC, United States
| | - Chang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Eric T. Weimer
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, University of North Carolina Hospitals, Chapel Hill, NC, United States
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States
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2
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Li L, Huang KL, Gao Y, Cui Y, Wang G, Elrod ND, Li Y, Chen YE, Ji P, Peng F, Russell WK, Wagner EJ, Li W. An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability. Nat Genet 2021; 53:994-1005. [PMID: 33986536 DOI: 10.1038/s41588-021-00864-5] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/05/2021] [Indexed: 12/14/2022]
Abstract
Genome-wide association studies have identified thousands of noncoding variants associated with human traits and diseases. However, the functional interpretation of these variants is a major challenge. Here, we constructed a multi-tissue atlas of human 3'UTR alternative polyadenylation (APA) quantitative trait loci (3'aQTLs), containing approximately 0.4 million common genetic variants associated with the APA of target genes, identified in 46 tissues isolated from 467 individuals (Genotype-Tissue Expression Project). Mechanistically, 3'aQTLs can alter poly(A) motifs, RNA secondary structure and RNA-binding protein-binding sites, leading to thousands of APA changes. Our CRISPR-based experiments indicate that such 3'aQTLs can alter APA regulation. Furthermore, we demonstrate that mapping 3'aQTLs can identify APA regulators, such as La-related protein 4. Finally, 3'aQTLs are colocalized with approximately 16.1% of trait-associated variants and are largely distinct from other QTLs, such as expression QTLs. Together, our findings show that 3'aQTLs contribute substantially to the molecular mechanisms underlying human complex traits and diseases.
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Affiliation(s)
- Lei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Kai-Lieh Huang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Yipeng Gao
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
| | - Ya Cui
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Gao Wang
- The Gertrude H. Sergievsky Center and Department of Neurology, Columbia University, New York, NY, USA
| | - Nathan D Elrod
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Yumei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Yiling Elaine Chen
- Department of Statistics, University of California, Los Angeles, CA, USA
| | - Ping Ji
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Fanglue Peng
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA.
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3
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Baxter-Lowe LA. The changing landscape of HLA typing: Understanding how and when HLA typing data can be used with confidence from bench to bedside. Hum Immunol 2021; 82:466-477. [PMID: 34030895 DOI: 10.1016/j.humimm.2021.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022]
Abstract
Human leukocyte antigen (HLA) genes are extraordinary for their extreme diversity and widespread impact on human health and disease. More than 30,000 HLA alleles have been officially named and more alleles continue to be discovered at a rapid pace. HLA typing systems which have been developed to detect HLA diversity have advanced rapidly and are revolutionizing our understanding of HLA's clinical importance. However, continuous improvements in knowledge and technology have created challenges for clinicians and scientists. This review explains how differences in HLA typing systems can impact the HLA types that are assigned. The consequences of differences in laboratory testing methods and reference databases are described. The challenges of using HLA types that are not equivalent are illustrated. A fundamental understanding of the continual expansion of our understanding of HLA diversity and limitations in some of the typing data is essential for using typing data appropriately in clinical and research settings.
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Affiliation(s)
- Lee Ann Baxter-Lowe
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, USA; Department of Pathology, University of Southern California, USA.
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4
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Population-scale genetic control of alternative polyadenylation and its association with human diseases. QUANTITATIVE BIOLOGY 2021. [DOI: 10.15302/j-qb-021-0252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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5
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Liu C. A long road/read to rapid high-resolution HLA typing: The nanopore perspective. Hum Immunol 2020; 82:488-495. [PMID: 32386782 DOI: 10.1016/j.humimm.2020.04.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 01/18/2023]
Abstract
Next-generation sequencing (NGS) has been widely adopted for clinical HLA typing and advanced immunogenetics researches. Current methodologies still face challenges in resolving cis-trans ambiguity involving distant variant positions, and the turnaround time is affected by testing volume and batching. Nanopore sequencing may become a promising addition to the existing options for HLA typing. The technology delivered by the MinION sequencer of Oxford Nanopore Technologies (ONT) can record the ionic current changes during the translocation of DNA/RNA strands through transmembrane pores and translate the signals to sequence reads. It features simple and flexible library preparations, long sequencing reads, portable and affordable sequencing devices, and rapid, real-time sequencing. However, the error rate of the sequencing reads is high and remains a hurdle for its broad application. This review article will provide a brief overview of this technology and then focus on the opportunities and challenges of using nanopore sequencing for high-resolution HLA typing and immunogenetics research.
