151
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Hickey G, Monlong J, Ebler J, Novak AM, Eizenga JM, Gao Y, Marschall T, Li H, Paten B, Abel HJ, Antonacci-Fulton LL, Asri M, Baid G, Baker CA, Belyaeva A, Billis K, Bourque G, Buonaiuto S, Carroll A, Chaisson MJP, Chang PC, Chang XH, Cheng H, Chu J, Cody S, Colonna V, Cook DE, Cook-Deegan RM, Cornejo OE, Diekhans M, Doerr D, Ebert P, Ebler J, Eichler EE, Eizenga JM, Fairley S, Fedrigo O, Felsenfeld AL, Feng X, Fischer C, Flicek P, Formenti G, Frankish A, Fulton RS, Gao Y, Garg S, Garrison E, Garrison NA, Giron CG, Green RE, Groza C, Guarracino A, Haggerty L, Hall IM, Harvey WT, Haukness M, Haussler D, Heumos S, Hickey G, Hoekzema K, Hourlier T, Howe K, Jain M, Jarvis ED, Ji HP, Kenny EE, Koenig BA, Kolesnikov A, Korbel JO, Kordosky J, Koren S, Lee H, Lewis AP, Li H, Liao WW, Lu S, Lu TY, Lucas JK, Magalhães H, Marco-Sola S, Marijon P, Markello C, Marschall T, Martin FJ, McCartney A, McDaniel J, Miga KH, Mitchell MW, Monlong J, Mountcastle J, Munson KM, Mwaniki MN, Nattestad M, Novak AM, Nurk S, Olsen HE, Olson ND, Paten B, Pesout T, Phillippy AM, Popejoy AB, Porubsky D, Prins P, Puiu D, Rautiainen M, Regier AA, Rhie A, Sacco S, Sanders AD, Schneider VA, Schultz BI, Shafin K, Sibbesen JA, Sirén J, Smith MW, Sofia HJ, Tayoun ANA, Thibaud-Nissen F, Tomlinson C, Tricomi FF, Villani F, Vollger MR, Wagner J, Walenz B, Wang T, Wood JMD, Zimin AV, Zook JM. Pangenome graph construction from genome alignments with Minigraph-Cactus. Nat Biotechnol 2024; 42:663-673. [PMID: 37165083 PMCID: PMC10638906 DOI: 10.1038/s41587-023-01793-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 04/18/2023] [Indexed: 05/12/2023]
Abstract
Pangenome references address biases of reference genomes by storing a representative set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles determined by variant callers can be used to construct pangenome graphs, but advances in long-read sequencing are leading to widely available, high-quality phased assemblies. Constructing a pangenome graph directly from assemblies, as opposed to variant calls, leverages the graph's ability to represent variation at different scales. Here we present the Minigraph-Cactus pangenome pipeline, which creates pangenomes directly from whole-genome alignments, and demonstrate its ability to scale to 90 human haplotypes from the Human Pangenome Reference Consortium. The method builds graphs containing all forms of genetic variation while allowing use of current mapping and genotyping tools. We measure the effect of the quality and completeness of reference genomes used for analysis within the pangenomes and show that using the CHM13 reference from the Telomere-to-Telomere Consortium improves the accuracy of our methods. We also demonstrate construction of a Drosophila melanogaster pangenome.
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Affiliation(s)
- Glenn Hickey
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- These authors contributed equally: Glenn Hickey, Jean Monlong
| | - Jean Monlong
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- These authors contributed equally: Glenn Hickey, Jean Monlong
| | - Jana Ebler
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Adam M. Novak
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jordan M. Eizenga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Yan Gao
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - Haley J. Abel
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Mobin Asri
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - Carl A. Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, McGill University, Montreal, QC, Canada
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Silvia Buonaiuto
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | | | - Mark J. P. Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | | | - Xian H. Chang
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Haoyu Cheng
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Justin Chu
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah Cody
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Vincenza Colonna
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | | | - Robert M. Cook-Deegan
- Arizona State University, Barrett and O’Connor Washington Center, Washington, DC, USA
| | - Omar E. Cornejo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Daniel Doerr
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Peter Ebert
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Core Unit Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jana Ebler
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Jordan M. Eizenga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Susan Fairley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Adam L. Felsenfeld
- National Institutes of Health (NIH)–National Human Genome Research Institute, Bethesda, MD, USA
| | - Xiaowen Feng
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Christian Fischer
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Robert S. Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Yan Gao
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shilpa Garg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Copenhagen, Denmark
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Nanibaa’ A. Garrison
- Institute for Society and Genetics, College of Letters and Science, University of California, Los Angeles, Los Angeles, CA, USA
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Carlos Garcia Giron
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Richard E. Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
- Dovetail Genomics, Scotts Valley, CA, USA
| | - Cristian Groza
- Quantitative Life Sciences, McGill University, Montreal, QC, Canada
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Genomics Research Centre, Human Technopole, Milan, Italy
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ira M. Hall
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Genomic Health, Yale University School of Medicine, New Haven, CT, USA
| | - William T. Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Simon Heumos
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
- Biomedical Data Science, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Glenn Hickey
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- These authors contributed equally: Glenn Hickey, Jean Monlong
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Miten Jain
- Northeastern University, Boston, MA, USA
| | - Erich D. Jarvis
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Hanlee P. Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Barbara A. Koenig
- Program in Bioethics and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | | | - Jan O. Korbel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Jennifer Kordosky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - HoJoon Lee
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexandra P. Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Wen-Wei Liao
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Genomic Health, Yale University School of Medicine, New Haven, CT, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Shuangjia Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Tsung-Yu Lu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Julian K. Lucas
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Hugo Magalhães
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Santiago Marco-Sola
- Computer Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
- Departament d’Arquitectura de Computadors i Sistemes Operatius, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pierre Marijon
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Charles Markello
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Tobias Marschall
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Fergal J. Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ann McCartney
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer McDaniel
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - Jean Monlong
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- These authors contributed equally: Glenn Hickey, Jean Monlong
| | | | - Katherine M. Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | | | - Adam M. Novak
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hugh E. Olsen
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Nathan D. Olson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Trevor Pesout
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alice B. Popejoy
- Department of Public Health Sciences, University of California, Davis, Davis, CA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Daniela Puiu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Mikko Rautiainen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Allison A. Regier
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Ashley D. Sanders
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Valerie A. Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Baergen I. Schultz
- National Institutes of Health (NIH)–National Human Genome Research Institute, Bethesda, MD, USA
| | | | - Jonas A. Sibbesen
- Center for Health Data Science, University of Copenhagen, Copenhagen, Denmark
| | - Jouni Sirén
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Michael W. Smith
- National Institutes of Health (NIH)–National Human Genome Research Institute, Bethesda, MD, USA
| | - Heidi J. Sofia
- National Institutes of Health (NIH)–National Human Genome Research Institute, Bethesda, MD, USA
| | - Ahmad N. Abou Tayoun
- Al Jalila Genomics Center of Excellence, Al Jalila Children’s Specialty Hospital, Dubai, UAE
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Francesca Floriana Tricomi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Mitchell R. Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Justin Wagner
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Brian Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ting Wang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Aleksey V. Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Justin M. Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
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Mim RA, Soorajkumar A, Kosaji N, Rahman MM, Sarker S, Karuvantevida N, Eshaque TB, Rahaman MA, Islam A, Chowdhury MSJ, Shams N, Uddin KMF, Akter H, Uddin M. Expanding deep phenotypic spectrum associated with atypical pathogenic structural variations overlapping 15q11-q13 imprinting region. Brain Behav 2024; 14:e3437. [PMID: 38616334 PMCID: PMC11016631 DOI: 10.1002/brb3.3437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 04/16/2024] Open
Abstract
BACKGROUND The 15q11-q13 region is a genetic locus with genes subject to genomic imprinting, significantly influencing neurodevelopment. Genomic imprinting is an epigenetic phenomenon that causes differential gene expression based on the parent of origin. In most diploid organisms, gene expression typically involves an equal contribution from both maternal and paternal alleles, shaping the phenotype. Nevertheless, in mammals, including humans, mice, and marsupials, the functional equivalence of parental alleles is not universally maintained. Notably, during male and female gametogenesis, parental alleles may undergo differential marking or imprinting, thereby modifying gene expression without altering the underlying DNA sequence. Neurodevelopmental disorders, such as Prader-Willi syndrome (PWS) (resulting from the absence of paternally expressed genes in this region), Angelman syndrome (AS) (associated with the absence of the maternally expressed UBE3A gene), and 15q11-q13 duplication syndrome (resulting from the two common forms of duplications-either an extra isodicentric 15 chromosome or an interstitial 15 duplication), are the outcomes of genetic variations in this imprinting region. METHODS Conducted a genomic study to identify the frequency of pathogenic variants impacting the 15q11-q13 region in an ethnically homogenous population from Bangladesh. Screened all known disorders from the DECIPHER database and identified variant enrichment within this cohort. Using the Horizon analysis platform, performed enrichment analysis, requiring at least >60% overlap between a copy number variation and a disorder breakpoint. Deep clinical phenotyping was carried out through multiple examination sessions to evaluate a range of clinical symptoms. RESULTS This study included eight individuals with clinically suspected PWS/AS, all previously confirmed through chromosomal microarray analysis, which revealed chromosomal breakpoints within the 15q11-q13 region. Among this cohort, six cases (75%) exhibited variable lengths of deletions, whereas two cases (25%) showed duplications. These included one type 2 duplication, one larger atypical duplication, one shorter type 2 deletion, one larger type 1 deletion, and four cases with atypical deletions. Furthermore, thorough clinical assessments led to the diagnosis of four PWS patients, two AS patients, and two individuals with 15q11-q13 duplication syndrome. CONCLUSION Our deep phenotypic observations identified a spectrum of clinical features that overlap and are unique to PWS, AS, and Dup15q syndromes. Our findings establish genotype-phenotype correlation for patients impacted by variable structural variations within the 15q11-q13 region.
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Affiliation(s)
- Rabeya Akter Mim
- Genetics and Genomic Medicine Centre (GGMC)NeuroGen HealthcareDhakaBangladesh
| | - Anjana Soorajkumar
- Center for Applied and Translational Genomics (CATG)Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai HealthDubaiUAE
| | - Noor Kosaji
- Center for Applied and Translational Genomics (CATG)Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai HealthDubaiUAE
| | - Muhammad Mizanur Rahman
- Department of Paediatric NeurologyBangabandhu Sheikh Mujib Medical UniversityDhakaBangladesh
| | - Shaoli Sarker
- Genetics and Genomic Medicine Centre (GGMC)NeuroGen HealthcareDhakaBangladesh
- Bangladesh Shishu Hospital and InstituteDhakaBangladesh
| | - Noushad Karuvantevida
- Center for Applied and Translational Genomics (CATG)Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai HealthDubaiUAE
| | | | - Md Atikur Rahaman
- Genetics and Genomic Medicine Centre (GGMC)NeuroGen HealthcareDhakaBangladesh
| | - Amirul Islam
- Genetics and Genomic Medicine Centre (GGMC)NeuroGen HealthcareDhakaBangladesh
- GenomeArc Inc.MississaugaOntarioCanada
| | - Mohammod Shah Jahan Chowdhury
- Genetics and Genomic Medicine Centre (GGMC)NeuroGen HealthcareDhakaBangladesh
- Ministry of Health and Family WelfareDhakaBangladesh
| | - Nusrat Shams
- Genetics and Genomic Medicine Centre (GGMC)NeuroGen HealthcareDhakaBangladesh
- National Institute of Neuroscience and HospitalDhakaBangladesh
| | - K. M. Furkan Uddin
- Genetics and Genomic Medicine Centre (GGMC)NeuroGen HealthcareDhakaBangladesh
| | - Hosneara Akter
- Genetics and Genomic Medicine Centre (GGMC)NeuroGen HealthcareDhakaBangladesh
| | - Mohammed Uddin
- Center for Applied and Translational Genomics (CATG)Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai HealthDubaiUAE
- GenomeArc Inc.MississaugaOntarioCanada
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153
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Kang Y, Hepojoki J, Maldonado RS, Mito T, Terzioglu M, Manninen T, Kant R, Singh S, Othman A, Verma R, Uusimaa J, Wartiovaara K, Kareinen L, Zamboni N, Nyman TA, Paetau A, Kipar A, Vapalahti O, Suomalainen A. Ancestral allele of DNA polymerase gamma modifies antiviral tolerance. Nature 2024; 628:844-853. [PMID: 38570685 PMCID: PMC11041766 DOI: 10.1038/s41586-024-07260-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 02/29/2024] [Indexed: 04/05/2024]
Abstract
Mitochondria are critical modulators of antiviral tolerance through the release of mitochondrial RNA and DNA (mtDNA and mtRNA) fragments into the cytoplasm after infection, activating virus sensors and type-I interferon (IFN-I) response1-4. The relevance of these mechanisms for mitochondrial diseases remains understudied. Here we investigated mitochondrial recessive ataxia syndrome (MIRAS), which is caused by a common European founder mutation in DNA polymerase gamma (POLG1)5. Patients homozygous for the MIRAS variant p.W748S show exceptionally variable ages of onset and symptoms5, indicating that unknown modifying factors contribute to disease manifestation. We report that the mtDNA replicase POLG1 has a role in antiviral defence mechanisms to double-stranded DNA and positive-strand RNA virus infections (HSV-1, TBEV and SARS-CoV-2), and its p.W748S variant dampens innate immune responses. Our patient and knock-in mouse data show that p.W748S compromises mtDNA replisome stability, causing mtDNA depletion, aggravated by virus infection. Low mtDNA and mtRNA release into the cytoplasm and a slow IFN response in MIRAS offer viruses an early replicative advantage, leading to an augmented pro-inflammatory response, a subacute loss of GABAergic neurons and liver inflammation and necrosis. A population databank of around 300,000 Finnish individuals6 demonstrates enrichment of immunodeficient traits in carriers of the POLG1 p.W748S mutation. Our evidence suggests that POLG1 defects compromise antiviral tolerance, triggering epilepsy and liver disease. The finding has important implications for the mitochondrial disease spectrum, including epilepsy, ataxia and parkinsonism.
