1
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Mouratidis I, Baltoumas FA, Chantzi N, Patsakis M, Chan CS, Montgomery A, Konnaris MA, Aplakidou E, Georgakopoulos GC, Das A, Chartoumpekis DV, Kovac J, Pavlopoulos GA, Georgakopoulos-Soares I. kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species. Comput Struct Biotechnol J 2024; 23:1919-1928. [PMID: 38711760 PMCID: PMC11070822 DOI: 10.1016/j.csbj.2024.04.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 05/08/2024] Open
Abstract
The decrease in sequencing expenses has facilitated the creation of reference genomes and proteomes for an expanding array of organisms. Nevertheless, no established repository that details organism-specific genomic and proteomic sequences of specific lengths, referred to as kmers, exists to our knowledge. In this article, we present kmerDB, a database accessible through an interactive web interface that provides kmer-based information from genomic and proteomic sequences in a systematic way. kmerDB currently contains 202,340,859,107 base pairs and 19,304,903,356 amino acids, spanning 54,039 and 21,865 reference genomes and proteomes, respectively, as well as 6,905,362 and 149,305,183 genomic and proteomic species-specific sequences, termed quasi-primes. Additionally, we provide access to 5,186,757 nucleic and 214,904,089 peptide sequences absent from every genome and proteome, termed primes. kmerDB features a user-friendly interface offering various search options and filters for easy parsing and searching. The service is available at: www.kmerdb.com.
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Affiliation(s)
- Ioannis Mouratidis
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Fotis A. Baltoumas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, 16672, Greece
| | - Nikol Chantzi
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Michail Patsakis
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Candace S.Y. Chan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Austin Montgomery
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Maxwell A. Konnaris
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Statistics, The Pennsylvania State University, University Park, PA, USA
| | - Eleni Aplakidou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, 16672, Greece
- Department of Basic Sciences, School of Medicine, University of Crete, Heraklion, Greece
| | - George C. Georgakopoulos
- National Technical University of Athens, School of Electrical and Computer Engineering, Athens, Greece
| | - Anshuman Das
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Dionysios V. Chartoumpekis
- Service of Endocrinology, Diabetology and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Georgios A. Pavlopoulos
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, 16672, Greece
- Center for New Biotechnologies and Precision Medicine, School of Medicine, National and Kapodistrian University of Athens, Athens, 11527, Greece
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
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2
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Aplakidou E, Vergoulidis N, Chasapi M, Venetsianou NK, Kokoli M, Panagiotopoulou E, Iliopoulos I, Karatzas E, Pafilis E, Georgakopoulos-Soares I, Kyrpides NC, Pavlopoulos GA, Baltoumas FA. Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Comput Struct Biotechnol J 2024; 23:2011-2033. [PMID: 38765606 PMCID: PMC11101950 DOI: 10.1016/j.csbj.2024.04.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.
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Affiliation(s)
- Eleni Aplakidou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nikolaos Vergoulidis
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Chasapi
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nefeli K. Venetsianou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Kokoli
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Eleni Panagiotopoulou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Ioannis Iliopoulos
- Department of Basic Sciences, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Evangelos Karatzas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Evangelos Pafilis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Nikos C. Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Georgios A. Pavlopoulos
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Center of New Biotechnologies & Precision Medicine, Department of Medicine, School of Health Sciences, National and Kapodistrian University of Athens, Greece
- Hellenic Army Academy, 16673 Vari, Greece
| | - Fotis A. Baltoumas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
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3
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Zhu Y, Zhang H, Shao R, Wu X, Ding Y, Li Y, Wang W, Li B, Lu P, Ma Z. Comprehensive pan-cancer analysis of KLRB1-CLEC2D pair and identification of small molecule inhibitors to disrupt their interaction. Int Immunopharmacol 2024; 140:112908. [PMID: 39133960 DOI: 10.1016/j.intimp.2024.112908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 07/25/2024] [Accepted: 08/05/2024] [Indexed: 09/01/2024]
Abstract
The interplay between immune checkpoints KLRB1 and CLEC2D is crucial for tumor progression and immune evasion, yet the interaction dynamics are not fully understood. This study aims to elucidate the interaction across various cancers and identify small molecule inhibitors that can disrupt it. We perform a comprehensive pan-cancer analysis of the KLRB1-CLEC2D pair, including mRNA expression patterns, pathological stages, survival outcomes, and single-cell omics, immune infiltration, copy number variations, and DNA methylation profiles. Our findings reveal a consistently higher CLEC2D/KLRB1 ratio in most cancer types compared to normal tissues, and this ratio also increased with advancing pathological stages. Lower KLRB1 expression correlated with higher mortality in most cancers, opposite to CLEC2D. Expression variations were attributed to differential lymphocyte infiltration, CNV, and DNA methylation. Structure-based virtual screening analysis identified compounds including forsythiaside A and RGD peptides as effective inhibitors of the KLRB1-CLEC2D interaction, validated through microscale thermophoresis. This research advances understanding of the KLRB1-CLEC2D interaction within the tumor microenvironment and introduces novel therapeutic strategies to modulate this interaction.
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Affiliation(s)
- Yaoyao Zhu
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Huajie Zhang
- Department of Public Health and Health Management, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Ruoyang Shao
- Department of Public Health and Health Management, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Xintong Wu
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Yike Ding
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Yanzi Li
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Weiwei Wang
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Bingqing Li
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Peiyuan Lu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China.
| | - Zhongrui Ma
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China.