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Affiliation(s)
- Chang Liu
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63105, United States.
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6
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Mariella E, Marotta F, Grassi E, Gilotto S, Provero P. The Length of the Expressed 3' UTR Is an Intermediate Molecular Phenotype Linking Genetic Variants to Complex Diseases. Front Genet 2019; 10:714. [PMID: 31475030 PMCID: PMC6707137 DOI: 10.3389/fgene.2019.00714] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/05/2019] [Indexed: 11/13/2022] Open
Abstract
In the last decades, genome-wide association studies (GWAS) have uncovered tens of thousands of associations between common genetic variants and complex diseases. However, these statistical associations can rarely be interpreted functionally and mechanistically. As the majority of the disease-associated variants are located far from coding sequences, even the relevant gene is often unclear. A way to gain insight into the relevant mechanisms is to study the genetic determinants of intermediate molecular phenotypes, such as gene expression and transcript structure. We propose a computational strategy to discover genetic variants affecting the relative expression of alternative 3′ untranslated region (UTR) isoforms, generated through alternative polyadenylation, a widespread posttranscriptional regulatory mechanism known to have relevant functional consequences. When applied to a large dataset in which whole genome and RNA sequencing data are available for 373 European individuals, 2,530 genes with alternative polyadenylation quantitative trait loci (apaQTL) were identified. We analyze and discuss possible mechanisms of action of these variants, and we show that they are significantly enriched in GWAS hits, in particular those concerning immune-related and neurological disorders. Our results point to an important role for genetically determined alternative polyadenylation in affecting predisposition to complex diseases, and suggest new ways to extract functional information from GWAS data.
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Affiliation(s)
- Elisa Mariella
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Federico Marotta
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Elena Grassi
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Stefano Gilotto
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Paolo Provero
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy.,Center for Tranlational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy
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7
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Carey BS, Poulton KV, Poles A. Factors affecting HLA expression: A review. Int J Immunogenet 2019; 46:307-320. [PMID: 31183978 DOI: 10.1111/iji.12443] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/26/2019] [Accepted: 05/03/2019] [Indexed: 12/22/2022]
Abstract
The detection and semiquantitative measurement of circulating human leucocyte antigen (HLA)-specific antibodies is essential for the management of patients before and after transplantation. In addition, the pretransplant cross-match to assess the reactivity of recipient HLA antibody against donor lymphocytes has long been the gold standard to prevent hyperacute rejection. Whilst both of these tests assume that recipient HLA-specific antibody is the only variable in the assessment of transplant risk, this is not the case. Transplant immunologists recognize that some HLA antigens are expressed at levels a magnitude lower than others (e.g., HLA-C, HLA-DQ), but within loci, and between different cell types there are many factors that influence HLA expression in both resting and activated cells. HLA is not usually expressed without the specific promoter proteins NLRC5, for HLA class I, and CIITA, for class II. The quantity of HLA protein production is then affected by factors including promoter region polymorphisms, alternative exon splice sites, methylation and microRNA-directed degradation. Different loci are influenced by multiple combinations of these control mechanisms making prediction of HLA regulation difficult, but an ability to measure the cellular expression of each HLA antigen, in conjunction with knowledge of circulating HLA-specific antibody, would lead to a more informed algorithm to assess transplant risk.