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MESH Headings
- Animals
- Female
- Humans
- Male
- Mice
- Age of Onset
- Alleles
- COVID-19/immunology
- COVID-19/virology
- COVID-19/genetics
- DNA Polymerase gamma/genetics
- DNA Polymerase gamma/immunology
- DNA Polymerase gamma/metabolism
- DNA, Mitochondrial/immunology
- DNA, Mitochondrial/metabolism
- Encephalitis Viruses, Tick-Borne/immunology
- Encephalitis, Tick-Borne/genetics
- Encephalitis, Tick-Borne/immunology
- Encephalitis, Tick-Borne/virology
- Founder Effect
- Gene Knock-In Techniques
- Herpes Simplex/genetics
- Herpes Simplex/immunology
- Herpes Simplex/virology
- Herpesvirus 1, Human/immunology
- Immune Tolerance/genetics
- Immune Tolerance/immunology
- Immunity, Innate/genetics
- Immunity, Innate/immunology
- Interferon Type I/immunology
- Mitochondrial Diseases/enzymology
- Mitochondrial Diseases/genetics
- Mitochondrial Diseases/immunology
- Mutation
- RNA, Mitochondrial/immunology
- RNA, Mitochondrial/metabolism
- SARS-CoV-2/immunology
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Affiliation(s)
- Yilin Kang
- Stem Cell and Metabolism Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jussi Hepojoki
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
| | - Rocio Sartori Maldonado
- Stem Cell and Metabolism Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Takayuki Mito
- Stem Cell and Metabolism Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mügen Terzioglu
- Stem Cell and Metabolism Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tuula Manninen
- Stem Cell and Metabolism Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ravi Kant
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Sachin Singh
- Department of Immunology, Institute of Clinical Medicine, University of Oslo and Rikshospitalet Oslo, Oslo, Norway
| | - Alaa Othman
- Swiss Multi-Omics Center, ETH Zürich, Zürich, Switzerland
| | - Rohit Verma
- Stem Cell and Metabolism Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Johanna Uusimaa
- Research Unit of Clinical Medicine and Medical Research Center, University of Oulu, Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Unit of Child Neurology, Oulu University Hospital, Oulu, Finland
| | - Kirmo Wartiovaara
- Stem Cell and Metabolism Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Helsinki University Hospital, HUS Diagnostics, Helsinki, Finland
| | - Lauri Kareinen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Finnish Food Safety Authority, Helsinki, Finland
| | - Nicola Zamboni
- Swiss Multi-Omics Center, ETH Zürich, Zürich, Switzerland
| | - Tuula Anneli Nyman
- Department of Immunology, Institute of Clinical Medicine, University of Oslo and Rikshospitalet Oslo, Oslo, Norway
| | - Anders Paetau
- Stem Cell and Metabolism Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Helsinki University Hospital, HUS Diagnostics, Helsinki, Finland
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anja Kipar
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Helsinki University Hospital, HUS Diagnostics, Helsinki, Finland
| | - Anu Suomalainen
- Stem Cell and Metabolism Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Helsinki University Hospital, HUS Diagnostics, Helsinki, Finland.
- HiLife, University of Helsinki, Helsinki, Finland.
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154
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Zhang W, Dong L, Li Y, Chen N, Zhu F. Detection of the HLA-C*07:04:29 allele in a Chinese individual. HLA 2024; 103:e15460. [PMID: 38566358 DOI: 10.1111/tan.15460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
HLA-C*07:04:29 differs from HLA-C*07:04:01:01 by a single substitution in exon 4.
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Affiliation(s)
- Wei Zhang
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
| | - Lina Dong
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
| | - Ying Li
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
| | - Nanying Chen
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
| | - Faming Zhu
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
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155
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Li Z, Li Y, Wang L, Gao P, Wang X. Characterization of the novel HLA-C*06:376N allele by Pacific Biosciences HiFi sequencing in a Chinese individual. HLA 2024; 103:e15459. [PMID: 38575366 DOI: 10.1111/tan.15459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024]
Abstract
HLA-C*06:376N differs from HLA-C*06:02:01:01 by seven nucleotide changes in exon 2, intron 2, and exon 3.
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Affiliation(s)
- Zihang Li
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yankun Li
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Liying Wang
- Department of Orthodontics, Stomatological Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Peng Gao
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaoning Wang
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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156
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Lee JK, Lee HW, Lee S, Lim S, Kang ES. Identification of the novel HLA-B*13:191 allele by next-generation sequencing. HLA 2024; 103:e15467. [PMID: 38575367 DOI: 10.1111/tan.15467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 03/21/2024] [Accepted: 03/24/2024] [Indexed: 04/06/2024]
Abstract
The novel HLA-B*13:191 allele was detected during the HLA typing for kidney transplantation.
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Affiliation(s)
- Jong Kwon Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hyun-Woo Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sookyeon Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sori Lim
- Technical Support Division, BioTIDE Co., Seoul, South Korea
| | - Eun-Suk Kang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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157
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Dhuyser A, Pérès M, Clément S, Morel T, Aarnink A. The novel HLA-DRB1*11:323 allele characterized by two different sequencing-based typing techniques. HLA 2024; 103:e15413. [PMID: 38575349 DOI: 10.1111/tan.15413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 04/06/2024]
Abstract
The novel allele HLA-DRB1*11:323 differs from HLA-DRB1*11:01:02:01 by one non-synonymous nucleotide substitution in exon 2.
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Affiliation(s)
- Adèle Dhuyser
- HLA and Histocompatibility Laboratory, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- IMoPA 6, UMR7365 CNRS, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Michaël Pérès
- HLA and Histocompatibility Laboratory, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Sandra Clément
- HLA and Histocompatibility Laboratory, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Thomas Morel
- HLA and Histocompatibility Laboratory, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Alice Aarnink
- HLA and Histocompatibility Laboratory, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- IMoPA 6, UMR7365 CNRS, Université de Lorraine, Vandœuvre-lès-Nancy, France
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158
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Barriteau CM, Lindholm PF, Hartman K, Pugh J, Sumugod RD, Ramsey G. Weak or discrepant RhD phenotypes: Laboratory management strategies for local patient populations. Transfusion 2024; 64:765-767. [PMID: 38593299 DOI: 10.1111/trf.17796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/23/2024] [Accepted: 02/29/2024] [Indexed: 04/11/2024]
Affiliation(s)
- Christina M Barriteau
- Division of Hematology and Oncology, Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Blood Bank, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Paul F Lindholm
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Blood Bank, Northwestern Memorial Hospital, Chicago, Illinois, USA
| | - Karyn Hartman
- Blood Bank, Northwestern Central DuPage Hospital, Winfield, Illinois, USA
| | - Johnathon Pugh
- Blood Bank, Northwestern Memorial Hospital, Chicago, Illinois, USA
| | | | - Glenn Ramsey
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Blood Bank, Northwestern Memorial Hospital, Chicago, Illinois, USA
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159
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Vellnow N, Gossmann TI, Waxman D. The pseudoentropy of allele frequency trajectories, the persistence of variation, and the effective population size. Biosystems 2024; 238:105176. [PMID: 38479654 DOI: 10.1016/j.biosystems.2024.105176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 03/24/2024]
Abstract
To concisely describe how genetic variation, at individual loci or across whole genomes, changes over time, and to follow transitory allelic changes, we introduce a quantity related to entropy, that we term pseudoentropy. This quantity emerges in a diffusion analysis of the mean time a mutation segregates in a population. For a neutral locus with an arbitrary number of alleles, the mean time of segregation is generally proportional to the pseudoentropy of initial allele frequencies. After the initial time point, pseudoentropy generally decreases, but other behaviours are possible, depending on the genetic diversity and selective forces present. For a biallelic locus, pseudoentropy and entropy coincide, but they are distinct quantities with more than two alleles. Thus for populations with multiple biallelic loci, the language of entropy suffices. Then entropy, combined across loci, serves as a concise description of genetic variation. We used individual based simulations to explore how this entropy behaves under different evolutionary scenarios. In agreement with predictions, the entropy associated with unlinked neutral loci decreases over time. However, deviations from free recombination and neutrality have clear and informative effects on the entropy's behaviour over time. Analysis of publicly available data of a natural D. melanogaster population, that had been sampled over seven years, using a sliding-window approach, yielded considerable variation in entropy trajectories of different genomic regions. These mostly follow a pattern that suggests a substantial effective population size and a limited effect of positive selection on genome-wide diversity over short time scales.
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Affiliation(s)
- Nikolas Vellnow
- TU Dortmund University, Computational Systems Biology, Faculty of Biochemical and Chemical Engineering, Emil-Figge-Str. 66, 44227 Dortmund, Germany.
| | - Toni I Gossmann
- TU Dortmund University, Computational Systems Biology, Faculty of Biochemical and Chemical Engineering, Emil-Figge-Str. 66, 44227 Dortmund, Germany.
| | - David Waxman
- Fudan University, Centre for Computational Systems Biology, ISTBI, 220 Handan Road, Shanghai 200433, People's Republic of China.
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160
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Lion J, Larivière S, Desoutter J, Guillaume N. Characterisation of the novel HLA-B*58:02:04 allele by next-generation sequencing. HLA 2024; 103:e15487. [PMID: 38629729 DOI: 10.1111/tan.15487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/19/2024]
Abstract
HLA-B*58:02:04 differs from HLA-B*58:02:01 by one synonymous nucleotide in codon 215 in exon 4.
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Affiliation(s)
- Julien Lion
- Department Histocompatibility, Amiens University Medical Centre, Amiens, France
| | - Sylvie Larivière
- Department Histocompatibility, Amiens University Medical Centre, Amiens, France
| | - Judith Desoutter
- Department Histocompatibility, Amiens University Medical Centre, Amiens, France
| | - Nicolas Guillaume
- Department Histocompatibility, Amiens University Medical Centre, Amiens, France
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161
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Abdolsamadi M, Rasouli S, Alizadeh Severi A, Khirehgesh MR, Safari F, Mahdieh N, Khazaie H, Soleymani B, Akbari B. The Association Between the 5-Hydroxytryptamine Receptor 2A Gene Variants rs6311 and rs6313 and Obstructive Sleep Apnea in the Iranian Kurdish Population. Genet Test Mol Biomarkers 2024; 28:159-164. [PMID: 38657123 DOI: 10.1089/gtmb.2023.0272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
Introduction: Sleep is one of the most significant parts of everyone's life. Most people sleep for about one-third of their lives. Sleep disorders negatively impact the quality of life. Obstructive sleep apnea (OSA) is a severe sleep disorder that significantly impacts the patient's life and their family members. This study aimed to investigate the relationship between rs6313 and rs6311 polymorphisms in the serotonin receptor type 2A gene and OSA in the Kurdish population. Materials and Methods: The study's population comprises 100 OSA sufferers and 100 healthy people. Polysomnography diagnostic tests were done on both the patient and control groups. The polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) was used to investigate the relationship between OSA and LEPR gene polymorphisms. Results: Statistical analysis showed a significant relationship between genotype frequencies of patient and control groups of rs6311 with OSA in dominant [odds ratio (OR) = 5.203, p < 0.001) and codominant models (OR = 9.7, p < 0.001). Also, there was a significant relationship between genotype frequencies of patient and control groups of rs6313 with OSA in dominant (OR = 10.565, p < 0.001) and codominant models (OR = 5.938, p < 0.001). Conclusions: Findings from the study demonstrated that the two polymorphisms rs6311 and rs6313 could be effective at causing OSA; however, there was no correlation between the severity of the disease and either of the two polymorphisms.
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Affiliation(s)
- Mohammad Abdolsamadi
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Science, Kermanshah, Iran
| | - Sharareh Rasouli
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Science, Kermanshah, Iran
| | - Ali Alizadeh Severi
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Science, Kermanshah, Iran
| | - Mohammad Reza Khirehgesh
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Fatemeh Safari
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nejat Mahdieh
- Cardiogenetic Research Laboratory, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Habibolah Khazaie
- Sleep Disorders Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Bijan Soleymani
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Bahman Akbari
- Sleep Disorders Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
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162
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Zhu N, Xue WJ, An L, Yan XF, Zheng J. The novel HLA-DPB1*1500:01N allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual. HLA 2024; 103:e15483. [PMID: 38605645 DOI: 10.1111/tan.15483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 04/02/2024] [Indexed: 04/13/2024]
Abstract
HLA-DPB1*1500:01N differs from HLA-DPB1*05:01:01:01 by one nucleotide in exon 3.