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4
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Meyer KJ, Mercer HE, Roos BR, Fingert JH, Anderson MG. Minimal phenotypes in transgenic mice with the human LOXL1/LOXL1-AS1 locus associated with exfoliation glaucoma. Vision Res 2024; 223:108464. [PMID: 39151208 PMCID: PMC11381136 DOI: 10.1016/j.visres.2024.108464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/31/2024] [Accepted: 07/31/2024] [Indexed: 08/18/2024]
Abstract
Exfoliation syndrome is a leading cause of secondary glaucoma worldwide. Among the risk-factors for exfoliation syndrome and exfoliation glaucoma that have been investigated, a genetic association with 15q24.1 is among the most striking. The leading candidates for the causal gene at this locus are LOXL1 and/or LOXL1-AS1, but studies have not yet coalesced in establishing, or ruling out, either candidate. Here, we contribute to studies of the 15q24.1 locus by making a partially humanized mouse model in which 166 kb of human genomic DNA from the 15q24.1 locus was introduced into the mouse genome via BAC transgenesis (B6-Tg(RP11-71M11)Andm). Transgenic expression of human genes in the BAC was only detectable for LOXL1-AS1. One cohort of 34 mice (21 experimental hemizygotes and 13 non-carrier control littermates) was assessed by slit-lamp exams and SD-OCT imaging at early (1-2 months) and mid (4-5 months) time points; fundus exams were performed at 5 months of age. A second smaller cohort (3 hemizygotes) were aged extensively (>12 months) to screen for overt abnormalities. Across all genotypes and ages, 136 slit-lamp exams, 128 SD-OCT exams, and 42 fundus exams detected no overt indices of exfoliation syndrome. Quantitatively, small, but statistically significant, age-related declines in ganglion cell complex thickness and total retinal thickness were detected in the hemizygotes at 4 months of age. Overall, this study demonstrates complexity in gene regulation from the 15q24.1 locus and suggests that LOXL1-AS1 is unlikely to be a monogenic cause of exfoliation syndrome but may contribute to glaucomatous retinal damage.
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Affiliation(s)
- Kacie J Meyer
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, United States; Institute for Vision Research, University of Iowa, Iowa City, IA, United States
| | - Hannah E Mercer
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, United States; Institute for Vision Research, University of Iowa, Iowa City, IA, United States
| | - Ben R Roos
- Institute for Vision Research, University of Iowa, Iowa City, IA, United States; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - John H Fingert
- Institute for Vision Research, University of Iowa, Iowa City, IA, United States; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Michael G Anderson
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, United States; Institute for Vision Research, University of Iowa, Iowa City, IA, United States; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States; Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, IA, United States.
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5
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Hayashi Y, Kaneko J, Ito-Matsuoka Y, Takehara A, Funakoshi M, Maezawa S, Shirane K, Furuya S, Matsui Y. Control of epigenomic landscape and development of fetal male germ cells through L-serine metabolism. iScience 2024; 27:110702. [PMID: 39262797 PMCID: PMC11388182 DOI: 10.1016/j.isci.2024.110702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/02/2024] [Accepted: 08/06/2024] [Indexed: 09/13/2024] Open
Abstract
Sex-specific metabolic characteristics emerge in the mouse germ line after reaching the genital ridges around embryonic day 10.5, coinciding with sexual differentiation. However, the impact of such metabolic characteristics on germ cell development remains unclear. In this study, we observed the specific upregulation in male fetal germ cells of D-3-phosphoglycerate dehydrogenase (PHGDH), the primary enzyme in the serine-glycine-one-carbon metabolism, along with an increase in a downstream metabolite, S-adenosylmethionine (SAM), crucial for protein and nucleic acid methylation. Inhibiting PHGDH in fetal testes resulted in reduced SAM levels in germ cells, accompanied by increases in the number of mouse vasa homolog (MVH/VASA)-positive germ cells and the promyelocytic leukemia zinc finger (PLZF)-positive undifferentiated spermatogonia ratio. Furthermore, PHGDH inhibition led to a decrease in the methylation of histone H3 and DNA, resulting in aberrations in gene expression profiles. In summary, our findings underscore the significant role of certain metabolic mechanisms in the development of male germ cells.
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Affiliation(s)
- Yohei Hayashi
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
- Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Jintaro Kaneko
- School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Yumi Ito-Matsuoka
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Asuka Takehara
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Mayuka Funakoshi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Yamazaki 2641, Noda, Chiba 278-8510, Japan
| | - So Maezawa
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Yamazaki 2641, Noda, Chiba 278-8510, Japan
| | - Kenjiro Shirane
- Department of Genome Biology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shigeki Furuya
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Yasuhisa Matsui
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
- Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
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6
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Ochoa S, Hsu AP, Oler AJ, Kumar D, Chauss D, van Hamburg JP, van Laar GG, Oikonomou V, Ganesan S, Ferré EMN, Schmitt MM, DiMaggio T, Barber P, Constantine GM, Rosen LB, Auwaerter PG, Gandhi B, Miller JL, Eisenberg R, Rubinstein A, Schussler E, Balliu E, Shashi V, Neth O, Olbrich P, Le KM, Mamia N, Laakso S, Nevalainen PI, Grönholm J, Seppänen MRJ, Boon L, Uzel G, Franco LM, Heller T, Winer KK, Ghosh R, Seifert BA, Walkiewicz M, Notarangelo LD, Zhou Q, Askentijevich I, Gahl W, Dalgard CL, Perera L, Afzali B, Tas SW, Holland SM, Lionakis MS. A deep intronic splice-altering AIRE variant causes APECED syndrome through antisense oligonucleotide-targetable pseudoexon inclusion. Sci Transl Med 2024; 16:eadk0845. [PMID: 39292801 DOI: 10.1126/scitranslmed.adk0845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/28/2024] [Indexed: 09/20/2024]
Abstract
Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) is a life-threatening monogenic autoimmune disorder primarily caused by biallelic deleterious variants in the autoimmune regulator (AIRE) gene. We prospectively evaluated 104 patients with clinically diagnosed APECED syndrome and identified 17 patients (16%) from 14 kindreds lacking biallelic AIRE variants in exons or flanking intronic regions; 15 had Puerto Rican ancestry. Through whole-genome sequencing, we identified a deep intronic AIRE variant (c.1504-818 G>A) cosegregating with the disease in all 17 patients. We developed a culture system of AIRE-expressing primary patient monocyte-derived dendric cells and demonstrated that c.1504-818 G>A creates a cryptic splice site and activates inclusion of a 109-base pair frame-shifting pseudoexon. We also found low-level AIRE expression in patient-derived lymphoblastoid cell lines (LCLs) and confirmed pseudoexon inclusion in independent extrathymic AIRE-expressing cell lines. Through protein modeling and transcriptomic analyses of AIRE-transfected human embryonic kidney 293 and thymic epithelial cell 4D6 cells, we showed that this variant alters the carboxyl terminus of the AIRE protein, abrogating its function. Last, we developed an antisense oligonucleotide (ASO) that reversed pseudoexon inclusion and restored the normal AIRE transcript sequence in LCLs. Thus, our findings revealed c.1504-818 G>A as a founder APECED-causing AIRE variant in the Puerto Rican population and uncovered pseudoexon inclusion as an ASO-reversible genetic mechanism underlying APECED.