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Affiliation(s)
- B Sean Carey
- Histocompatibility and Immunogenetics, Combined Laboratory, University Hospitals Plymouth, Plymouth, UK
| | | | - Anthony Poles
- Histocompatibility and Immunogenetics, Combined Laboratory, University Hospitals Plymouth, Plymouth, UK
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8
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Misra MK, Damotte V, Hollenbach JA. The immunogenetics of neurological disease. Immunology 2018; 153:399-414. [PMID: 29159928 PMCID: PMC5838423 DOI: 10.1111/imm.12869] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/09/2017] [Accepted: 11/14/2017] [Indexed: 12/18/2022] Open
Abstract
Genes encoding antigen-presenting molecules within the human major histocompatibility complex (MHC) account for the highest component of genetic risk for many neurological diseases, such as multiple sclerosis, neuromyelitis optica, Parkinson's disease, Alzheimer's disease, schizophrenia, myasthenia gravis and amyotrophic lateral sclerosis. Myriad genetic, immunological and environmental factors may contribute to an individual's susceptibility to neurological disease. Here, we review and discuss the decades long research on the influence of genetic variation at the MHC locus and the role of immunogenetic killer cell immunoglobulin-like receptor (KIR) loci in neurological diseases, including multiple sclerosis, neuromyelitis optica, Parkinson's disease, Alzheimer's disease, schizophrenia, myasthenia gravis and amyotrophic lateral sclerosis. The findings of immunogenetic association studies are consistent with a polygenic model of inheritance in the heterogeneous and multifactorial nature of complex traits in various neurological diseases. Future investigation is highly recommended to evaluate both coding and non-coding variation in immunogenetic loci using high-throughput high-resolution next-generation sequencing technologies in diverse ethnic groups to fully appreciate their role in neurological diseases.
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Affiliation(s)
- Maneesh K. Misra
- Department of NeurologySan Francisco School of MedicineUniversity of CaliforniaSan FranciscoCAUSA
| | - Vincent Damotte
- Department of NeurologySan Francisco School of MedicineUniversity of CaliforniaSan FranciscoCAUSA
| | - Jill A. Hollenbach
- Department of NeurologySan Francisco School of MedicineUniversity of CaliforniaSan FranciscoCAUSA
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9
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Hollenbach JA, Oksenberg JR. The immunogenetics of multiple sclerosis: A comprehensive review. J Autoimmun 2015; 64:13-25. [PMID: 26142251 DOI: 10.1016/j.jaut.2015.06.010] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 06/23/2015] [Indexed: 12/21/2022]
Abstract
Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system and common cause of non-traumatic neurological disability in young adults. The likelihood for an individual to develop MS is strongly influenced by her or his ethnic background and family history of disease, suggesting that genetic susceptibility is a key determinant of risk. Over 100 loci have been firmly associated with susceptibility, whereas the main signal genome-wide maps to the class II region of the human leukocyte antigen (HLA) gene cluster and explains up to 10.5% of the genetic variance underlying risk. HLA-DRB1*15:01 has the strongest effect with an average odds ratio of 3.08. However, complex allelic hierarchical lineages, cis/trans haplotypic effects, and independent protective signals in the class I region of the locus have been described as well. Despite the remarkable molecular dissection of the HLA region in MS, further studies are needed to generate unifying models to account for the role of the MHC in disease pathogenesis. Driven by the discovery of combinatorial associations of Killer-cell Immunoglobulin-like Receptor (KIR) and HLA alleles with infectious, autoimmune diseases, transplantation outcome and pregnancy, multi-locus immunogenomic research is now thriving. Central to immunity and critically important for human health, KIR molecules and their HLA ligands are encoded by complex genetic systems with extraordinarily high levels of sequence and structural variation and complex expression patterns. However, studies to-date of KIR in MS have been few and limited to very low resolution genotyping. Application of modern sequencing methodologies coupled with state of the art bioinformatics and analytical approaches will permit us to fully appreciate the impact of HLA and KIR variation in MS.