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Affiliation(s)
- Ning Zhu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
- Department of Laboratory, Shanghai Tissuebank Biotechnology Co., Ltd, Shanghai, China
| | - Wu-Jun Xue
- Department of Kidney Transplantation, Hospital of Nephrology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Lin An
- Department of Laboratory, Shanghai Tissuebank Biotechnology Co., Ltd, Shanghai, China
| | - Xiao-Fei Yan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
| | - Jin Zheng
- Department of Kidney Transplantation, Hospital of Nephrology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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163
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Loginova M, Obukhov I, Paramonov I. Identification of the novel HLA-C allele, HLA-C*07:02:150. HLA 2024; 103:e15471. [PMID: 38566402 DOI: 10.1111/tan.15471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/04/2024]
Abstract
A novel HLA-C*07 allele, now officially designated HLA-C*07:02:150, was identified by next-generation sequencing.
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Affiliation(s)
- Maria Loginova
- Research Laboratory of Applied Immunogenetics, Federal State Budget Research Institution: Kirov Hematology and Blood Transfusion Research Institute under the Federal Medicine and Biology Agency, Kirov, Russia
- Department of Microbiology, Federal State Budget Educational Institution of Higher Professional Education: Vyatka State University, Kirov, Russia
| | - Ivan Obukhov
- Research Laboratory of Applied Immunogenetics, Federal State Budget Research Institution: Kirov Hematology and Blood Transfusion Research Institute under the Federal Medicine and Biology Agency, Kirov, Russia
| | - Igor Paramonov
- Research Laboratory of Applied Immunogenetics, Federal State Budget Research Institution: Kirov Hematology and Blood Transfusion Research Institute under the Federal Medicine and Biology Agency, Kirov, Russia
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164
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He Y, Dong L, Chen N, Zhang W, Zhu F. Identification of two novel HLA-DRB1 alleles, HLA-DRB1*08:03:13 and HLA-DRB1*08:119. HLA 2024; 103:e15462. [PMID: 38568165 DOI: 10.1111/tan.15462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
Compared with HLA-DRB1*08:03:02:01, the alleles HLA-DRB1*08:03:13 and HLA-DRB1*08:119 each show one nucleotide substitution, respectively.
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Affiliation(s)
- Yizhen He
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
| | - Lina Dong
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
| | - Nanying Chen
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
| | - Wei Zhang
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
| | - Faming Zhu
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
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165
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Biswas M, Hossain MS, Ahmed Rupok T, Hossain MS, Sukasem C. The association of CYP2C19 LoF alleles with adverse clinical outcomes in stroke patients taking clopidogrel: An updated meta-analysis. Clin Transl Sci 2024; 17:e13792. [PMID: 38581109 PMCID: PMC10997845 DOI: 10.1111/cts.13792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/11/2024] [Accepted: 03/15/2024] [Indexed: 04/08/2024] Open
Abstract
The aggregated risk of recurrent stroke in stroke/transient ischemic attack (TIA) patients carrying CYP2C19 LoF alleles who take clopidogrel has not been investigated recently, and the available research is limited. This study aimed to perform an updated meta-analysis to assess the association between CYP2C19 LoF alleles and the risk of recurrent stroke in patients taking clopidogrel. Databases were searched for the literature on eligible studies. The end points were recurrent stroke, composite vascular events, and bleeding events. Odds ratios (ORs) were calculated using RevMan software, where p < 0.05 was considered statistically significant. Patients carrying CYP2C19 LoF alleles who were treated with clopidogrel had a significantly increased risk of recurrent ischemic stroke compared with non-carriers (OR 2.18, 96% CI 1.80-2.63; p < 0.00001). The risk of recurrent stroke was only significantly different in Asian patients (OR 2.29, 96% CI 1.88-2.80; p < 0.00001) but not in patients of other ethnicities; however, there were a limited number of studies in other ethnic groups. Both observational studies (OR 2.83, 96% CI 2.20-3.65; p < 0.00001) and RCTs (OR 1.48, 96% CI 1.10-1.98; p = 0.009) found associations with a significantly increased risk of recurrent ischemic stroke. Asian stroke patients or TIA patients carrying CYP2C19 LoF alleles and taking clopidogrel were at a significantly higher risk of recurrent ischemic stroke than non-carriers. Significantly increased risk of recurrent ischemic stroke was found in both observational studies and RCTs.
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Affiliation(s)
- Mohitosh Biswas
- Department of PharmacyUniversity of RajshahiRajshahiBangladesh
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi HospitalMahidol UniversityBangkokThailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC)Ramathibodi HospitalBangkokThailand
| | | | | | | | - Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi HospitalMahidol UniversityBangkokThailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC)Ramathibodi HospitalBangkokThailand
- Pharmacogenomics and Precision Medicine, The Preventive Genomics & Family Check‐up Services Center, Bumrungrad International HospitalBangkokThailand
- Faculty of Pharmaceutical SciencesBurapha UniversitySaensuk, MueangChonburiThailand
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166
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Sang LN, An L, Ding PP, Xue HC, Xing HZ. The novel HLA-DPA1*02:117 allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual. HLA 2024; 103:e15456. [PMID: 38575336 DOI: 10.1111/tan.15456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024]
Abstract
HLA-DPA1*02:117 differs from HLA-DPA1*02:02:02:01 by one nucleotide in exon 2.
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Affiliation(s)
- Li-Na Sang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lin An
- Department of Laboratory, Shanghai Tissuebank Biotechnology Co., Ltd, Shanghai, China
| | - Pei-Pei Ding
- Department of Laboratory, Shanghai Tissuebank Biotechnology Co., Ltd, Shanghai, China
| | - Han-Chun Xue
- Department of Laboratory, Shanghai Tissuebank Biotechnology Co., Ltd, Shanghai, China
| | - Hai-Zhou Xing
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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167
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Tileklioğlu E, Ertabaklar H. [Genetic Diversity of Blastocystis in Diarrheal Cases: Identification of Subtypes and Alleles]. MIKROBIYOL BUL 2024; 58:196-208. [PMID: 38676586 DOI: 10.5578/mb.202498207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2024]
Abstract
Blastocystis spp. are the most common intestinal protozoan parasites detected in human stool samples. While identified long before today, its pathogenicity remains controversial. It is generally asymptomatic but in symptomatic cases, many gastrointestinal symptoms, especially diarrhea, have been associated with Blastocystis infection. In recent years, the relationship between the symptoms observed in cases and Blastocystis subtypes (ST) has been reported. The aim of this study was to detect Blastocystis in diarrheal cases admitted to the Aydın Adnan Menderes University Faculty of Medicine, Department of Parasitology Laboratory, to determine subtypes and allele diversity and to investigate its relationship with clinical symptoms. For this purpose, diarrheal stool samples of 200 cases were included in the study and their demographic characteristics (age, gender, residence) and clinical findings (abdominal pain, dyspepsia, nausea-vomiting, weakness, weight loss, anal itching, rash, urticaria) were recorded. Blastocystis was detected by direct microscope method (DM) and by molecular analyses which were performed with polymerase chain reaction (PCR). Subtype diversity was determined based on DNA sequence analysis by PCR targeting the Blastocystis ribosomal ribonucleic acid small subunit (SSU rRNA) gene. In addition, alleles related to Blastocystis subtypes were determined and statistically compared between all data and clinical findings. In the current study, Blastocystis was detected in 31 (15.5%) samples by DM and in 35 (17.5%) samples by PCR specific to the Blastocystis SSU rRNA gene among 200 diarrheal stool samples. No statistical difference was detected between Blastocystis and demographic characteristics. Dyspepsia and nausea-vomiting symptoms differed significantly in cases with Blastocystis compared to negative ones (p= 0.0025, p= 0.0498). Blastocystis subtype was detected in 33 samples by SSU rRNA sequence analysis, and the subtype distribution was ST1 (n= 10, 30.3%), ST2 (n= 4, 12.1%) and ST3 (n= 19, 57.6%). In the statistical evaluation between clinical findings and Blastocystis subtypes, a relationship was found between dyspepsia and Blastocystis ST3 (p= 0.0039). The allele diversity of Blastocystis subtypes was determined as allele 4 (10/10) in all ST1, allele 11 (2/4) and 12 (2/4) in ST2, allele 34 (14/19), 36 (4/19), and 38 (1/19) in ST3. In conclusion, our study provides important data on the molecular epidemiological characteristics of the Blastocystis by determining positivity, subtypes and alleles in diarrheal cases. Therefore, within the scope of the one health approach, comprehensive molecular epidemiological studies are required to determine the presence and genotypes of Blastocystis in human, animal and environmental samples.
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Affiliation(s)
- Evren Tileklioğlu
- Aydın Adnan Menderes University Faculty of Medicine, Department of Parasitology, Aydın, Türkiye
| | - Hatice Ertabaklar
- Aydın Adnan Menderes University Faculty of Medicine, Department of Parasitology, Aydın, Türkiye
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168
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Tao S, Norman PJ, You X, Kichula KM, Dong L, Chen N, He Y, Chen C, Zhang W, Zhu F. High-resolution KIR and HLA genotyping in three Chinese ethnic minorities reveals distinct origins. HLA 2024; 103:e15482. [PMID: 38625090 PMCID: PMC11027949 DOI: 10.1111/tan.15482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 03/05/2024] [Accepted: 04/02/2024] [Indexed: 04/17/2024]
Abstract
Polymorphism of killer-cell immunoglobulin-like receptors (KIRs) and their HLA class I ligands impacts the effector activity of cytotoxic NK cell and T cell subsets. Therefore, understanding the extent and implications of KIR and HLA class I genetic polymorphism across various populations is important for immunological and medical research. In this study, we conducted a high-resolution investigation of KIR and HLA class I diversity in three distinct Chinese ethnic minority populations. We studied the She, Yugur, and Tajik, and compared them with the Zhejiang Han population (Zhe), which represents the majority Southern Han ethnicity. Our findings revealed that the Tajik population exhibited the most diverse KIR copy number, allele, and haplotype diversity among the four populations. This diversity aligns with their proposed ancestral origin, closely resembling that of Iranian populations, with a relatively higher presence of KIR-B genes, alleles, and haplotypes compared with the other Chinese populations. The Yugur population displayed KIR distributions similar to those of the Tibetans and Southeast Asians, whereas the She population resembled the Zhe and other East Asians, as confirmed by genetic distance analysis of KIR. Additionally, we identified 12.9% of individuals across the three minority populations as having KIR haplotypes characterized by specific gene block insertions or deletions. Genetic analysis based on HLA alleles yielded consistent results, even though there were extensive variations in HLA alleles. The observed variations in KIR interactions, such as higher numbers of 2DL1-C2 interactions in Tajik and Yugur populations and of 2DL3-C1 interactions in the She population, are likely shaped by demographic and evolutionary mechanisms specific to their local environments. Overall, our findings offer valuable insights into the distribution of KIR and HLA diversity among three distinct Chinese ethnic minority populations, which can inform future clinical and population studies.
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Affiliation(s)
- Sudan Tao
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
| | - Paul J. Norman
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States
| | - Xuan You
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
| | - Katherine M. Kichula
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States
| | - Lina Dong
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
| | - Nanying Chen
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
| | - Yizhen He
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
| | - Chen Chen
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
| | - Wei Zhang
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
| | - Faming Zhu
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
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169
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Sakaue S, Weinand K, Isaac S, Dey KK, Jagadeesh K, Kanai M, Watts GFM, Zhu Z, Brenner MB, McDavid A, Donlin LT, Wei K, Price AL, Raychaudhuri S. Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles. Nat Genet 2024; 56:615-626. [PMID: 38594305 DOI: 10.1038/s41588-024-01682-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 02/07/2024] [Indexed: 04/11/2024]
Abstract
Translating genome-wide association study (GWAS) loci into causal variants and genes requires accurate cell-type-specific enhancer-gene maps from disease-relevant tissues. Building enhancer-gene maps is essential but challenging with current experimental methods in primary human tissues. Here we developed a nonparametric statistical method, SCENT (single-cell enhancer target gene mapping), that models association between enhancer chromatin accessibility and gene expression in single-cell or nucleus multimodal RNA sequencing and ATAC sequencing data. We applied SCENT to 9 multimodal datasets including >120,000 single cells or nuclei and created 23 cell-type-specific enhancer-gene maps. These maps were highly enriched for causal variants in expression quantitative loci and GWAS for 1,143 diseases and traits. We identified likely causal genes for both common and rare diseases and linked somatic mutation hotspots to target genes. We demonstrate that application of SCENT to multimodal data from disease-relevant human tissue enables the scalable construction of accurate cell-type-specific enhancer-gene maps, essential for defining noncoding variant function.