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Affiliation(s)
- Sebastian Ochoa
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Amy P Hsu
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Dhaneshwar Kumar
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Daniel Chauss
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Jan Piet van Hamburg
- Departments of Rheumatology and Clinical Immunology and Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, 1105 AZ, Netherlands
| | - Gustaaf G van Laar
- Departments of Rheumatology and Clinical Immunology and Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, 1105 AZ, Netherlands
| | - Vasileios Oikonomou
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Sundar Ganesan
- Biological Imaging Section, Research Technologies Branch, NIAID, NIH, Bethesda, MD 20892, USA
| | - Elise M N Ferré
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Monica M Schmitt
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Tom DiMaggio
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Princess Barber
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | | | - Lindsey B Rosen
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Paul G Auwaerter
- Sherrilyn and Ken Fisher Center for Environmental Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bhumika Gandhi
- Division of Internal Medicine-Pediatrics, Department of Medicine, Medstar Georgetown University Hospital, Washington, DC 20007, USA
| | - Jennifer L Miller
- Division of Pediatric Endocrinology, Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Rachel Eisenberg
- Division of Allergy and Immunology, Department of Pediatrics, Montefiore Medical Center, Bronx, NY 10467, USA
| | - Arye Rubinstein
- Division of Allergy and Immunology, Department of Pediatrics, Montefiore Medical Center, Bronx, NY 10467, USA
- Department of Microbiology and Immunology, Montefiore Medical Center, Bronx, NY 10467, USA
| | - Edith Schussler
- Division of Pulmonary, Allergy, and Immunology, Department of Pediatrics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Erjola Balliu
- Department of Endocrinology, Diabetes and Metabolism, Lakeland Regional Health Grasslands Campus, Lakeland, FL 33803, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
- Undiagnosed Diseases Network, Duke University Medical Center, Durham, NC 27710, USA
| | - Olaf Neth
- Inborn Errors of Immunity Laboratory, Biomedicine Institute in Seville (IBiS), University of Seville/CSIC, "Red de Investigación Translacional en Infectología Pediátrica," Paediatric Infectious Diseases, Rheumatology and Immunology Unit, Virgen del Rocío University Hospital, Seville 41013, Spain
| | - Peter Olbrich
- Inborn Errors of Immunity Laboratory, Biomedicine Institute in Seville (IBiS), University of Seville/CSIC, "Red de Investigación Translacional en Infectología Pediátrica," Paediatric Infectious Diseases, Rheumatology and Immunology Unit, Virgen del Rocío University Hospital, Seville 41013, Spain
- Departamento de Farmacología, Pediatría y Radiología, Facultad de Medicina, Universidad de Sevilla, Seville 41004, Spain
| | - Kim My Le
- Translational Immunology Research Program, University of Helsinki, Helsinki 00014, Finland
- Pediatric Research Center, New Children's Hospital, University of Helsinki and HUS Helsinki University Hospital, Helsinki 00290, Finland
| | - Nanni Mamia
- Pediatric Research Center, New Children's Hospital, University of Helsinki and HUS Helsinki University Hospital, Helsinki 00290, Finland
| | - Saila Laakso
- Pediatric Research Center, New Children's Hospital, University of Helsinki and HUS Helsinki University Hospital, Helsinki 00290, Finland
- Folkhälsan Research Center, Helsinki 00250, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
| | | | - Juha Grönholm
- Translational Immunology Research Program, University of Helsinki, Helsinki 00014, Finland
- Pediatric Research Center, New Children's Hospital, University of Helsinki and HUS Helsinki University Hospital, Helsinki 00290, Finland
| | - Mikko R J Seppänen
- Translational Immunology Research Program, University of Helsinki, Helsinki 00014, Finland
- Pediatric Research Center, New Children's Hospital, University of Helsinki and HUS Helsinki University Hospital, Helsinki 00290, Finland
- European Reference Network Rare Immunodeficiency Autoinflammatory and Autoimmune Diseases Network (ERN RITA) Core Center, Utrecht, 3584 CX, Netherlands
| | | | - Gulbu Uzel
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Luis M Franco
- Functional Immunogenomics Unit, Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Theo Heller
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Karen K Winer
- Pediatric Growth and Nutrition Branch, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Rajarshi Ghosh
- Centralized Sequencing Program, Division of Intramural Research, NIAID, NIH, Bethesda, MD 20892, USA
| | - Bryce A Seifert
- Centralized Sequencing Program, Division of Intramural Research, NIAID, NIH, Bethesda, MD 20892, USA
| | - Magdalena Walkiewicz
- Centralized Sequencing Program, Division of Intramural Research, NIAID, NIH, Bethesda, MD 20892, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Qing Zhou
- Inflammatory Disease Section, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Ivona Askentijevich
- Inflammatory Disease Section, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - William Gahl
- Medical Genetics Branch, National Human Genome Research Institute, and NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD 20892, USA
| | - Cliffton L Dalgard
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Sander W Tas
- Departments of Rheumatology and Clinical Immunology and Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, 1105 AZ, Netherlands
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Michail S Lionakis
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
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7
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Dong J, Brown S, Truong K. Nearby and non-nested genes in the human genome have more similar genotype tissue expression. PLoS One 2024; 19:e0307360. [PMID: 39292702 PMCID: PMC11410254 DOI: 10.1371/journal.pone.0307360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 07/03/2024] [Indexed: 09/20/2024] Open
Abstract
Neighboring genes within a shared promoter arrangement (i.e. opposite direction with the neighboring ends as the transcriptional start sites) are expected to have a high similarity in genotype tissue expression due to the potential overlap in the promoter region. This raises the question of whether similarity in expression profiles depends on orientation of the neighboring genes and whether there exist thresholds of locality where the similarity diminishes. Thus, in this work, we compared genotype tissue expression profiles at different genomic orientations and localities. Interestingly, there exist gene pairs in the human genome with very high or low expression similarity. Shorter chromosomes tend to have more similarly expressed genes. Also, a cluster of 3 adjacent genes within the average range of 20 to 60 kilobase pairs can have very similar expression profiles regardless of their orientations. However, when genes are nested and in opposite orientations, a lower than expected similarity was observed. Lastly, in cases where genotype tissue expression data does not exist or have low read counts (e.g. non-coding RNA), our identified influencing range can be a first estimate of the genotype tissue expression.