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Affiliation(s)
- Jill A Hollenbach
- Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA.
| | - Jorge R Oksenberg
- Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
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10
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Hartmann N, Luesink E, Khokhlovich E, Szustakowski JD, Baeriswyl L, Peterson J, Scherer A, Nanguneri NR, Staedtler F. The use of haplotype-specific transcripts improves sample annotation consistency. Biomark Res 2014; 2:17. [PMID: 25285214 PMCID: PMC4184161 DOI: 10.1186/2050-7771-2-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 08/27/2014] [Indexed: 11/10/2022] Open
Abstract
Background Exact sample annotation in expression microarray datasets is essential for any type of pharmacogenomics research. Results Candidate markers were explored through the application of Hartigans’ dip test statistics to a publically available human whole genome microarray dataset. The marker performance was tested on 188 serial samples from 53 donors and of variable tissue origin from five public microarray datasets. A qualified transcript marker panel consisting of three probe sets for human leukocyte antigens HLA-DQA1 (2 probe sets) and HLA-DRB4 identified sample donor identifier inconsistencies in six of the 188 test samples. About 3% of the test samples require root-cause analysis due to unresolvable inaccuracies. Conclusions The transcript marker panel consisting of HLA-DQA1 and HLA-DRB4 represents a robust, tissue-independent composite marker to assist control donor annotation concordance at the transcript level. Allele-selectivity of HLA genes renders them good candidates for “fingerprinting” with donor specific expression pattern.
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Affiliation(s)
- Nicole Hartmann
- Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland
| | - Evert Luesink
- Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland
| | - Edward Khokhlovich
- Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland
| | - Joseph D Szustakowski
- Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland
| | - Lukas Baeriswyl
- Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland
| | - Joshua Peterson
- Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland
| | | | - Nirmala R Nanguneri
- Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland
| | - Frank Staedtler
- Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland
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11
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Corso C, Pisapia L, Citro A, Cicatiello V, Barba P, Cigliano L, Abrescia P, Maffei A, Manco G, Del Pozzo G. EBP1 and DRBP76/NF90 binding proteins are included in the major histocompatibility complex class II RNA operon. Nucleic Acids Res 2011; 39:7263-75. [PMID: 21624892 PMCID: PMC3167597 DOI: 10.1093/nar/gkr278] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Major histocompatibility complex class II mRNAs encode heterodimeric proteins involved in the presentation of exogenous antigens during an immune response. Their 3'UTRs bind a protein complex in which we identified two factors: EBP1, an ErbB3 receptor-binding protein and DRBP76, a double-stranded RNA binding nuclear protein, also known as nuclear factor 90 (NF90). Both are well-characterized regulatory factors of several mRNA molecules processing. Using either EBP1 or DRBP76/NF90-specific knockdown experiments, we established that the two proteins play a role in regulating the expression of HLA-DRA, HLA-DRB1 and HLA-DQA1 mRNAs levels. Our study represents the first indication of the existence of a functional unit that includes different transcripts involved in the adaptive immune response. We propose that the concept of 'RNA operon' may be suitable for our system in which MHCII mRNAs are modulated via interaction of their 3'UTR with same proteins.