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Affiliation(s)
- Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathryn Weinand
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Shakson Isaac
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Kushal K Dey
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Karthik Jagadeesh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Masahiro Kanai
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Gerald F M Watts
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Zhu Zhu
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael B Brenner
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Andrew McDavid
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Laura T Donlin
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alkes L Price
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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170
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Pliota P, Marvanova H, Koreshova A, Kaufman Y, Tikanova P, Krogull D, Hagmüller A, Widen SA, Handler D, Gokcezade J, Duchek P, Brennecke J, Ben-David E, Burga A. Selfish conflict underlies RNA-mediated parent-of-origin effects. Nature 2024; 628:122-129. [PMID: 38448590 PMCID: PMC10990930 DOI: 10.1038/s41586-024-07155-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/02/2024] [Indexed: 03/08/2024]
Abstract
Genomic imprinting-the non-equivalence of maternal and paternal genomes-is a critical process that has evolved independently in many plant and mammalian species1,2. According to kinship theory, imprinting is the inevitable consequence of conflictive selective forces acting on differentially expressed parental alleles3,4. Yet, how these epigenetic differences evolve in the first place is poorly understood3,5,6. Here we report the identification and molecular dissection of a parent-of-origin effect on gene expression that might help to clarify this fundamental question. Toxin-antidote elements (TAs) are selfish elements that spread in populations by poisoning non-carrier individuals7-9. In reciprocal crosses between two Caenorhabditis tropicalis wild isolates, we found that the slow-1/grow-1 TA is specifically inactive when paternally inherited. This parent-of-origin effect stems from transcriptional repression of the slow-1 toxin by the PIWI-interacting RNA (piRNA) host defence pathway. The repression requires PIWI Argonaute and SET-32 histone methyltransferase activities and is transgenerationally inherited via small RNAs. Remarkably, when slow-1/grow-1 is maternally inherited, slow-1 repression is halted by a translation-independent role of its maternal mRNA. That is, slow-1 transcripts loaded into eggs-but not SLOW-1 protein-are necessary and sufficient to counteract piRNA-mediated repression. Our findings show that parent-of-origin effects can evolve by co-option of the piRNA pathway and hinder the spread of selfish genes that require sex for their propagation.
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Affiliation(s)
- Pinelopi Pliota
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Hana Marvanova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Alevtina Koreshova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Yotam Kaufman
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Polina Tikanova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Daniel Krogull
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Andreas Hagmüller
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Sonya A Widen
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Dominik Handler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Joseph Gokcezade
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Peter Duchek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Eyal Ben-David
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Alejandro Burga
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
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171
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Loginova M, Druzhinina S, Paramonov I. Detection of the novel HLA-B*55:01:31, HLA-C*07:1113 alleles and confirmation of HLA-C*12:392. HLA 2024; 103:e15466. [PMID: 38568169 DOI: 10.1111/tan.15466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 03/21/2024] [Accepted: 03/24/2024] [Indexed: 04/05/2024]
Abstract
Novel HLA-B*55:01:31, HLA-C*07:1113 alleles and confirmatory HLA-C*12:392 allele were detected during the HLA typing process.
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Affiliation(s)
- Maria Loginova
- Federal State Budget Research Institution, Kirov Hematology and Blood Transfusion Research Institute under the Federal Medicine and Biology Agency, Kirov, Russia
- Federal State Budget Educational Institution of Higher Professional Education, Vyatka State University, Kirov, Russia
| | - Svetlana Druzhinina
- Federal State Budget Research Institution, Kirov Hematology and Blood Transfusion Research Institute under the Federal Medicine and Biology Agency, Kirov, Russia
| | - Igor Paramonov
- Federal State Budget Research Institution, Kirov Hematology and Blood Transfusion Research Institute under the Federal Medicine and Biology Agency, Kirov, Russia
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172
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Dhuyser A, Pérès M, Clément S, Morel T, Aarnink A. The novel HLA-DRB1*03:210 allele characterised by two different sequencing-based typing techniques. HLA 2024; 103:e15412. [PMID: 38568180 DOI: 10.1111/tan.15412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 04/05/2024]
Abstract
The novel allele HLA-DRB1*03:210 differs from HLA-DRB1*03:01:01:01 by one non-synonymous nucleotide substitution in exon 3.
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Affiliation(s)
- Adèle Dhuyser
- HLA and Histocompatibility Laboratory, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- IMoPA 6, UMR7365 CNRS, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Michaël Pérès
- HLA and Histocompatibility Laboratory, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Sandra Clément
- HLA and Histocompatibility Laboratory, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Thomas Morel
- HLA and Histocompatibility Laboratory, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Alice Aarnink
- HLA and Histocompatibility Laboratory, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- IMoPA 6, UMR7365 CNRS, Université de Lorraine, Vandœuvre-lès-Nancy, France
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173
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Dong L, Chen C, He Y, Zhang W, Zhu F. Identification of the novel HLA-DPA1*02:02:15 allele by next-generation sequencing. HLA 2024; 103:e15469. [PMID: 38575354 DOI: 10.1111/tan.15469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
The novel HLA-DPA1*02:02:15 allele differs from HLA-DPA1*02:02:02:01 by one nucleotide substitution in exon 1.
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Affiliation(s)
- Lina Dong
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
| | - Chen Chen
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
| | - Yizhen He
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
| | - Wei Zhang
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
| | - Faming Zhu
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
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174
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Veller C, Coop GM. Interpreting population- and family-based genome-wide association studies in the presence of confounding. PLoS Biol 2024; 22:e3002511. [PMID: 38603516 PMCID: PMC11008796 DOI: 10.1371/journal.pbio.3002511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 01/19/2024] [Indexed: 04/13/2024] Open
Abstract
A central aim of genome-wide association studies (GWASs) is to estimate direct genetic effects: the causal effects on an individual's phenotype of the alleles that they carry. However, estimates of direct effects can be subject to genetic and environmental confounding and can also absorb the "indirect" genetic effects of relatives' genotypes. Recently, an important development in controlling for these confounds has been the use of within-family GWASs, which, because of the randomness of mendelian segregation within pedigrees, are often interpreted as producing unbiased estimates of direct effects. Here, we present a general theoretical analysis of the influence of confounding in standard population-based and within-family GWASs. We show that, contrary to common interpretation, family-based estimates of direct effects can be biased by genetic confounding. In humans, such biases will often be small per-locus, but can be compounded when effect-size estimates are used in polygenic scores (PGSs). We illustrate the influence of genetic confounding on population- and family-based estimates of direct effects using models of assortative mating, population stratification, and stabilizing selection on GWAS traits. We further show how family-based estimates of indirect genetic effects, based on comparisons of parentally transmitted and untransmitted alleles, can suffer substantial genetic confounding. We conclude that, while family-based studies have placed GWAS estimation on a more rigorous footing, they carry subtle issues of interpretation that arise from confounding.
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Affiliation(s)
- Carl Veller
- Department of Ecology & Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Graham M. Coop
- Department of Evolution and Ecology, and Center for Population Biology, University of California, Davis, California, United States of America
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175
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Thun GA, Gueuning M, Sigurdardottir S, Meyer E, Gourri E, Schneider L, Merki Y, Trost N, Neuenschwander K, Engström C, Frey BM, Meyer S, Mattle-Greminger MP. Novel regulatory variant in ABO intronic RUNX1 binding site inducing A 3 phenotype. Vox Sang 2024; 119:377-382. [PMID: 38226545 DOI: 10.1111/vox.13580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 01/17/2024]
Abstract
BACKGROUND AND OBJECTIVES Mixed-field agglutination in ABO phenotyping (A3, B3) has been linked to genetically different blood cell populations such as in chimerism, or to rare variants in either ABO exon 7 or regulatory regions. Clarification of such cases is challenging and would greatly benefit from sequencing technologies that allow resolving full-gene haplotypes at high resolution. MATERIALS AND METHODS We used long-read sequencing by Oxford Nanopore Technologies to sequence the entire ABO gene, amplified in two overlapping long-range PCR fragments, in a blood donor presented with A3B phenotype. Confirmation analyses were carried out by Sanger sequencing and included samples from other family members. RESULTS Our data revealed a novel heterozygous g.10924C>A variant on the ABO*A allele located in the transcription factor binding site for RUNX1 in intron 1 (+5.8 kb site). Inheritance was shown by the results of the donor's mother, who shared the novel variant and the anti-A specific mixed-field agglutination. CONCLUSION We discovered a regulatory variant in the 8-bp RUNX1 motif of ABO, which extends current knowledge of three other variants affecting the same motif and also leading to A3 or B3 phenotypes. Overall, long-range PCR combined with nanopore sequencing proved powerful and showed great potential as an emerging strategy for resolving cases with cryptic ABO phenotypes.
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Affiliation(s)
- Gian Andri Thun
- Department of Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Morgan Gueuning
- Department of Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Sonja Sigurdardottir
- Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Eduardo Meyer
- Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Elise Gourri
- Department of Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
- Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Linda Schneider
- Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Yvonne Merki
- Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Nadine Trost
- Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Kathrin Neuenschwander
- Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Charlotte Engström
- Department of Immunohematology, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Beat M Frey
- Department of Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
- Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
- Department of Immunohematology, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Stefan Meyer
- Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Maja P Mattle-Greminger
- Department of Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
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176
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AlZahrani S, Alharbi H, Bamrdouf R, Ajebi A, Mohammed A. Identification of the novel HLA-C allele, HLA-C*12:351Q, using next-generation sequencing. HLA 2024; 103:e15493. [PMID: 38647251 DOI: 10.1111/tan.15493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024]
Abstract
The novel allele HLA-C*12:351Q differs from HLA-C*12:02:02:01 by a single nucleotide deletion in exon 5.
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Affiliation(s)
- Saber AlZahrani
- Histocompatibility & Immunogenetics Laboratory, King Fahad Specialist Hospital, Dammam, Saudi Arabia
| | - Hassan Alharbi
- Histocompatibility & Immunogenetics Laboratory, King Fahad Specialist Hospital, Dammam, Saudi Arabia
| | - Rafah Bamrdouf
- Histocompatibility & Immunogenetics Laboratory, King Fahad Specialist Hospital, Dammam, Saudi Arabia
| | - Ali Ajebi
- Histocompatibility & Immunogenetics Laboratory, King Fahad Specialist Hospital, Dammam, Saudi Arabia
| | - Amani Mohammed
- Histocompatibility & Immunogenetics Laboratory, King Fahad Specialist Hospital, Dammam, Saudi Arabia
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177
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Carrillo A, Manzur MJ, Juri Ayub M. Saliva direct PCR protocol for HLA-DQB1*02 genotyping. Int J Immunogenet 2024; 51:89-92. [PMID: 38296826 DOI: 10.1111/iji.12656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/22/2023] [Accepted: 01/22/2024] [Indexed: 02/02/2024]
Abstract
Celiac disease (CD) is an immune disorder, that is triggered by gluten ingestion in genetically predisposed individuals. The HLA-DQB1*02 allele is the main predisposing genetic factor and a candidate for first-line genotyping screening. We designed and validated a simple, DNA purification-free PCR protocol directly from crude saliva, enabling the detection of the DQB1*02 allele. This assay also distinguishes homozygous from heterozygous carriers. We propose this method for use in mass screening and/or epidemiological studies.
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Affiliation(s)
- Angeles Carrillo
- Laboratorio de Desarrollo de Diagnósticos Moleculares, Área Biología Molecular, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
| | - María Jimena Manzur
- Laboratorio de Desarrollo de Diagnósticos Moleculares, Área Biología Molecular, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
| | - Maximiliano Juri Ayub
- Laboratorio de Desarrollo de Diagnósticos Moleculares, Área Biología Molecular, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
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178
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Lara MK, Brabec JL, Hernan AE, Scott RC, Tyler AL, Mahoney JM. Network-based analysis predicts interacting genetic modifiers from a meta-mapping study of spike-wave discharge in mice. Genes Brain Behav 2024; 23:e12879. [PMID: 38444174 PMCID: PMC10915378 DOI: 10.1111/gbb.12879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 11/29/2023] [Accepted: 12/19/2023] [Indexed: 03/07/2024]
Abstract
Absence seizures are characterized by brief lapses in awareness accompanied by a hallmark spike-and-wave discharge (SWD) electroencephalographic pattern and are common to genetic generalized epilepsies (GGEs). While numerous genes have been associated with increased risk, including some Mendelian forms with a single causal allele, most cases of GGE are idiopathic and there are many unknown genetic modifiers of GGE influencing risk and severity. In a previous meta-mapping study, crosses between transgenic C57BL/6 and C3HeB/FeJ strains, each carrying one of three SWD-causing mutations (Gabrg2tm1Spet(R43Q) , Scn8a8j or Gria4spkw1 ), demonstrated an antagonistic epistatic interaction between loci on mouse chromosomes 2 and 7 influencing SWD. These results implicate universal modifiers in the B6 background that mitigate SWD severity through a common pathway, independent of the causal mutation. In this study, we prioritized candidate modifiers in these interacting loci. Our approach integrated human genome-wide association results with gene interaction networks and mouse brain gene expression to prioritize candidate genes and pathways driving variation in SWD outcomes. We considered candidate genes that are functionally associated with human GGE risk genes and genes with evidence for coding or non-coding allele effects between the B6 and C3H backgrounds. Our analyses output a summary ranking of gene pairs, one gene from each locus, as candidates for explaining the epistatic interaction. Our top-ranking gene pairs implicate microtubule function, cytoskeletal stability and cell cycle regulation as novel hypotheses about the source of SWD variation across strain backgrounds, which could clarify underlying mechanisms driving differences in GGE severity in humans.