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Affiliation(s)
- Jiahong Dong
- Edward S. Rogers, Sr. Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Stephen Brown
- Edward S. Rogers, Sr. Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Kevin Truong
- Edward S. Rogers, Sr. Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
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8
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Kelchtermans J, March ME, Hakonarson H, McGrath-Morrow SA. Phenotype wide association study links bronchopulmonary dysplasia with eosinophilia in children. Sci Rep 2024; 14:21391. [PMID: 39271728 PMCID: PMC11399246 DOI: 10.1038/s41598-024-72348-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 09/05/2024] [Indexed: 09/15/2024] Open
Abstract
Bronchopulmonary dysplasia (BPD) is a common complication of preterm birth. Despite this, genetic drivers of BPD are poorly understood. The objective of this study is to better understand the impact of single nucleotide polymorphisms (SNPs) previously associated with BPD by examining associations with other phenotypes. We drew pediatric subjects from the biorepository at the Center for Applied Genomics to identify associations between these SNPs and 2,146 imputed phenotypes. Methylation data, external cohorts, and in silico validation methods were used to corroborate significant associations. We identified 60 SNPs that were previously associated with BPD. We found a significant association between rs3771150 and rs3771171 and mean eosinophil percentage in a European cohort of 6,999 patients and replicated this in external cohorts. Both SNPs were also associated with asthma, COPD and FEV1/FVC ratio. These SNPs displayed associations with methylation probes and were functionally linked to ST2 (IL1RL1) levels in blood and lung tissue. Our findings support a genetic justification for the epidemiological link between BPD and asthma. Given the well-established link between ST2 and type 2 inflammation in asthma, these findings provide a rationale for future studies exploring the role of type 2 inflammation in the pathogenesis of BPD.
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Affiliation(s)
- Jelte Kelchtermans
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- The Center of Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Division of Pulmonary and Sleep Medicine, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA, 19104, USA.
| | - Michael E March
- The Center of Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Center of Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Pulmonary and Sleep Medicine, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA, 19104, USA
| | - Sharon A McGrath-Morrow
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Pulmonary and Sleep Medicine, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA, 19104, USA
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9
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Moon N, Morgan CP, Marx-Rattner R, Jeng A, Johnson RL, Chikezie I, Mannella C, Sammel MD, Epperson CN, Bale TL. Stress increases sperm respiration and motility in mice and men. Nat Commun 2024; 15:7900. [PMID: 39261485 PMCID: PMC11391062 DOI: 10.1038/s41467-024-52319-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 09/02/2024] [Indexed: 09/13/2024] Open
Abstract
Semen quality and fertility has declined over the last 50 years, corresponding to ever-increasing environmental stressors. However, the cellular mechanisms involved and their impact on sperm functions remain unknown. In a repeated sampling human cohort study, we identify a significant effect of prior perceived stress to increase sperm motility 2-3 months following stress, timing that expands upon our previous studies revealing significant stress-associated changes in sperm RNA important for fertility. We mechanistically examine this post-stress timing in mice using an in vitro stress model in the epididymal epithelial cells responsible for sperm maturation and find 7282 differentially H3K27me3 bound DNA regions involving genes critical for mitochondrial and metabolic pathways. Further, prior stress exposure significantly changes the composition and size of epithelial cell-secreted extracellular vesicles that when incubated with mouse sperm, increase mitochondrial respiration and sperm motility, adding to our prior work showing impacts on embryo development. Together, these studies identify a time-dependent, translational signaling pathway that communicates stress experience to sperm, ultimately affecting reproductive functions.
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Affiliation(s)
- Nickole Moon
- Department of Psychiatry, University of Colorado Anschutz Medical Campus School of Medicine, Aurora, CO, 80045, USA
- Department of Pharmacology, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Christopher P Morgan
- Department of Pharmacology, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Ruth Marx-Rattner
- Department of Pharmacology, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Alyssa Jeng
- Department of Psychiatry, University of Colorado Anschutz Medical Campus School of Medicine, Aurora, CO, 80045, USA
| | - Rachel L Johnson
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Ijeoma Chikezie
- Department of Pharmacology, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Carmen Mannella
- Department of Physiology, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Mary D Sammel
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - C Neill Epperson
- Department of Psychiatry, University of Colorado Anschutz Medical Campus School of Medicine, Aurora, CO, 80045, USA
| | - Tracy L Bale
- Department of Psychiatry, University of Colorado Anschutz Medical Campus School of Medicine, Aurora, CO, 80045, USA.
- Department of Pharmacology, University of Maryland Baltimore, Baltimore, MD, 21201, USA.
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10
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Ghodke-Puranik Y, Olferiev M, Crow MK. Systemic lupus erythematosus genetics: insights into pathogenesis and implications for therapy. Nat Rev Rheumatol 2024:10.1038/s41584-024-01152-2. [PMID: 39232240 DOI: 10.1038/s41584-024-01152-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2024] [Indexed: 09/06/2024]
Abstract
Systemic lupus erythematosus (SLE) is a prime example of how the interplay between genetic and environmental factors can trigger systemic autoimmunity, particularly in young women. Although clinical disease can take years to manifest, risk is established by the unique genetic makeup of an individual. Genome-wide association studies have identified almost 200 SLE-associated risk loci, yet unravelling the functional effect of these loci remains a challenge. New analytic tools have enabled researchers to delve deeper, leveraging DNA sequencing and cell-specific and immune pathway analysis to elucidate the immunopathogenic mechanisms. Both common genetic variants and rare non-synonymous mutations can interact to increase SLE risk. Notably, variants strongly associated with SLE are often located in genome super-enhancers that regulate MHC class II gene expression. Additionally, the 3D conformations of DNA and RNA contribute to genome regulation and innate immune system activation. Improved therapies for SLE are urgently needed and current and future knowledge from genetic and genomic research should provide new tools to facilitate patient diagnosis, enhance the identification of therapeutic targets and optimize testing of agents.