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Affiliation(s)
- Carmela Corso
- Institute of Genetics and Biophysics ‘A. Buzzati Traverso’, CNR, Via Pietro Castellino 111, 80131, Naples, Department of Biological Science, University of Naples Federico II, Via Mezzocannone 8, 80134, Naples and Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Laura Pisapia
- Institute of Genetics and Biophysics ‘A. Buzzati Traverso’, CNR, Via Pietro Castellino 111, 80131, Naples, Department of Biological Science, University of Naples Federico II, Via Mezzocannone 8, 80134, Naples and Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Alessandra Citro
- Institute of Genetics and Biophysics ‘A. Buzzati Traverso’, CNR, Via Pietro Castellino 111, 80131, Naples, Department of Biological Science, University of Naples Federico II, Via Mezzocannone 8, 80134, Naples and Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Valeria Cicatiello
- Institute of Genetics and Biophysics ‘A. Buzzati Traverso’, CNR, Via Pietro Castellino 111, 80131, Naples, Department of Biological Science, University of Naples Federico II, Via Mezzocannone 8, 80134, Naples and Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
- *To whom correspondence should be addressed. Valeria Cicatiello. Tel: +390816132455; Fax: +390816132718;
| | - Pasquale Barba
- Institute of Genetics and Biophysics ‘A. Buzzati Traverso’, CNR, Via Pietro Castellino 111, 80131, Naples, Department of Biological Science, University of Naples Federico II, Via Mezzocannone 8, 80134, Naples and Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Luisa Cigliano
- Institute of Genetics and Biophysics ‘A. Buzzati Traverso’, CNR, Via Pietro Castellino 111, 80131, Naples, Department of Biological Science, University of Naples Federico II, Via Mezzocannone 8, 80134, Naples and Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Paolo Abrescia
- Institute of Genetics and Biophysics ‘A. Buzzati Traverso’, CNR, Via Pietro Castellino 111, 80131, Naples, Department of Biological Science, University of Naples Federico II, Via Mezzocannone 8, 80134, Naples and Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Antonella Maffei
- Institute of Genetics and Biophysics ‘A. Buzzati Traverso’, CNR, Via Pietro Castellino 111, 80131, Naples, Department of Biological Science, University of Naples Federico II, Via Mezzocannone 8, 80134, Naples and Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Giuseppe Manco
- Institute of Genetics and Biophysics ‘A. Buzzati Traverso’, CNR, Via Pietro Castellino 111, 80131, Naples, Department of Biological Science, University of Naples Federico II, Via Mezzocannone 8, 80134, Naples and Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
- *To whom correspondence should be addressed. Valeria Cicatiello. Tel: +390816132455; Fax: +390816132718;
| | - Giovanna Del Pozzo
- Institute of Genetics and Biophysics ‘A. Buzzati Traverso’, CNR, Via Pietro Castellino 111, 80131, Naples, Department of Biological Science, University of Naples Federico II, Via Mezzocannone 8, 80134, Naples and Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
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12
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Horton R, Gibson R, Coggill P, Miretti M, Allcock RJ, Almeida J, Forbes S, Gilbert JGR, Halls K, Harrow JL, Hart E, Howe K, Jackson DK, Palmer S, Roberts AN, Sims S, Stewart CA, Traherne JA, Trevanion S, Wilming L, Rogers J, de Jong PJ, Elliott JF, Sawcer S, Todd JA, Trowsdale J, Beck S. Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project. Immunogenetics 2008; 60:1-18. [PMID: 18193213 PMCID: PMC2206249 DOI: 10.1007/s00251-007-0262-2] [Citation(s) in RCA: 235] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 10/29/2007] [Indexed: 02/05/2023]
Abstract
The human major histocompatibility complex (MHC) is contained within about 4 Mb on the short arm of chromosome 6 and is recognised as the most variable region in the human genome. The primary aim of the MHC Haplotype Project was to provide a comprehensively annotated reference sequence of a single, human leukocyte antigen-homozygous MHC haplotype and to use it as a basis against which variations could be assessed from seven other similarly homozygous cell lines, representative of the most common MHC haplotypes in the European population. Comparison of the haplotype sequences, including four haplotypes not previously analysed, resulted in the identification of >44,000 variations, both substitutions and indels (insertions and deletions), which have been submitted to the dbSNP database. The gene annotation uncovered haplotype-specific differences and confirmed the presence of more than 300 loci, including over 160 protein-coding genes. Combined analysis of the variation and annotation datasets revealed 122 gene loci with coding substitutions of which 97 were non-synonymous. The haplotype (A3-B7-DR15; PGF cell line) designated as the new MHC reference sequence, has been incorporated into the human genome assembly (NCBI35 and subsequent builds), and constitutes the largest single-haplotype sequence of the human genome to date. The extensive variation and annotation data derived from the analysis of seven further haplotypes have been made publicly available and provide a framework and resource for future association studies of all MHC-associated diseases and transplant medicine.