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Affiliation(s)
- Montana Kay Lara
- Department of Neurological SciencesUniversity of VermontBurlingtonVermontUSA
| | - Jeffrey L. Brabec
- Department of Neurological SciencesUniversity of VermontBurlingtonVermontUSA
| | - Amanda E. Hernan
- Department of Neurological SciencesUniversity of VermontBurlingtonVermontUSA
- Division of NeuroscienceNemours Children's HealthWilmingtonDelawareUSA
- Department of Psychological and Brain SciencesUniversity of DelawareNewarkDelawareUSA
| | - Rod C. Scott
- Division of NeuroscienceNemours Children's HealthWilmingtonDelawareUSA
- Department of Psychological and Brain SciencesUniversity of DelawareNewarkDelawareUSA
| | | | - J. Matthew Mahoney
- Department of Neurological SciencesUniversity of VermontBurlingtonVermontUSA
- The Jackson LaboratoryBar HarborMaineUSA
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179
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Lin Z, Li J, Luo W. A DLB patient with complicated CAA interruptions and intermediate alleles of 43 CAG/CAA repeats in TBP. Acta Neurol Belg 2024; 124:695-697. [PMID: 37632648 DOI: 10.1007/s13760-023-02351-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/10/2023] [Indexed: 08/28/2023]
Affiliation(s)
- Zhiru Lin
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Jiaxiang Li
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Wei Luo
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.
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180
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Tao S, You X, Wang J, Zhang W, He J, Zhu F. Determination for KIR genotype and allele copy number via real-time quantitative PCR method. Immunogenetics 2024; 76:137-143. [PMID: 38206349 DOI: 10.1007/s00251-023-01331-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024]
Abstract
Killer cell immunoglobulin-like receptor (KIR) and human leukocyte antigen (HLA) play crucial roles in regulating NK cell activity. Here, we report a real-time quantitative PCR (qPCR) to genotype all KIR genes and their copy numbers simultaneously. With 18 pairs of locus-specific primers, we identified KIR genes by Ct values and determined KIR copy number using the 2-∆Ct method. Haplotypes were assigned based on KIR gene copy numbers. The real-time qPCR results were consistent with the NGS method, except for one sample with KIR2DL5 discrepancy. qPCR is a multiplex method that can identify KIR copy number, which helps obtain a relatively accurate haplotype structure, facilitating increased KIR research in laboratories where NGS or other high-resolution methods are not available.
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Affiliation(s)
- Sudan Tao
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People's Republic of China
| | - Xuan You
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People's Republic of China
| | - Jielin Wang
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People's Republic of China
| | - Wei Zhang
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People's Republic of China
| | - Ji He
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People's Republic of China
| | - Faming Zhu
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People's Republic of China.
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181
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Moriya A, Otsuka K, Naoi R, Terahata M, Takeda K, Kondo S, Adachi-Yamada T. Creation of Knock-In Alleles of Insulin Receptor Tagged by Fluorescent Proteins mCherry or EYFP in Fruit Fly Drosophila melanogaster. Zoolog Sci 2024; 41:230-243. [PMID: 38587918 DOI: 10.2108/zs230075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/19/2023] [Indexed: 04/10/2024]
Abstract
The insulin/insulin-like growth factor-like signaling (IIS) pathway is highly conserved across metazoans and regulates numerous physiological functions, including development, metabolism, fecundity, and lifespan. The insulin receptor (InR), a crucial membrane receptor in the IIS pathway, is known to be ubiquitously expressed in various tissues, albeit at generally low levels, and its subcellular localization remains incompletely characterized. In this study, we employed CRISPR-mediated mutagenesis in the fruit fly Drosophila to create knock-in alleles of InR tagged with fluorescent proteins (InR::mCherry or InR::EYFP). By inserting the coding sequence of the fluorescent proteins mCherry or EYFP near the end of the coding sequence of the endogenous InR gene, we could trace the natural InR protein through their fluorescence. As an example, we investigated epithelial cells of the male accessory gland (AG), an internal reproductive organ, and identified two distinct patterns of InR::mCherry localization. In young AG, InR::mCherry accumulated on the basal plasma membrane between cells, whereas in mature AG, it exhibited intracellular localization as multiple puncta, indicating endocytic recycling of InR during cell growth. In the AG senescence accelerated by the mutation of Diuretic hormone 31 (Dh31), the presence of InR::mCherry puncta was more pronounced compared to the wild type. These findings raise expectations for the utility of the newly created InR::mCherry/EYFP alleles for studying the precise expression levels and subcellular localization of InR. Furthermore, this fluorescently tagged allele approach can be extended to investigate other membrane receptors with low abundance, facilitating the direct examination of their true expression and localization.
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Affiliation(s)
- Ayano Moriya
- Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Department of Life Science, Faculty of Science, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan
| | - Kei Otsuka
- Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Department of Life Science, Faculty of Science, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan
- Department of Life Science, Faculty of Science, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan
| | - Riku Naoi
- Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Department of Life Science, Faculty of Science, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan
| | - Mayu Terahata
- Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Department of Life Science, Faculty of Science, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan
| | - Koji Takeda
- Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Department of Life Science, Faculty of Science, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan
- Department of Life Science, Faculty of Science, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan
| | - Shu Kondo
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Katsushika-ku, Tokyo 125-8585, Japan
| | - Takashi Adachi-Yamada
- Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Department of Life Science, Faculty of Science, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan,
- Department of Life Science, Faculty of Science, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan
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182
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Li J, Bank C. Dominance and multi-locus interaction. Trends Genet 2024; 40:364-378. [PMID: 38453542 DOI: 10.1016/j.tig.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 03/09/2024]
Abstract
Dominance is usually considered a constant value that describes the relative difference in fitness or phenotype between heterozygotes and the average of homozygotes at a focal polymorphic locus. However, the observed dominance can vary with the genetic background of the focal locus. Here, alleles at other loci modify the observed phenotype through position effects or dominance modifiers that are sometimes associated with pathogen resistance, lineage, sex, or mating type. Theoretical models have illustrated how variable dominance appears in the context of multi-locus interaction (epistasis). Here, we review empirical evidence for variable dominance and how the observed patterns may be captured by proposed epistatic models. We highlight how integrating epistasis and dominance is crucial for comprehensively understanding adaptation and speciation.
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Affiliation(s)
- Juan Li
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland; Swiss Institute for Bioinformatics, Lausanne, Switzerland.
| | - Claudia Bank
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland; Swiss Institute for Bioinformatics, Lausanne, Switzerland
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183
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Dhuyser A, Pérès M, Clément S, Morel T, Aarnink A. The novel HLA-B*44:48:02 allele characterised by two different sequencing-based typing techniques. HLA 2024; 103:e15399. [PMID: 38568109 DOI: 10.1111/tan.15399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 04/05/2024]
Abstract
The novel allele HLA-B*44:48:02 differs from HLA-B*44:48:01 by one synonymous nucleotide substitution in exon 3.
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Affiliation(s)
- Adèle Dhuyser
- HLA and histocompatibility laboratory, CHRU de Nancy, Vandoeuvre les Nancy, France
- IMoPA 6, UMR7365 CNRS, Université de Lorraine, Vandoeuvre-les-Nancy, France
| | - Michaël Pérès
- HLA and histocompatibility laboratory, CHRU de Nancy, Vandoeuvre les Nancy, France
| | - Sandra Clément
- HLA and histocompatibility laboratory, CHRU de Nancy, Vandoeuvre les Nancy, France
| | - Thomas Morel
- HLA and histocompatibility laboratory, CHRU de Nancy, Vandoeuvre les Nancy, France
| | - Alice Aarnink
- HLA and histocompatibility laboratory, CHRU de Nancy, Vandoeuvre les Nancy, France
- IMoPA 6, UMR7365 CNRS, Université de Lorraine, Vandoeuvre-les-Nancy, France
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184
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Shirizadeh A, Razavi Z, Saeedi V, Faradmal J, Roshanaei G, Hajilooi M, Morahan G, Solgi G. Family-based association of HLA-DRB1 and DQB1 alleles and haplotypes in a group of Iranian Type 1 diabetes children. HLA 2024; 103:e15446. [PMID: 38575369 DOI: 10.1111/tan.15446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/06/2024] [Accepted: 03/09/2024] [Indexed: 04/06/2024]
Abstract
This family-based study was conducted in a group of Iranians with Type 1 diabetes (T1D) to investigate the transmission from parents of risk and non-risk HLA alleles and haplotypes, and to estimate the genetic risk score for this disease within this population. A total of 240 T1D subjects including 111 parent-child trios (111 children with T1D, 133 siblings, and 222 parents) and 330 ethnically matched healthy individuals were recruited. High-resolution HLA typing for DRB1/DQB1 loci was performed for all study subjects (n = 925) using polymerase chain reaction-sequence-specific oligonucleotide probe method. The highest predisposing effect on developing T1D was conferred by the following haplotypes both in all subjects and in probands compared to controls: DRB1*04:05-DQB1*03:02 (Pc = 2.97e-06 and Pc = 6.04e-10, respectively), DRB1*04:02-DQB1*03:02 (Pc = 5.94e-17 and Pc = 3.86e-09, respectively), and DRB1*03:01-DQB1*02:01 (Pc = 8.26e-29 and Pc = 6.56e-16, respectively). Conversely, the major protective haplotypes included DRB1*13:01-DQB1*06:03 (Pc = 6.99e-08), DRB1*15:01-DQB1*06:02 (Pc = 2.97e-06) in the cases versus controls. Also, DRB1*03:01-DQB1*02:01/DRB1*04:02|05-DQB1*03:02 and DRB1*03:01-DQB1*02:01/DRB1*03:01-DQB1*02:01 diplotypes conferred the highest predisposing effect in the cases (Pc = 8.65e-17 and Pc = 6.26e-08, respectively) and in probands (Pc = 5.4e-15 and Pc = 0.001, respectively) compared to controls. Transmission disequilibrium test showed that the highest risk was conferred by DRB1*04:02-DQB1*03:02 (Pc = 3.26e-05) and DRB1*03:01-DQB1*02:01 (Pc = 1.78e-12) haplotypes and the highest protection by DRB1*14:01-DQB1*05:03 (Pc = 8.66e-05), DRB1*15:01-DQB1*06:02 (Pc = 0.002), and DRB1*11:01-DQB1*03:01 (Pc = 0.0003) haplotypes. Based on logistic regression analysis, carriage of risk haplotypes increased the risk of T1D development 24.5 times in the Iranian population (p = 5.61e-13). Also, receiver operating characteristic curve analysis revealed a high predictive power of those risk haplotypes in discrimination of susceptible from healthy individuals (area under curve: 0.88, p = 5.5e-32). Our study highlights the potential utility of genetic risk assessment based on HLA diplotypes for predicting T1D risk in individuals, particularly among family members of affected children in our population.
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Affiliation(s)
- Ata Shirizadeh
- Immunology Department, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Zahra Razavi
- Pediatrics Department, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Vahid Saeedi
- Pediatric Endocrinology and Metabolism Department, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Javad Faradmal
- Biostatistics Department, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ghodratollah Roshanaei
- Biostatistics Department, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mehrdad Hajilooi
- Immunology Department, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Grant Morahan
- Centre for Medical Research, University of Western Australia, Perth, Western Australia, Australia
| | - Ghasem Solgi
- Immunology Department, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
- Cancer Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
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185
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Policarpo M, Legendre L, Germon I, Lafargeas P, Espinasa L, Rétaux S, Casane D. The nature and distribution of putative non-functional alleles suggest only two independent events at the origins of Astyanax mexicanus cavefish populations. BMC Ecol Evol 2024; 24:41. [PMID: 38556874 PMCID: PMC10983663 DOI: 10.1186/s12862-024-02226-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 03/14/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Several studies suggested that cavefish populations of Astyanax mexicanus settled during the Late Pleistocene. This implies that the cavefish's most conspicuous phenotypic changes, blindness and depigmentation, and more cryptic characters important for cave life, evolved rapidly. RESULTS Using the published genomes of 47 Astyanax cavefish from la Cueva de El Pachón, El Sótano de la Tinaja, La Cueva Chica and El Sótano de Molino, we searched for putative loss-of-function mutations in previously defined sets of genes, i.e., vision, circadian clock and pigmentation genes. Putative non-functional alleles for four vision genes were identified. Then, we searched genome-wide for putative non-functional alleles in these four cave populations. Among 512 genes with segregating putative non-functional alleles in cavefish that are absent in surface fish, we found an enrichment in visual perception genes. Among cavefish populations, different levels of shared putative non-functional alleles were found. Using a subset of 12 genes for which putative loss-of-function mutations were found, we extend the analysis of shared pseudogenes to 11 cave populations. Using a subset of six genes for which putative loss-of-function mutations were found in the El Sótano del Toro population, where extensive hybridization with surface fish occurs, we found a correlation between the level of eye regression and the amount of putative non-functional alleles. CONCLUSIONS We confirm that very few putative non-functional alleles are present in a large set of vision genes, in accordance with the recent origin of Astyanax mexicanus cavefish. Furthermore, the genome-wide analysis indicates an enrichment of putative loss-of-function alleles in genes with vision-related GO-terms, suggesting that visual perception may be the function chiefly impacted by gene losses related to the shift from a surface to a cave environment. The geographic distribution of putative loss-of-function alleles newly suggests that cave populations from Sierra de Guatemala and Sierra de El Abra share a common origin, albeit followed by independent evolution for a long period. It also supports that populations from the Micos area have an independent origin. In El Sótano del Toro, the troglomorphic phenotype is maintained despite massive introgression of the surface genome.