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Affiliation(s)
- Yogita Ghodke-Puranik
- Mary Kirkland Center for Lupus Research, Hospital for Special Surgery and Weill Cornell Medicine, New York, NY, USA
| | - Mikhail Olferiev
- Mary Kirkland Center for Lupus Research, Hospital for Special Surgery and Weill Cornell Medicine, New York, NY, USA
| | - Mary K Crow
- Mary Kirkland Center for Lupus Research, Hospital for Special Surgery and Weill Cornell Medicine, New York, NY, USA.
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11
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Jiao K, Zhu B, Chang X, Guo J, Fu J, Song X, Yu X, Zhang X, Dong J, Yan W, Luan X, Wang Z, Han H, Du L, Yu L, Zhang Y, Zhang J, Chen Y, Hu J, Zhao Z, Kang J, Tan S, Wang Z, Mao S, Qian F, Luo R, Liu C, Huang Z, Li G, Li X, Luo L, Li D, Zhou Y, Hu X, Yu X, Shi Y, Jiang J, Zhang J, Cheng N, Wang N, Xia X, Yue D, Gao M, Xi J, Luo S, Lu J, Zhao C, Ke Q, Ma M, Zhu W. High-risk screening for late-onset Pompe disease in China: An expanded multicenter study. J Inherit Metab Dis 2024. [PMID: 39227307 DOI: 10.1002/jimd.12793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 09/05/2024]
Abstract
Late-onset Pompe disease (LOPD) is caused by a genetic deficiency of the lysosomal enzyme acid alpha-glucosidase (GAA), leading to progressive limb-girdle weakness and respiratory impairment. The insidious onset of non-specific early symptoms often prohibits timely diagnosis. This study aimed to validate the high-risk screening criteria for LOPD in the Chinese population. A total of 726 patients were included, including 96 patients under 14 years of age. Dried blood spots (DBS) and tandem mass spectrometry (MS/MS) were employed to evaluate serum GAA activity. Forty-four patients exhibited a decreased GAA activity, 16 (2.2%) of which were confirmed as LOPD by genetic testing. Three previously unreported GAA mutations were also identified. The median diagnostic delay was shortened to 3 years, which excelled the previous retrospective studies. At diagnosis, most patients exhibited impaired respiratory function and/or limb-girdle weakness. Elevated serum creatine kinase (CK) levels were more frequently observed in patients who manifested before age 16. Overall, high-risk screening is a feasible and efficient method to identify LOPD patients at an early stage. Patients over 1 year of age with either weakness in axial and/or proximal limb muscles, or unexplained respiratory distress shall be subject to GAA enzymatic test, while CK levels above 2 times the upper normal limit shall be an additional criterion for patients under 16. This modified high-risk screening criteria for LOPD requires further validation in larger Chinese cohorts.
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Affiliation(s)
- Kexin Jiao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
| | - Bochen Zhu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
| | - Xueli Chang
- Department of Neurology, First Hospital, Shanxi Medical University, Taiyuan, China
| | - Junhong Guo
- Department of Neurology, First Hospital, Shanxi Medical University, Taiyuan, China
| | - Jun Fu
- Department of Neurology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Xueqin Song
- Department of Neurology, Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xuen Yu
- Department of Neurology, Institute of Neurology, Anhui University of Traditional Chinese Medicine, Hefei, China
| | - Xiaoge Zhang
- Department of Neurology, Northwest Women's and Children's Hospital, Xi'an, China
| | - Jihong Dong
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wang Yan
- Department of Neurology, Ningbo No.2 Hospital, Ningbo, China
| | - Xinghua Luan
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Zhiqiang Wang
- Department of Neurology, The First Affiliated Hospital of Fujian Medical University, Fujian, China
| | - Hong Han
- Department of Neurology, Children's Hospital of Shanxi Province, Taiyuan, China
| | - Lijun Du
- Department of Neurology, Children's Hospital of Shanxi Province, Taiyuan, China
| | - Liqiang Yu
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yali Zhang
- Department of Neurology, Chifeng Municipal Hospital, Chifeng, China
| | - Jingjing Zhang
- Department of Neurology, Chifeng Municipal Hospital, Chifeng, China
| | - Yan Chen
- Department of Neurology, Tongji Hospital of Tongji University, Shanghai, China
| | - Jing Hu
- Department of Neuromuscular Disease, Hebei Medical University Third Hospital, Shijiazhuang, China
| | - Zhe Zhao
- Department of Neuromuscular Disease, Hebei Medical University Third Hospital, Shijiazhuang, China
| | - Juan Kang
- Department of Neurology, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Song Tan
- Department of Neurology, Sichuan Provincial People's Hospital, Sichuan Academy of Medical Sciences, Chengdu, China
| | - Zhiyun Wang
- Department of Neurology, Tianjin First Central Hospital, Nankai University, Tianjin, China
| | - Shanshan Mao
- Department of Neurology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Fangyuan Qian
- Department of Neurology, ZhongDa Hospital, Southeast University, Nanjing, China
| | - Ronghua Luo
- Department of Neurology, West China Second Hospital of Sichuan University, Chengdu, China
| | - Changxia Liu
- Department of Neurology, Yancheng First Hospital, Affiliated Hospital of Nanjing University Medical School, The First people's Hospital of Yancheng, Jiangsu, China
| | - Zhengyu Huang
- Department of Neurology, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Gang Li
- Department of Neurology, Shanghai Dongfang Hospital, Tongji University, Shanghai, China
| | - Xia Li
- Department of Neurology, Xi'an Children's Hospital, China
| | - Lijun Luo
- Department of Neurology, Wuhan No.1 Hospital, Wuhan, China
| | - Dong Li
- Department of Pediatric Neurology, Tianjin Children's Hospital, Tianjin University Children's Hospital, Tianjin, China
| | - Yuanlin Zhou
- Department of Neurology, Taizhou Hospital of Zhejiang Province, Taizhou, China
| | - Xiafei Hu
- Department of Neurology, Taizhou Hospital of Zhejiang Province, Taizhou, China
| | - Xuefan Yu
- Department of Neurology, The First Hospital of Jilin University, Changchun, China
| | - Yongguang Shi
- Department of Neurology, The First Hospital of Jilin University, Changchun, China
| | - Jianming Jiang
- Department of Neurology, Changhai Hospital, Shanghai, China
| | - Jialong Zhang
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Nachuan Cheng
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Ningning Wang
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xingyu Xia
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Dongyue Yue
- Department of Neurology, Jing'an District Center Hospital of Shanghai, Shanghai, China