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Affiliation(s)
- Roger Horton
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Richard Gibson
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Penny Coggill
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Marcos Miretti
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Richard J. Allcock
- School of Surgery and Pathology, University of Western Australia, Nedlands, 6009 WA Australia
| | - Jeff Almeida
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Simon Forbes
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - James G. R. Gilbert
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Karen Halls
- The Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
| | - Jennifer L. Harrow
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Elizabeth Hart
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Kevin Howe
- CRUK Cambridge Research Institute, Robinson Way, Cambridge, CB2 0RE UK
| | - David K. Jackson
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Sophie Palmer
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Anne N. Roberts
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Addenbrooke’s Hospital, Cambridge, CB2 0XY UK
| | - Sarah Sims
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - C. Andrew Stewart
- National Cancer Institute, P.O. Box B., 567/206, Frederick, MD 21702 USA
| | - James A. Traherne
- Department of Pathology, Immunology Division, University of Cambridge, Cambridge, CB2 1QP UK
| | - Steve Trevanion
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Laurens Wilming
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Jane Rogers
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Pieter J. de Jong
- Children’s Hospital Oakland Research Institute, Oakland, CA 94609-1673 USA
| | - John F. Elliott
- Alberta Diabetes Institute (ADI), Department of Medical Microbiology and Immunology, Division of Dermatology and Cutaneous Sciences, University of Alberta, Edmonton, AB T6G 2H7 Canada
| | - Stephen Sawcer
- Department of Clinical Neurosciences, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 2QQ UK
| | - John A. Todd
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Addenbrooke’s Hospital, Cambridge, CB2 0XY UK
| | - John Trowsdale
- Department of Pathology, Immunology Division, University of Cambridge, Cambridge, CB2 1QP UK
| | - Stephan Beck
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BD UK
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13
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Hwang JY, Hirono I, Aoki T. Cloning and expression of a novel serine protease from Japanese flounder, Paralichthys olivaceus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2007; 31:587-95. [PMID: 17084451 DOI: 10.1016/j.dci.2006.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2005] [Revised: 06/28/2006] [Accepted: 07/04/2006] [Indexed: 05/12/2023]
Abstract
Two different cDNA clones of Japanese flounder (types I-1 and I-2) with lengths of 1096 and 1572bp, respectively, were found to encode the same serine protease consisting of 244 identical amino acid residues with three putative N-glycosylation sites, an 18-amino acid signal peptide and a 2-amino acid activation peptide. The amino acid sequence of the Japanese flounder serine protease shares 39-44% identity to known hematopoietic serine proteases. Genomic analysis showed that two different clones were alternatively spliced from the same gene. A phylogenetic tree analysis showed that the Japanese flounder serine protease clustered with a hypothetical fugu protein and this cluster belonged to the neutrophil serine protease family cluster, which includes myeloblastin, N-elastase, and azurocidin. Expression of the Japanese flounder serine protease gene was observed to be up-regulated in head kidney cells after infection with Hirame rhabdovirus and LPS induction. In situ hybridization indicated that cells expressing Japanese flounder serine protease are different from CD8(+) and immunoglobulin(+) cells.