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Affiliation(s)
- Maxime Policarpo
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement Et Écologie, 91190, Gif-Sur-Yvette, France
- Present Address: Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Laurent Legendre
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement Et Écologie, 91190, Gif-Sur-Yvette, France
| | - Isabelle Germon
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement Et Écologie, 91190, Gif-Sur-Yvette, France
| | - Philippe Lafargeas
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement Et Écologie, 91190, Gif-Sur-Yvette, France
| | - Luis Espinasa
- School of Science, Marist College, Poughkeepsie, NY, USA
| | - Sylvie Rétaux
- Institut de Neuroscience Paris-Saclay, Université Paris-Saclay and CNRS, 91400, Saclay, France.
| | - Didier Casane
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement Et Écologie, 91190, Gif-Sur-Yvette, France.
- Université Paris Cité, UFR Sciences du Vivant, 75013, Paris, France.
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186
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Mohamed AS, Salama AF, Sabaa MA, Toraih E, Elshazli RM. GEMIN4 Variants: Risk Profiling, Bioinformatics, and Dynamic Simulations Uncover Susceptibility to Bladder Carcinoma. Arch Med Res 2024; 55:102970. [PMID: 38401326 DOI: 10.1016/j.arcmed.2024.102970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/11/2024] [Accepted: 02/13/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND The relationship between GEMIN4 genetic variants and cancer, especially bladder carcinoma (BLCA), has been explored without conclusive results. This study aims to elucidate the link between GEMIN4 polymorphisms and BLCA susceptibility through genetic analyses, bioinformatics, and molecular dynamics (MD) simulations. METHODS A cohort of 249 participants (121 BLCA patients and 128 unrelated controls) was enrolled. PCR was employed for allelic discrimination of GEMIN4 variants, followed by subgroup stratification, haplotype analyses, structural prediction using the AlphaFold2 prediction tool, subsequent MD simulations, structural analysis, and residue interaction mapping using Desmond, UCSF ChimeraX, and Cytoscape softwares. RESULTS The rs.2740348*G variant demonstrated a protective role against BLCA in allelic (OR = 0.55, p = 0.002) and recessive (OR = 0.54, p = 0.017) models, whereas the rs.7813*T variant increased BLCA risk under the recessive model (OR = 1.90, p = 0.019). Haplotype analysis revealed a significant association between GEMIN4 haplotype (rs.2740348*C/rs.7813*T) with increased BLCA risk (OR = 2.01, p = 0.004). Univariate analysis revealed associations of the variants with albumin levels and absolute neutrophil count in BLCA patients. Pathogenicity evaluation categorized p.Gln450Glu as neutral and p.Arg1033Cys as deleterious. MD simulations revealed structural alterations and conformational shifts in the GEMIN4 protein induced by the Glu450 and Cys1033 mutations. CONCLUSIONS The study highlights the dual role of GEMIN4 variants in BLCA susceptibility, with rs.2740348 conferring protection and rs.7813 increasing risk. The Glu450 residue positively impacted protein stability, while Cys1033 had a detrimental effect on protein function. These findings underscore the significance of GEMIN4 variants in BLCA susceptibility and pave the way for future diagnostic and therapeutic initiatives.
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Affiliation(s)
- Abdallah S Mohamed
- Biochemistry Division, Department of Chemistry, Faculty of Science, Tanta University, Tanta, Egypt
| | - Afrah F Salama
- Biochemistry Division, Department of Chemistry, Faculty of Science, Tanta University, Tanta, Egypt
| | - Magdy A Sabaa
- Department of Urology, Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Eman Toraih
- Endocrine and Oncology Division, Department of Surgery, Tulane University School of Medicine, New Orleans, LA, USA; Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt.
| | - Rami M Elshazli
- Biochemistry and Molecular Genetics Unit, Department of Basic Sciences, Faculty of Physical Therapy, Horus University - Egypt, New Damietta, Egypt.
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187
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Rico-Torres CP, Valenzuela-Moreno LF, Robles-González E, Cruz-Tamayo AA, Huchin-Cab M, Pérez-Flores J, Xicoténcatl-García L, Luna-Pastén H, Ortiz-Alegría LB, Cañedo-Solares I, Cedillo-Peláez C, García-Lacy F, Caballero-Ortega H. Genotyping of Toxoplasma gondii in domestic animals from Campeche, México, reveals virulent genotypes and a recombinant ROP5 allele. Parasitology 2024; 151:363-369. [PMID: 38379406 PMCID: PMC11044059 DOI: 10.1017/s0031182024000106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/27/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024]
Abstract
Toxoplasma gondii has at least 318 genotypes distributed worldwide, and tropical regions usually have greater genetic diversity. Campeche is a state located in the southeastern region of México and has favourable climate conditions for the replication and dissemination of this protozoan, similar to those in South American countries where broad genetic diversity has been described. Thus, in this study, 4 T. gondii isolates were obtained from tissues of stray dogs and free-range chickens in Campeche, México, and were genotyped by Mn-PCR-RFLP with 10 typing markers (SAG1, altSAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico) and 5 virulence markers (CS3, ROP16, ROP17, ROP18 and ROP5) to provide new information about the distribution and virulence prediction of T. gondii genotypes. Two isolates of T. gondii genotype #116 and 2 of genotype #38 were obtained from stray dogs and chickens, respectively. The parasite load found in these species was between <50 and more than 35 000 tachyzoites per mg of tissue. Virulence marker genotyping revealed a recombinant 1&3 ROP5 RFLP pattern in 2 ToxoDB #116 isolates with no prediction of virulence in a murine model, while in the 2 ToxoDB #38 isolates, the ROP18/ROP5 combination predicted high virulence. Considering all the typed markers, there is a predominance of type I and III alleles, as constantly reported for the isolates characterized in various regions of México. It is crucial to determine their phenotype to corroborate the genetic virulence profile of the T. gondii isolates obtained in this study.
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Affiliation(s)
| | | | | | | | - Miguel Huchin-Cab
- Facultad de Ciencias Agropecuarias, Universidad Autónoma de Campeche, México
| | - Jonathan Pérez-Flores
- Departamento de Observación y Estudio de la Tierra, la Atmósfera y el Océano, El Colegio de la Frontera Sur, México
| | | | - Héctor Luna-Pastén
- Laboratorio de Inmunología Experimental, Instituto Nacional de Pediatría, México
| | | | - Irma Cañedo-Solares
- Laboratorio de Inmunología Experimental, Instituto Nacional de Pediatría, México
| | | | - Fernando García-Lacy
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, México
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188
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Aloui C, Neumann L, Bergametti F, Sartori E, Herbreteau M, Maillard A, Coste T, Morel H, Hervé D, Chabriat H, Timsit S, Viakhireva I, Denoyer Y, Allibert R, Demurger F, Gollion C, Vermersch P, Marchelli F, Blugeon C, Lemoine S, Tourtier-Bellosta C, Brouazin A, Leutenegger AL, Pipiras E, Tournier-Lasserve E. An AluYa5 Insertion in the 3'UTR of COL4A1 and Cerebral Small Vessel Disease. JAMA Netw Open 2024; 7:e247034. [PMID: 38630472 PMCID: PMC11024774 DOI: 10.1001/jamanetworkopen.2024.7034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/19/2024] [Indexed: 04/19/2024] Open
Abstract
Importance Cerebral small vessel diseases (CSVDs) account for one-fifth of stroke cases. Numerous familial cases remain unresolved after routine screening of known CSVD genes. Objective To identify novel genes and mechanisms associated with familial CSVD. Design, Setting, and Participants This 2-stage study involved linkage analysis and a case-control study; linkage analysis and whole exome and genome sequencing were used to identify candidate gene variants in 2 large families with CSVD (9 patients with CSVD). Then, a case-control analysis was conducted on 246 unrelated probands, including probands from these 2 families and 244 additional probands. All probands (clinical onset Main Outcomes and Measures A pathogenic AluYa5 insertion was identified within the COL4A1 3'UTR in the 2 large families with CSVD. Reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR), Western blot, and long-read RNA sequencing were used to investigate outcomes associated with the insertion using patient fibroblasts. Clinical and magnetic resonance imaging features of probands with variants and available relatives were assessed. Results Among 246 probands (141 females [57.3%]; median [IQR] age at referral, 56 [49-64] years), 7 patients of French ancestry carried the insertion. This insertion was absent in 467 healthy French individuals in a control group (odds ratio, ∞; 95% CI, 2.78 to ∞; P = 5 × 10-4) and 10 847 individuals from the gnomAD structural variant database (odds ratio, ∞; 95% CI, 64.77 to ∞; P = 2.42 × 10-12). In these 7 patients' families, 19 family members with CSVD carried the insertion. RT-qPCR and Western blot showed an upregulation of COL4A1 mRNA (10.6-fold increase; 95% CI, 1.4-fold to 17.1-fold increase) and protein levels (2.8-fold increase; 95% CI, 2.1-fold to 3.5-fold increase) in patient vs control group fibroblasts. Long-read RNA sequencing data showed that the insertion was associated with perturbation in the use of canonical COL4A1 polyadenylation signals (approximately 87% of isoforms transcribed from the wild type allele vs 5% of isoforms transcribed from the allele with the insertion used the 2 distal canonical polyadenylation signals). The main clinical feature of individuals with CSVD was the recurrence of pontine ischemic lesions starting at an early age (17 of 19 patients [89.5%]). Conclusions and relevance This study found a novel mechanism associated with COL4A1 upregulation and a highly penetrant adult-onset CSVD. These findings suggest that quantitative alterations of the cerebrovascular matrisome are associated with CSVD pathogenesis, with diagnostic and therapeutic implications.
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Affiliation(s)
- Chaker Aloui
- NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France
| | - Lisa Neumann
- NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France
| | - Françoise Bergametti
- NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France
| | - Eric Sartori
- Service de Neurologie, Centre Hospitalier Bretagne Sud, Lorient, France
| | - Marc Herbreteau
- Service de Neurologie, Centre Hospitalier Bretagne Sud, Lorient, France
| | - Arnaud Maillard
- Assistance Publique-Hôpitaux de Paris, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, Paris, France
| | - Thibault Coste
- NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France
- Assistance Publique-Hôpitaux de Paris, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, Paris, France
| | - Hélène Morel
- NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France
- Assistance Publique-Hôpitaux de Paris, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, Paris, France
| | - Dominique Hervé
- NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France
- Assistance Publique-Hôpitaux de Paris, Service de Neurologie, Hôpital Lariboisière, Paris, France
| | - Hugues Chabriat
- NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France
- Assistance Publique-Hôpitaux de Paris, Service de Neurologie, Hôpital Lariboisière, Paris, France
| | - Serge Timsit
- Service de Neurologie Vasculaire, Centre Hospitalier Régional Universitaire de Brest, Brest, France
| | - Irina Viakhireva
- Service de Neurologie Vasculaire, Centre Hospitalier Régional Universitaire de Brest, Brest, France
| | - Yves Denoyer
- Service de Neurologie, Centre Hospitalier Bretagne Sud, Lorient, France
- Université de Rennes, Laboratoire Traitement du Signal et de l'Image, Institut National de la Santé Et de la Recherche Médicale Unité Mixte de Recherche 1099, Rennes, France
| | - Rémi Allibert
- Service de Neurologie, Unité Neurovasculaire, Centre Hospitalier Universitaire de Saint Etienne, Saint Etienne, France
| | - Florence Demurger
- Service de Neurologie, Unité Neurovasculaire, Centre Hospitalier Bretagne Atlantique, Vannes, France
| | - Cedric Gollion
- Service de Neurologie, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Patrick Vermersch
- Univ. Lille, Institut National de la Santé Et de la Recherche Médicale Unité Mixte de Recherche 1172 LilNCog, Centre Hospitalier Universitaire Lille, Fédérations Hospitalo-Universitaire Precise, Lille, France
| | - Florence Marchelli
- Assistance Publique-Hôpitaux de Paris, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, Paris, France
| | - Corinne Blugeon
- GenomiqueENS, Institut de Biologie de l’Ecole Normale Supérieur, Département de biologie, École Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé Et de la Recherche Médicale, Université Paris Sciences et Lettres, Paris, France
| | - Sophie Lemoine
- GenomiqueENS, Institut de Biologie de l’Ecole Normale Supérieur, Département de biologie, École Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé Et de la Recherche Médicale, Université Paris Sciences et Lettres, Paris, France
| | | | - Alexis Brouazin
- Service de neurologie, Centre Hospitalier de Cornouaille, Quimper, France
| | - Anne-Louise Leutenegger
- NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France
| | - Eva Pipiras
- NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France
- Assistance Publique-Hôpitaux de Paris, Hôpitaux Jean Verdier et Armand Trousseau, Université Sorbonne Paris Nord, Bobigny, France
| | - Elisabeth Tournier-Lasserve
- NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France
- Assistance Publique-Hôpitaux de Paris, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, Paris, France
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189
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Liu P, Wilson P, Redquest B, Keobouasone S, Manseau M. Seq2Sat and SatAnalyzer toolkit: Towards comprehensive microsatellite genotyping from sequencing data. Mol Ecol Resour 2024; 24:e13929. [PMID: 38289068 DOI: 10.1111/1755-0998.13929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 03/06/2024]
Abstract
Accurate and efficient microsatellite loci genotyping is an essential process in population genetics that is also used in various demographic analyses. Protocols for next-generation sequencing of microsatellite loci enable high-throughput and cross-compatible allele scoring, common issues that are not addressed by conventional capillary-based approaches. To improve this process, we have developed an all-in-one software, called Seq2Sat (sequence to microsatellite), in C++ to support automated microsatellite genotyping. It directly takes raw reads of microsatellite amplicons and conducts read quality control before inferring genotypes based on depth-of-read, read ratio, sequence composition and length. We have also developed a module for sex identification based on sex chromosome-specific locus amplicons. To allow for greater user access and complement autoscoring, we developed SatAnalyzer (microsatellite analyzer), a user-friendly web-based platform that conducts reads-to-report analyses by calling Seq2Sat for genotype autoscoring and produces interactive genotype graphs for manual editing. SatAnalyzer also allows users to troubleshoot multiplex optimization by analysing read quality and distribution across loci and samples in support of high-quality library preparation. To evaluate its performance, we benchmarked our toolkit Seq2Sat/SatAnalyzer against a conventional capillary gel method and existing microsatellite genotyping software, MEGASAT, using two datasets. Results showed that SatAnalyzer can achieve >99.70% genotyping accuracy and Seq2Sat is ~5 times faster than MEGASAT despite many more informative tables and figures being generated. Seq2Sat and SatAnalyzer are freely available on github (https://github.com/ecogenomicscanada/Seq2Sat) and dockerhub (https://hub.docker.com/r/rocpengliu/satanalyzer).