| | - Mingshi Gao
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jianying Xi
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Sushan Luo
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiahong Lu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Chongbo Zhao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Qing Ke
- Department of Neurology, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Mingming Ma
- Department of Neurology, First Hospital, Shanxi Medical University, Taiyuan, China
| | - Wenhua Zhu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
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12
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Umhoefer JM, Arce MM, Dajani R, Belk JA, Mowery CT, Nguyen V, Gowen BG, Simeonov DR, Curie GL, Corn JE, Chang HY, Marson A. Deciphering regulation of FOXP3 expression in human conventional T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.30.610436. [PMID: 39282425 PMCID: PMC11398386 DOI: 10.1101/2024.08.30.610436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
Abstract
FOXP3 is a lineage-defining transcription factor that controls differentiation and maintenance of suppressive function of regulatory T cells (Tregs). Foxp3 is exclusively expressed in Tregs in mice. However, in humans, FOXP3 is not only constitutively expressed in Tregs; it is also transiently expressed in stimulated CD4+CD25- conventional T cells (Tconvs)1-3. Mechanisms governing the expression of FOXP3 in human Tconvs are not understood. Here, we performed CRISPR interference (CRISPRi) screens using a 15K-member gRNA library tiling 39 kb downstream of the FOXP3 transcriptional start site (TSS) to 85 kb upstream of the TSS in Treg and Tconvs. The FOXP3 promoter and conserved non-coding sequences (CNS0, CNS1, CNS2 and CNS3), characterized as enhancer elements in murine Tregs, were required for maintenance of FOXP3 in human Tregs. In contrast, FOXP3 in human Tconvs depended on regulation at CNS0 and a novel Tconv-specific noncoding sequence (TcNS+) located upstream of CNS0. Arrayed validations of these sites identified an additional repressive cis-element overlapping with the PPP1R3F promoter (TcNS-). Pooled CRISPR knockouts revealed multiple transcription factors required for proper expression of FOXP3 in Tconvs, including GATA3, STAT5, IRF4, ETS1 and DNA methylation-associated regulators DNMT1 and MBD2. Analysis of ChIP-seq and ATAC-seq paired with knock-out (KO) of GATA3, STAT5, IRF4, and ETS1 revealed regulation of CNS0 and TcNS+ accessibility. Collectively, this work identified Treg-shared and Tconv-specific cis-elements and the trans-factors that interact with them, building a network of regulators controlling FOXP3 expression in human Tconvs.
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Affiliation(s)
- Jennifer M Umhoefer
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
- Biomedical Sciences graduate program, University of California, San Francisco, CA, USA
| | - Maya M Arce
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
- Biomedical Sciences graduate program, University of California, San Francisco, CA, USA
| | - Rama Dajani
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Julia A Belk
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Cody T Mowery
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
- Biomedical Sciences graduate program, University of California, San Francisco, CA, USA
| | - Vinh Nguyen
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin G Gowen
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Dimitre R Simeonov
- Department of Medicine, University of California, San Francisco, CA, USA
- Biomedical Sciences graduate program, University of California, San Francisco, CA, USA
| | - Gemma L Curie
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jacob E Corn
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, Switzerland
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
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13
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Lieberman-Cribbin W, Domingo-Relloso A, Glabonjat RA, Schilling K, Cole SA, O'Leary M, Best LG, Zhang Y, Fretts AM, Umans JG, Goessler W, Navas-Acien A, Tellez-Plaza M, Kupsco A. An epigenome-wide study of selenium status and DNA methylation in the Strong Heart Study. ENVIRONMENT INTERNATIONAL 2024; 191:108955. [PMID: 39154409 DOI: 10.1016/j.envint.2024.108955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 06/19/2024] [Accepted: 08/13/2024] [Indexed: 08/20/2024]
Abstract
BACKGROUND Selenium (Se) is an essential nutrient linked to adverse health endpoints at low and high levels. The mechanisms behind these relationships remain unclear and there is a need to further understand the epigenetic impacts of Se and their relationship to disease. We investigated the association between urinary Se levels and DNA methylation (DNAm) in the Strong Heart Study (SHS), a prospective study of cardiovascular disease (CVD) among American Indians adults. METHODS Selenium concentrations were measured in urine (collected in 1989-1991) using inductively coupled plasma mass spectrometry among 1,357 participants free of CVD and diabetes. DNAm in whole blood was measured cross-sectionally using the Illumina MethylationEPIC BeadChip (850 K) Array. We used epigenome-wide robust linear regressions and elastic net to identify differentially methylated cytosine-guanine dinucleotide (CpG) sites associated with urinary Se levels. RESULTS The mean (standard deviation) urinary Se concentration was 51.8 (25.1) μg/g creatinine. Across 788,368 CpG sites, five differentially methylated positions (DMP) (hypermethylated: cg00163554, cg18212762, cg11270656, and hypomethylated: cg25194720, cg00886293) were significantly associated with Se in linear regressions after accounting for multiple comparisons (false discovery rate p-value: 0.10). The top hypermethylated DMP (cg00163554) was annotated to the Disco Interacting Protein 2 Homolog C (DIP2C) gene, which relates to transcription factor binding. Elastic net models selected 425 hypo- and hyper-methylated DMPs associated with urinary Se, including three sites (cg00163554 [DIP2C], cg18212762 [MAP4K2], cg11270656 [GPIHBP1]) identified in linear regressions. CONCLUSIONS Urinary Se was associated with minimal changes in DNAm in adults from American Indian communities across the Southwest and the Great Plains in the United States, suggesting that other mechanisms may be driving health impacts. Future analyses should explore other mechanistic biomarkers in human populations, determine these relationships prospectively, and investigate the potential role of differentially methylated sites with disease endpoints.