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Affiliation(s)
- Jee Youn Hwang
- Laboratory of Genome Science, Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato, Tokyo 108-8477, Japan
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14
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Královicová J, Vorechovsky I. Position-dependent repression and promotion of DQB1 intron 3 splicing by GGGG motifs. THE JOURNAL OF IMMUNOLOGY 2006; 176:2381-8. [PMID: 16455996 DOI: 10.4049/jimmunol.176.4.2381] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Alternative splicing of HLA-DQB1 exon 4 is allele-dependent and results in variable expression of soluble DQbeta. We have recently shown that differential inclusion of this exon in mature transcripts is largely due to intron 3 variants in the branch point sequence (BPS) and polypyrimidine tract. To identify additional regulatory cis-elements that contribute to haplotype-specific splicing of DQB1, we systematically examined the effect of guanosine (G) repeats on intron 3 removal. We found that the GGG or GGGG repeats generally improved splicing of DQB1 intron 3, except for those that were adjacent to the 5' splice site where they had the opposite effect. The most prominent splicing enhancement was conferred by GGGG motifs arranged in tandem upstream of the BPS. Replacement of a G-rich segment just 5' of the BPS with a series of random sequences markedly repressed splicing, whereas substitutions of a segment further upstream that lacked the G-rich elements and had the same size did not result in comparable splicing inhibition. Systematic mutagenesis of both suprabranch guanosine quadruplets (G(4)) revealed a key role of central G residues in splicing enhancement, whereas cytosines in these positions had the most prominent repressive effects. Together, these results show a significant role of tandem G(4)NG(4) structures in splicing of both complete and truncated DQB1 intron 3, support position dependency of G repeats in splicing promotion and inhibition, and identify positively and negatively acting sequences that contribute to the haplotype-specific DQB1 expression.
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Affiliation(s)
- Jana Královicová
- Division of Human Genetics, University of Southampton, School of Medicine, UK
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15
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Borges A, García CC, Lugo E, Alfonzo MJ, Jowers MJ, Op den Camp HJM. Diversity of long-chain toxins in Tityus zulianus and Tityus discrepans venoms (Scorpiones, Buthidae): molecular, immunological, and mass spectral analyses. Comp Biochem Physiol C Toxicol Pharmacol 2006; 142:240-252. [PMID: 16356783 DOI: 10.1016/j.cbpc.2005.10.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Revised: 10/11/2005] [Accepted: 10/12/2005] [Indexed: 11/27/2022]
Abstract
In Venezuela, stings by Tityus zulianus scorpions produce cardiorespiratory arrest, whereas envenoming by Tityus discrepans involves gastrointestinal/pancreatic complications, suggesting structural and/or functional differences. We sought to compare their toxin repertoires through immunological, molecular, and mass spectral analyses. First, in vivo tests showed that neutralization of T. zulianus venom toxicity by the anti-T. discrepans antivenom was not complete. To compare T. discrepans and T. zulianus long-chain (sodium channel-active) toxins, their most toxic Sephadex G-50 fractions, TdII and TzII, were subjected to acid-urea PAGE, which showed differences in composition. Amplification of toxin-encoding mRNAs using a leader peptide-based oligonucleotide rendered cDNAs representing twelve T. discrepans and two T. zulianus distinct toxin transcripts, including only one shared component, indicating divergence between T. zulianus and T. discrepans 5' region-encoded, toxin signal peptides. A 3'-UTR polymorphism was also noticed among the transcripts encoding shared components Tz1 and Td4. MALDI-TOF MS profiling of TdII and TzII produced species-specific spectra, with seven of the individual masses matching those predicted by cDNA sequencing. Phylogenetic analysis showed that the unique T. zulianus transcript-encoded sequence, Tz2, is structurally related to Tityus serrulatus and Centruroides toxins. Together with previous reports, this work indicates that T. zulianus and T. discrepans toxin repertoires differ structurally and functionally.
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Affiliation(s)
- Adolfo Borges
- Sección de Biomembranas, Instituto de Medicina Experimental, Universidad Central de Venezuela, Caracas 1051, Venezuela.