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Affiliation(s)
- Peng Liu
- Science and Technology, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Paul Wilson
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | | | - Sonesinh Keobouasone
- Science and Technology, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Micheline Manseau
- Science and Technology, Environment and Climate Change Canada, Ottawa, Ontario, Canada
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190
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Sun Y, Wang Z, Kang Y, Li J, Liu Z. The novel HLA-C*03:94:02 allele identified by next-generation sequencing in a Chinese individual. HLA 2024; 103:e15453. [PMID: 38568176 DOI: 10.1111/tan.15453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/10/2024] [Accepted: 03/12/2024] [Indexed: 04/05/2024]
Abstract
HLA-C*03:94:02 differs from HLA-C*03:94:01 by a single nucleotide substitution in exon 2 (codon 17 GGA->GGG).
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Affiliation(s)
- Yamin Sun
- HLA Laboratory, Henan Red Cross Blood Center, Zhengzhou, Henan, China
- Henan Blood Safety Research Institute, Zhengzhou, Henan, China
| | - Ziqing Wang
- HLA Laboratory, Henan Red Cross Blood Center, Zhengzhou, Henan, China
- Henan Blood Safety Research Institute, Zhengzhou, Henan, China
| | - Yiqing Kang
- HLA Laboratory, Henan Red Cross Blood Center, Zhengzhou, Henan, China
- Henan Blood Safety Research Institute, Zhengzhou, Henan, China
| | - Jianbin Li
- HLA Laboratory, Henan Red Cross Blood Center, Zhengzhou, Henan, China
- Henan Blood Safety Research Institute, Zhengzhou, Henan, China
| | - Zheng Liu
- HLA Laboratory, Henan Red Cross Blood Center, Zhengzhou, Henan, China
- Henan Blood Safety Research Institute, Zhengzhou, Henan, China
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191
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Kambala A, Rajeh A, Joel MZ, Ma E, Cornman H, Zhang J, Kwatra SG. HLA DRB5∗01:01 is associated with pruritus in individuals with Fitzpatrick skin type IV-VI. J Am Acad Dermatol 2024; 90:855-857. [PMID: 38104778 DOI: 10.1016/j.jaad.2023.11.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/16/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023]
Affiliation(s)
- Anusha Kambala
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ahmad Rajeh
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marina Z Joel
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Emily Ma
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hannah Cornman
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jeni Zhang
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Shawn G Kwatra
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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192
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Karaosmanoglu B, Imren G, Utine E, Taylan Sekeroglu H, Taskiran EZ. Allele-specific antisense oligonucleotides for the treatment of BEST1-related dominantly inherited retinal diseases: An in vitro model. Exp Eye Res 2024; 241:109833. [PMID: 38369231 DOI: 10.1016/j.exer.2024.109833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 10/22/2023] [Accepted: 02/15/2024] [Indexed: 02/20/2024]
Abstract
Retinal dystrophies are a common health problem worldwide that are currently incurable due to the inability of retinal cells to regenerate. Inherited retinal diseases (IRDs) are a diverse group of disorders characterized by progressive vision loss caused by photoreceptor cell dysfunction. The eye has always been an attractive organ for the development of novel therapies due to its independent access to the systemic pathway. Moreover, anti-sense oligonucleotides (ASOs), which facilitate manipulation of unwanted mRNAs via degradation or splicing, are undergoing rapid development and have been clinically deployed for the treatment of several diseases. The primary aim of this study was to establish a reliable in vitro model utilizing induced photoreceptor-like cells (PRCs) for assessing the efficacy and safety of ASOs targeting the BEST1 gene. Despite advances in gene therapy, effective treatments for a broad range of IRDs remain limited. An additional aim was to develop an in vitro model for evaluating RNA-based therapeutics, specifically ASOs, for the treatment in IRDs. Firstly, a cell culture model was established by induction of PRCs from dermal fibroblasts via direct programming. The induced PRCs were characterized at both the transcriptomic and protein level. Then, a common single nucleotide polymorphism (SNP) was identified in the BEST1 gene (rs1800007) for targeting with ASOs. ASOs were designed using the GapmeR strategy to target multiple alleles of this SNP, which is potentially suitable for a large proportion of the population. The efficacy and possible off-target effects of these ASOs were also analyzed in the induced PRC model. The findings show that the selected ASOs achieved allele-specific mRNA degradation with virtually no off-target effects on the global transcriptome profile, indicating their potential as safe and effective therapeutic agents. The presented in vitro model is a valuable platform for testing personalized IRD treatments and should inspire further research on RNA-based therapeutics. To the best of our knowledge this study is the first to test RNA-based therapeutics involving the use of ASOs in an induced PRC model. Based on the present findings, it will be possible to establish an ex vivo disease model using dermal fibroblast samples from affected individuals. In other words, the disease model and the ASOs that were successfully designed in this study can serve as a useful platform for the testing of personalized treatments for IRDs.
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Affiliation(s)
- Beren Karaosmanoglu
- Hacettepe University, Faculty of Medicine, Department of Medical Genetics, Turkey
| | - Gozde Imren
- Hacettepe University, Faculty of Medicine, Department of Medical Genetics, Turkey
| | - Eda Utine
- Hacettepe University, Faculty of Medicine, Department of Pediatric Genetics, Turkey
| | | | - Ekim Z Taskiran
- Hacettepe University, Faculty of Medicine, Department of Medical Genetics, Turkey.
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193
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Sugio T, Uchida N, Miyawaki K, Ohno Y, Eto T, Mori Y, Yoshimoto G, Kikushige Y, Kunisaki Y, Mizuno S, Nagafuji K, Iwasaki H, Kamimura T, Ogawa R, Miyamoto T, Taniguchi S, Akashi K, Kato K. Prognostic impact of HLA supertype mismatch in single-unit cord blood transplantation. Bone Marrow Transplant 2024; 59:466-472. [PMID: 38238452 DOI: 10.1038/s41409-023-02183-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 11/26/2023] [Accepted: 12/12/2023] [Indexed: 04/06/2024]
Abstract
The "human leukocyte antigen (HLA) supertype" is a functional classification of HLA alleles, which was defined by structural features and peptide specificities, and has been reportedly associated with the clinical outcomes of viral infections and autoimmune diseases. Although the disparity in each HLA locus was reported to have no clinical significance in single-unit cord blood transplantation (sCBT), the clinical significance of the HLA supertype in sCBT remains unknown. Therefore, we retrospectively analyzed clinical data of 1603 patients who received sCBT in eight institutes in Japan between 2000 and 2017. Each HLA allele was categorized into 19 supertypes, and the prognostic effect of disparities was then assessed. An HLA-B supertype mismatch was identified as a poor prognostic factor (PFS: hazard ratio [HR] = 1.23, p = 0.00044) and was associated with a higher cumulative incidence (CI) of relapse (HR = 1.24, p = 0.013). However, an HLA-B supertype mismatch was not associated with the CI of acute and chronic graft-versus-host-disease. The multivariate analysis for relapse and PFS showed the significance of an HLA-B supertype mismatch independent of allelic mismatches, and other previously reported prognostic factors. HLA-B supertype-matched grafts should be selected in sCBT.
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Affiliation(s)
- Takeshi Sugio
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
- Divisions of Oncology and Hematology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Naoyuki Uchida
- Department of Hematology, Toranomon Hospital, Tokyo, Japan
| | - Kohta Miyawaki
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Yuju Ohno
- Department of Hematology, Kitakyushu Municipal Medical Center, Fukuoka, Japan
| | - Tetsuya Eto
- Department of Hematology, Hamanomachi Hospital, Fukuoka, Japan
| | - Yasuo Mori
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Goichi Yoshimoto
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Yoshikane Kikushige
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Yuya Kunisaki
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shinichi Mizuno
- Department of Health Sciences, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koji Nagafuji
- Department of Medicine, Kurume University School of Medicine, Fukuoka, Japan
| | - Hiromi Iwasaki
- Department of Hematology, National Hospital Organization Kyushu Medical Center, Fukuoka, Japan
| | | | - Ryosuke Ogawa
- Department of Hematology, JCHO Kyushu Hospital, Fukuoka, Japan
| | - Toshihiro Miyamoto
- Department of Hematology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Ishikawa, Japan
| | - Shuichi Taniguchi
- Department of Hematology, Toranomon Hospital, Tokyo, Japan
- Department of Hematology, Hamanomachi Hospital, Fukuoka, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Koji Kato
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan.
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194
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Hendrickson PG, Oristian KM, Browne MR, Luo L, Ma Y, Cardona DM, Nash JO, Ballester PL, Davidson S, Shlien A, Linardic CM, Kirsch DG. Spontaneous expression of the CIC::DUX4 fusion oncoprotein from a conditional allele potently drives sarcoma formation in genetically engineered mice. Oncogene 2024; 43:1223-1230. [PMID: 38413794 PMCID: PMC11027086 DOI: 10.1038/s41388-024-02984-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/07/2024] [Accepted: 02/14/2024] [Indexed: 02/29/2024]
Abstract
CIC::DUX4 sarcoma (CDS) is a rare but highly aggressive undifferentiated small round cell sarcoma driven by a fusion between the tumor suppressor Capicua (CIC) and DUX4. Currently, there are no effective treatments and efforts to identify and translate better therapies are limited by the scarcity of patient tumor samples and cell lines. To address this limitation, we generated three genetically engineered mouse models of CDS (Ch7CDS, Ai9CDS, and TOPCDS). Remarkably, chimeric mice from all three conditional models developed spontaneous soft tissue tumors and disseminated disease in the absence of Cre-recombinase. The penetrance of spontaneous (Cre-independent) tumor formation was complete irrespective of bi-allelic Cic function and the distance between adjacent loxP sites. Characterization of soft tissue and presumed metastatic tumors showed that they consistently expressed the CIC::DUX4 fusion protein and many downstream markers of the disease credentialing the models as CDS. In addition, tumor-derived cell lines were generated and ChIP-seq was preformed to map fusion-gene specific binding using an N-terminal HA epitope tag. These datasets, along with paired H3K27ac ChIP-sequencing maps, validate CIC::DUX4 as a neomorphic transcriptional activator. Moreover, they are consistent with a model where ETS family transcription factors are cooperative and redundant drivers of the core regulatory circuitry in CDS.
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Affiliation(s)
- Peter G Hendrickson
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | | | - MaKenna R Browne
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
- Developmental and Stem Cell Biology Program, Duke University Medical Center, Durham, NC, USA
| | - Lixia Luo
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Yan Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Diana M Cardona
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Joshua O Nash
- Program in Genetics and Genome Biology, The Hospital for Sick Children (SickKids), University of Toronto, Toronto, ON, Canada
- Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Pedro L Ballester
- Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Scott Davidson
- Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children (SickKids), University of Toronto, Toronto, ON, Canada
- Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Corinne M Linardic
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - David G Kirsch
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA.
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA.