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Affiliation(s)
- Wil Lieberman-Cribbin
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA.
| | - Arce Domingo-Relloso
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA; Department of Biostatistics, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Ronald A Glabonjat
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Kathrin Schilling
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Shelley A Cole
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Marcia O'Leary
- Missouri Breaks Industries Research, Cheyenne River Sioux Tribe, Eagle Butte, SD 57625, USA
| | - Lyle G Best
- Missouri Breaks Industries Research, Cheyenne River Sioux Tribe, Eagle Butte, SD 57625, USA
| | - Ying Zhang
- Department of Biostatistics and Epidemiology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Amanda M Fretts
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Jason G Umans
- MedStar Health Research Institute, Hyattsville, MD, USA; Georgetown-Howard Universities Center for Clinical and Translational Science, Washington, DC, USA
| | | | - Ana Navas-Acien
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Maria Tellez-Plaza
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Allison Kupsco
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
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14
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van Megen WH, de Baaij JHF, Churchill GA, Devuyst O, Hoenderop JGJ, Korstanje R. Genetic drivers of age-related changes in urinary magnesium excretion. Physiol Genomics 2024; 56:634-647. [PMID: 39037434 DOI: 10.1152/physiolgenomics.00119.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/23/2024] Open
Abstract
Although age-dependent alterations in urinary magnesium (Mg2+) excretion have been described, the underlying mechanism remains elusive. As heritability significantly contributes to variations in urinary Mg2+ excretion, we measured urinary Mg2+ excretion at different ages in a cohort of genetically variable Diversity Outbred (DO) mice. Compared with animals aged 6 mo, an increase in Mg2+ excretion was observed at 12 and 18 mo. Quantitative trait locus (QTL) analysis revealed an association of a locus on chromosome 10 with Mg2+ excretion at 6 mo of age, with Oit3 (encoding oncoprotein-induced transcript 3; OIT3) as our primary candidate gene. To study the possible role of OIT3 in renal Mg2+ handling, we generated and characterized Oit3 knockout (Oit3-/-) mice. Although a slightly lower serum Mg2+ concentration was present in male Oit3-/- mice, this effect was not observed in female Oit3-/- mice. In addition, urinary Mg2+ excretion and the expression of renal magnesiotropic genes were unaltered in Oit3-/- mice. For animals aged 12 and 18 mo, QTL analysis revealed an association with a locus on chromosome 19, which contains the gene encoding TRPM6, a known Mg2+ channel involved in renal Mg2+ reabsorption. Comparison with RNA sequencing (RNA-Seq) data revealed that Trpm6 mRNA expression is inversely correlated with the QTL effect, implying that TRPM6 may be involved in age-dependent changes in urinary Mg2+ excretion in mice. In conclusion, we show here that variants in Oit3 and Trpm6 are associated with urinary Mg2+ excretion at distinct periods of life, although OIT3 is unlikely to affect renal Mg2+ handling.NEW & NOTEWORTHY Aging increased urinary magnesium (Mg2+) excretion in mice. We show here that variation in Oit3, a candidate gene for the locus associated with Mg2+ excretion in young mice, is unlikely to be involved as knockout of Oit3 did not affect Mg2+ excretion. Differences in the expression of the renal Mg2+ channel TRPM6 may contribute to the variation in urinary Mg2+ excretion in older mice.
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Affiliation(s)
- Wouter H van Megen
- Department of Medical Biosciences, Radboudumc, Nijmegen, The Netherlands
| | | | | | - Olivier Devuyst
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | | | - Ron Korstanje
- The Jackson Laboratory, Bar Harbor, Maine, United States
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15
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Haviland I, Hector RD, Swanson LC, Verran AS, Sherrill E, Frazier Z, Denny AM, Lucash J, Zhang B, Dubbs HA, Marsh ED, Weisenberg JL, Leonard H, Crippa M, Cogliati F, Russo S, Suter B, Rajaraman R, Percy AK, Schreiber JM, Demarest S, Benke TA, Chopra M, Yu TW, Olson HE. Deletions in the CDKL5 5' untranslated region lead to CDKL5 deficiency disorder. Am J Med Genet A 2024:e63843. [PMID: 39205479 DOI: 10.1002/ajmg.a.63843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/22/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024]
Abstract
Pathogenic variants in the cyclin-dependent kinase-like 5 (CDKL5) gene are associated with CDKL5 deficiency disorder (CDD), a severe X-linked developmental and epileptic encephalopathy. Deletions affecting the 5' untranslated region (UTR) of CDKL5, which involve the noncoding exon 1 and/or alternatively spliced first exons (exons 1a-e), are uncommonly reported. We describe genetic and phenotypic characteristics for 15 individuals with CDKL5 partial gene deletions affecting the 5' UTR. All individuals presented characteristic features of CDD, including medically refractory infantile-onset epilepsy, global developmental delay, and visual impairment. We performed RNA sequencing on fibroblast samples from three individuals with small deletions involving exons 1 and/or 1a/1b only. Results demonstrated reduced CDKL5 mRNA expression with no evidence of expression from alternatively spliced first exons. Our study broadens the genotypic spectrum for CDD by adding to existing evidence that deletions affecting the 5' UTR of the CDKL5 gene are associated with the disorder. We propose that smaller 5' UTR deletions may require additional molecular testing approaches such as RNA sequencing to determine pathogenicity.