| | - Carmen C García
- Sección de Biomembranas, Instituto de Medicina Experimental, Universidad Central de Venezuela, Caracas 1051, Venezuela
| | - Elizabeth Lugo
- Sección de Biomembranas, Instituto de Medicina Experimental, Universidad Central de Venezuela, Caracas 1051, Venezuela
| | - Marcelo J Alfonzo
- Sección de Biomembranas, Instituto de Medicina Experimental, Universidad Central de Venezuela, Caracas 1051, Venezuela
| | - Michael J Jowers
- Institute of Biomedical and Life Sciences, Division of Molecular Genetics, University of Glasgow, Glasgow G11 6NU, United Kingdom
| | - Huub J M Op den Camp
- Department of Microbiology, Faculty of Science, Radboud University Nijmegen, Tooernooiveld 1, Nijmegen, The Netherlands
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16
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Balas A, Aviles MJ, Alonso-Nieto M, Zarapuz L, Blanco L, García-Sánchez F, Vicario JL. HLA-DQA1 Introns 2 and 3 Sequencing: DQA1 Sequencing-Based Typing and Characterization of a Highly Polymorphic Microsatellite at Intron 3 of DQA1*0505. Hum Immunol 2005; 66:903-11. [PMID: 16216675 DOI: 10.1016/j.humimm.2005.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2005] [Indexed: 11/22/2022]
Abstract
DQA1 class II gene encodes the alpha-chain of the human leukocyte antigen (HLA)-DQ heterodimer. Sequencing-based typing (SBT) for HLA genes is the most powerful methodology described. However, most of the SBT procedures reported for HLA class II genes are not able to define complete exon 2 region. For that purpose, we have characterized introns 2 and 3 from most DQA1 alleles to design amplification procedures that were able to obtain complete exon 2 and 3 sequences from DQA1 genes. This coding information allowed us to reduce the number of ambiguities for DQA1 typing. DQA1 intron 2 and 3 characterization demonstrated the presence of two polymorphisms for alleles with the same exons 2 and 3 sequence from DQA1*05 group. Different samples including the DQA1*050101 alleles showed a single nucleotide polymorphism at position 53 of intron 2 (G53T). Additional haplotypic analysis showed the possible association of T53 allele with the Ax-Cw5-B18-DR17-DQ2 extended haplotype. On the other hand, DQA1*0505 sequencing from different control samples noticed the existence of a microsatellite (TTTC/AAAG)n located at position 126 of intron 3. Fragment length analysis demonstrated a high polymorphism for this short tandem repeat system (0505STR), defining alleles that ranged from 8 to 20 repetitions in our population.
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Affiliation(s)
- Antonio Balas
- Histocompatibility and Molecular Biology Department. Regional Transfusion Centre of Madrid, Madrid, Spain
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17
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Hoarau JJ, Festy F, Cesari M, Pabion M. A new splicing acceptor site and poly(A)+ sequence signal within DQA1*0401 and DQA1*0501 mRNA 3'UTR contribute to increase the extraordinary diversity of mRNA isoforms. Immunogenetics 2005; 57:182-8. [PMID: 15900489 DOI: 10.1007/s00251-005-0769-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2004] [Revised: 12/08/2004] [Indexed: 02/05/2023]
Abstract
In this paper, we have analysed the diversity of mRNA species generated by DQA1*0501 and DQA1*0401 alleles in homozygous B-lymphoblastoid cell lines. As we previously reported, six mRNA isoforms that differ in the 3'UTR have been identified in these cells. This diversity of mRNA species results both from the alternative use of two acceptor spliced sites and the differential selection of two poly(A)+ sequence signals by the processing machinery. In this report we describe a new acceptor sequence signal that allows generation of a new alternative spliced mRNA species. This acceptor sequence signal was also present in all of the seven DQA1 homozygous cell lines analysed. In addition, we have identified a previously undetected, non-conventional but functional, poly(A)+ sequence signal that lacks an identifiable AATAAA hexamer, one of the most important element of the core. This sequence signal allows the generation of two additional mRNA isoforms both in DQA1*0501 and DQA1*0401 homozygous cell lines but not in the others. We show that DQA1*0501 and DQA1*0401 primary transcripts can be processed into nine mRNA isoforms that differ in the 3'UTR. Finally, we summarized all the DQA1 mRNA species deriving from DQA1*0101, DQA1*0102, DQA1*0103, DQA1*0201, DQA1*0301, DQA1*0401 and DQA1*0501 alleles and shown in B-lymphoblastoid cell lines.
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Affiliation(s)
- J J Hoarau
- Brain Inflammation and Immunity Group, University of Cardiff-School of Medicine, CF14 4XN Cardiff, UK
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