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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195
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Honkanen L, Loechel R, Davison S, Donner J, Anderson H. Canine coat color E locus updates: Identification of a new MC1R variant causing 'sable' coat color in English Cocker Spaniels and a proposed update to the E locus dominance hierarchy. Anim Genet 2024; 55:291-295. [PMID: 38282569 DOI: 10.1111/age.13398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/21/2023] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
The coat color phenotype 'sable' occurs in the English Cocker Spaniel dog breed. It closely resembles other canine color patterns known as domino/grizzle/pied (eA allele) and grizzle/domino (eG allele) determined by variants in the melanocortin 1 receptor gene (MC1R; 'extension' or E locus), a key multi-allele regulator of coat color. We examined genetic variation in MC1R, and found one new non-synonymous variant, c.250G>A (p.(Asp84Asn)), consistently associated with the English Cocker Spaniel 'sable' phenotype. We propose calling this newly identified allele eH and further show that the eA , eH and eG (previously known as EG ) alleles associate with similar phenotypes in dogs impacting genotypes regulated by beta-defensin 103 gene (CBD103; K locus) and agouti signaling protein gene (ASIP; A locus) in the absence of the EM and E alleles. This suggests that all three alleles are putative reduced-function variants of the MC1R gene. We propose the revised and updated E locus dominance hierarchy to be EM > E > eA /eH /eG > e1-3 .
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Affiliation(s)
- Leena Honkanen
- Wisdom Panel, Mars Petcare Science & Diagnostics, Helsinki, Finland
| | | | - Stephen Davison
- Wisdom Panel, Mars Petcare Science & Diagnostics, Leicestershire, UK
| | - Jonas Donner
- Wisdom Panel, Mars Petcare Science & Diagnostics, Helsinki, Finland
| | - Heidi Anderson
- Wisdom Panel, Mars Petcare Science & Diagnostics, Helsinki, Finland
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196
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Tang W, Wang J, Dai T, Qiu H, Liu C, Chen S, Hu Z. Association of leptin receptor polymorphisms with susceptibility of non-small cell lung cancer: Evidence from 2249 subjects. Cancer Med 2024; 13:e7178. [PMID: 38659416 PMCID: PMC11043686 DOI: 10.1002/cam4.7178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Abstract
Non-small cell lung cancer (NSCLC) is increasing dramatically. It is believed that energy metabolism-related genes could play an important role in etiology of NSCLC. In this study, we sought to assess the correlation between three LEPR single nucleotide polymorphisms (rs1137101, rs1137100 and rs6588147) with NSCLS susceptibility. In total, 1193 NSCLC cases and 1056 controls were included. SNPscan™ genotyping method was used to analyze the genotypes of LEPR polymorphisms. Compared to rs6588147 GG in LEPR gene, this study identified a protective role of LEPR rs6588147 GA and GA/AA for the occurrence of NSCLC (GA vs. GG [p = 0.021] and GA/AA vs. GG [p = 0.030]). As well, we found that a protective role of LEPR rs6588147 for the occurrence of non-SCC subgroup (p < 0.05). By logistic regression analysis, we found that the rs6588147 A allele related genotypes might play a protective role for the occurrence of NSCLC in drinking, BMI ≥24 kg/m2, smoking and male subgroups. We also found that the rs1137101 A allele related genotypes played a protective role for the occurrence of NSCLC in male, younger participants (under 59 years) and overweight/obesity (BMI ≥24 kg/m2) subgroups. We found that LEPR Ars1037100Ars1037101Ars6588147 haplotype might play a protective role for the occurrence of NSCLC (p = 0.013). In addition, our findings indicated that LEPR rs1137100 G>A SNP might increase the risk of lymph node metastases (p = 0.038). This study highlights that LEPR rs6588147, rs1137101 genotypes and LEPR Ars1037100Ars1037101Ars6588147 haplotype are correlated with the occurrence of NSCLC. LEPR rs1137100 G>A SNP increases the risk of lymph node metastases.
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Affiliation(s)
- Weifeng Tang
- Departments of Esophageal Surgery and Thoracic SurgeryNanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical SchoolNanjing210008Jiangsu ProvinceChina
| | - Jian Wang
- Department of Cardiothoracic SurgeryAffiliated Yixing People's Hospital of Jiangsu UniversityYixingJiangsu ProvinceChina
| | - Ting Dai
- Department of PharmacyAffiliated Yixing People's Hospital of Jiangsu UniversityYixingJiangsu ProvinceChina
| | - Hao Qiu
- Department of Laboratory Medicine, School of MedicineJiangsu UniversityZhenjiangJiangsu ProvinceChina
| | - Chao Liu
- Department of Cardiothoracic SurgeryAffiliated People's Hospital of Jiangsu UniversityZhenjiangJiangsu ProvinceChina
| | - Shuchen Chen
- Department of Thoracic SurgeryFujian Medical University Union HospitalFuzhouFujian ProvinceChina
| | - Zhendong Hu
- Departments of Esophageal Surgery and Thoracic SurgeryNanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical SchoolNanjing210008Jiangsu ProvinceChina
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197
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Klementieva NV, Lunev EA, Shmidt AA, Loseva EM, Savchenko IM, Svetlova EA, Galkin II, Polikarpova AV, Usachev EV, Vassilieva SG, Marina VI, Dzhenkova MA, Romanova AD, Agutin AV, Timakova AA, Reshetov DA, Egorova TV, Bardina MV. RNA Interference Effectors Selectively Silence the Pathogenic Variant GNAO1 c.607 G > A In Vitro. Nucleic Acid Ther 2024; 34:90-99. [PMID: 38215303 DOI: 10.1089/nat.2023.0043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024] Open
Abstract
RNA interference (RNAi)-based therapeutics hold the potential for dominant genetic disorders, enabling sequence-specific inhibition of pathogenic gene products. We aimed to direct RNAi for the selective suppression of the heterozygous GNAO1 c.607 G > A variant causing GNAO1 encephalopathy. By screening short interfering RNA (siRNA), we showed that GNAO1 c.607G>A is a druggable target for RNAi. The si1488 candidate achieved at least twofold allelic discrimination and downregulated mutant protein to 35%. We created vectorized RNAi by incorporating the si1488 sequence into the short hairpin RNA (shRNA) in the adeno-associated virus (AAV) vector. The shRNA stem and loop were modified to improve the transcription, processing, and guide strand selection. All tested shRNA constructs demonstrated selectivity toward mutant GNAO1, while tweaking hairpin structure only marginally affected the silencing efficiency. The selectivity of shRNA-mediated silencing was confirmed in the context of AAV vector transduction. To conclude, RNAi effectors ranging from siRNA to AAV-RNAi achieve suppression of the pathogenic GNAO1 c.607G>A and discriminate alleles by the single-nucleotide substitution. For gene therapy development, it is crucial to demonstrate the benefit of these RNAi effectors in patient-specific neurons and animal models of the GNAO1 encephalopathy.
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Affiliation(s)
- Natalia V Klementieva
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | - Evgenii A Lunev
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna A Shmidt
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Irina M Savchenko
- Marlin Biotech LLC, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina A Svetlova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | - Ivan I Galkin
- Marlin Biotech LLC, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna V Polikarpova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | - Evgeny V Usachev
- Laboratory of Translational Biomedicine, Gamaleya National Research Center for Epidemiology, Moscow, Russia
| | - Svetlana G Vassilieva
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | | | - Marina A Dzhenkova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | - Anna D Romanova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
| | - Anton V Agutin
- State Budgetary Healthcare Institution of Moscow Region "Balashikha Hospital," Balashikha, Russia
| | - Anna A Timakova
- Institute for Regenerative Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | | | - Tatiana V Egorova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | - Maryana V Bardina
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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198
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Liao Y, Xie Q, Yin X, Li X, Xie J, Wu X, Tang S, Liu M, Zeng L, Pan Y, Yang J, Feng Z, Qin X, Zheng H. penA profile of Neisseria gonorrhoeae in Guangdong, China: Novel penA alleles are related to decreased susceptibility to ceftriaxone or cefixime. Int J Antimicrob Agents 2024; 63:107101. [PMID: 38325722 DOI: 10.1016/j.ijantimicag.2024.107101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 12/15/2023] [Accepted: 01/29/2024] [Indexed: 02/09/2024]
Abstract
BACKGROUND Resistance to extended-spectrum cephalosporins (ESCs) has become a public health concern with the spread of Neisseria gonorrhoeae and increasing antimicrobial resistance. Mutation of penA, encoding penicillin-binding protein 2, represents a mechanism of ESC resistance. This study sought to assess penA alleles and mutations associated with decreased susceptibility (DS) to ESCs in N. gonorrhoeae. MATERIALS AND METHODS In 2021, 347 gonococci were collected in Guangdong, China. Minimum inhibitory concentations (MICs) of ceftriaxone and cefixime were determined, and whole-genome sequencing and phylogenetic analysis were performed. Multi-locus sequence typing (MLST) and conventional resistance determinants such as penA, mtrR, PonA and PorB were analysed. penA was genotyped and sequence-aligned using PubMLST. RESULTS Genome-wide phylogenetic analysis revealed that the prevalence of DS to ESCs was highest in Clade 11.1 (100.0%), Clade 2 (66.7%) and Clade 0 (55.7%), and the leading cause was strains with penA-60.001 or new penA alleles in clades. The penA phylogenetic tree is divided into two branches: non-mosaic penA and mosaic penA. The latter contained penA-60.001, penA-10 and penA-34. penA profile analysis indicated that A311V and T483S are closely related to DS to ESCs in mosaic penA. The new alleles NEIS1753_2840 and NEIS1753_2837 are closely related to penA-60.001, with DS to ceftriaxone and cefixime of 100%. NEIS1753_2660, a derivative of penA-10 (A486V), has increased DS to ceftriaxone. NEIS1753_2846, a derivative of penA-34.007 (G546S), has increased DS to cefixime. CONCLUSION This study identified critical penA alleles related to elevated MICs, and trends of gonococcus-evolved mutated penA associated with DS to ESCs in Guangdong.
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Affiliation(s)
- Yiwen Liao
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Qinghui Xie
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaona Yin
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaoxiao Li
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Junhui Xie
- The Affiliated Cancer Hospital of Gannan Medical University, Ganzhou, Jiang Xi, China
| | - Xingzhong Wu
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Sanmei Tang
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Mingjing Liu
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Lihong Zeng
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yuying Pan
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jianjiang Yang
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhanqin Feng
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaolin Qin
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory for Sexually Transmitted Disease Control, Guangzhou, Guangdong, China
| | - Heping Zheng
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory for Sexually Transmitted Disease Control, Guangzhou, Guangdong, China.
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199
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Dhuyser A, Pérès M, Clément S, Morel T, Aarnink A. The novel HLA-A*30:01:23 allele characterised by two different sequencing-based typing techniques. HLA 2024; 103:e15408. [PMID: 38575359 DOI: 10.1111/tan.15408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 04/06/2024]
Abstract
The novel allele HLA-A*30:01:23 differs from HLA-A*30:01:01:01 by one synonymous nucleotide substitution in exon 2.
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Affiliation(s)
- Adèle Dhuyser
- HLA and Histocompatibility Laboratory, CHRU de Nancy, Vandoeuvre les Nancy, France
- IMoPA 6, UMR7365 CNRS, Université de Lorraine, Vandoeuvre-les-Nancy, France
| | - Michaël Pérès
- HLA and Histocompatibility Laboratory, CHRU de Nancy, Vandoeuvre les Nancy, France
| | - Sandra Clément
- HLA and Histocompatibility Laboratory, CHRU de Nancy, Vandoeuvre les Nancy, France
| | - Thomas Morel
- HLA and Histocompatibility Laboratory, CHRU de Nancy, Vandoeuvre les Nancy, France
| | - Alice Aarnink
- HLA and Histocompatibility Laboratory, CHRU de Nancy, Vandoeuvre les Nancy, France
- IMoPA 6, UMR7365 CNRS, Université de Lorraine, Vandoeuvre-les-Nancy, France
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200
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Al Agbar S, Sharma A, Cohoe E, Beaune D, Sidahmed AME. The novel HLA-DQA1*05:05:17:03 allele, identified in a potential organ donor. HLA 2024; 103:e15489. [PMID: 38647206 DOI: 10.1111/tan.15489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/03/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
HLA-DQA1*05:05:17:03 differs from HLA-DQA1*05:05:01:02 by a single base substitution in exon 1 and HLA-DQA1*05:05:17:01 within introns 1 and 2.
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Affiliation(s)
- Sabina Al Agbar
- Immunogenetics and Transplantation Laboratory, London Health Sciences Centre and Pathology and Laboratory Medicine, University Hospital, London, Ontario, Canada
| | - Arpit Sharma
- Immunogenetics and Transplantation Laboratory, London Health Sciences Centre and Pathology and Laboratory Medicine, University Hospital, London, Ontario, Canada
| | - Elsa Cohoe
- Immunogenetics and Transplantation Laboratory, London Health Sciences Centre and Pathology and Laboratory Medicine, University Hospital, London, Ontario, Canada
| | - David Beaune
- Immunogenetics and Transplantation Laboratory, London Health Sciences Centre and Pathology and Laboratory Medicine, University Hospital, London, Ontario, Canada
| | - Abubaker M E Sidahmed
- Immunogenetics and Transplantation Laboratory, London Health Sciences Centre and Pathology and Laboratory Medicine, University Hospital, London, Ontario, Canada
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