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Affiliation(s)
- Isabel Haviland
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ralph D Hector
- Simons Initiative for the Developing Brain & Patrick Wild Centre, Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Lindsay C Swanson
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Aubrie Soucy Verran
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Emma Sherrill
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Zoë Frazier
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - AnneMarie M Denny
- Division of Pediatric Neurology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Jenna Lucash
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Bo Zhang
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Holly A Dubbs
- Division of Child Neurology, Children's Hospital of Philadelphia, Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Eric D Marsh
- Division of Child Neurology, Children's Hospital of Philadelphia, Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Judith L Weisenberg
- Department of Pediatric Neurology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Helen Leonard
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Milena Crippa
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Francesca Cogliati
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Silvia Russo
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Bernhard Suter
- Division of Child Neurology, Texas Children's Hospital, Departments of Neurology and Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Rajsekar Rajaraman
- Division of Pediatric Neurology, UCLA Mattel Children's Hospital, Los Angeles, California, USA
| | - Alan K Percy
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - John M Schreiber
- Division of Epilepsy, Neurophysiology, and Critical Care Neurology, Children's National Hospital, Washington, DC, USA
| | - Scott Demarest
- Department of Pediatrics and Neurology, Precision Medicine Institute, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, Colorado, USA
| | - Timothy A Benke
- Department of Pediatrics, Pharmacology and Neurology, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, Colorado, USA
| | - Maya Chopra
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Timothy W Yu
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Heather E Olson
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Epilepsy and Clinical Neurophysiology, Boston Children's Hospital, Boston, Massachusetts, USA
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16
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Sullivan PJ, Quinn JMW, Wu W, Pinese M, Cowley MJ. SpliceVarDB: A comprehensive database of experimentally validated human splicing variants. Am J Hum Genet 2024:S0002-9297(24)00288-X. [PMID: 39226898 DOI: 10.1016/j.ajhg.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 08/03/2024] [Accepted: 08/06/2024] [Indexed: 09/05/2024] Open
Abstract
Variants that alter gene splicing are estimated to comprise up to a third of all disease-causing variants, yet they are hard to predict from DNA sequencing data alone. To overcome this, many groups are incorporating RNA-based analyses, which are resource intensive, particularly for diagnostic laboratories. There are thousands of functionally validated variants that induce mis-splicing; however, this information is not consolidated, and they are under-represented in ClinVar, which presents a barrier to variant interpretation and can result in duplication of validation efforts. To address this issue, we developed SpliceVarDB, an online database consolidating over 50,000 variants assayed for their effects on splicing in over 8,000 human genes. We evaluated over 500 published data sources and established a spliceogenicity scale to standardize, harmonize, and consolidate variant validation data generated by a range of experimental protocols. According to the strength of their supporting evidence, variants were classified as "splice-altering" (∼25%), "not splice-altering" (∼25%), and "low-frequency splice-altering" (∼50%), which correspond to weak or indeterminate evidence of spliceogenicity. Importantly, 55% of the splice-altering variants in SpliceVarDB are outside the canonical splice sites (5.6% are deep intronic). These variants can support the variant curation diagnostic pathway and can be used to provide the high-quality data necessary to develop more accurate in silico splicing predictors. The variants are accessible through an online platform, SpliceVarDB, with additional features for visualization, variant information, in silico predictions, and validation metrics. SpliceVarDB is a very large collection of splice-altering variants and is available at https://splicevardb.org.
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Affiliation(s)
- Patricia J Sullivan
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia; UNSW Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Julian M W Quinn
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Weilin Wu
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Mark Pinese
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia.
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17
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Ritchie SC, Taylor HJ, Liang Y, Manikpurage HD, Pennells L, Foguet C, Abraham G, Gibson JT, Jiang X, Liu Y, Xu Y, Kim LG, Mahajan A, McCarthy MI, Kaptoge S, Lambert SA, Wood A, Sim X, Collins FS, Denny JC, Danesh J, Butterworth AS, Di Angelantonio E, Inouye M. Integrated clinical risk prediction of type 2 diabetes with a multifactorial polygenic risk score. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.22.24312440. [PMID: 39228710 PMCID: PMC11370520 DOI: 10.1101/2024.08.22.24312440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Combining information from multiple GWASs for a disease and its risk factors has proven a powerful approach for development of polygenic risk scores (PRSs). This may be particularly useful for type 2 diabetes (T2D), a highly polygenic and heterogeneous disease where the additional predictive value of a PRS is unclear. Here, we use a meta-scoring approach to develop a metaPRS for T2D that incorporated genome-wide associations from both European and non-European genetic ancestries and T2D risk factors. We evaluated the performance of this metaPRS and benchmarked it against existing genome-wide PRS in 620,059 participants and 50,572 T2D cases amongst six diverse genetic ancestries from UK Biobank, INTERVAL, the All of Us Research Program, and the Singapore Multi-Ethnic Cohort. We show that our metaPRS was the most powerful PRS for predicting T2D in European population-based cohorts and had comparable performance to the top ancestry-specific PRS, highlighting its transferability. In UK Biobank, we show the metaPRS had stronger predictive power for 10-year risk than all individual risk factors apart from BMI and biomarkers of dysglycemia. The metaPRS modestly improved T2D risk stratification of QDiabetes risk scores for 10-year risk prediction, particularly when prioritising individuals for blood tests of dysglycemia. Overall, we present a highly predictive and transferrable PRS for T2D and demonstrate that the potential for PRS to incrementally improve T2D risk prediction when incorporated into UK guideline-recommended screening and risk prediction with a clinical risk score.
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Affiliation(s)
- Scott C Ritchie
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Henry J Taylor
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yujian Liang
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Hasanga D Manikpurage
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Lisa Pennells
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Carles Foguet
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Gad Abraham
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Joel T Gibson
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Xilin Jiang
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, US
| | - Yang Liu
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Yu Xu
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Lois G Kim
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
| | - Anubha Mahajan
- OMNI Human Genetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Mark I McCarthy
- OMNI Human Genetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Stephen Kaptoge
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Samuel A Lambert
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Angela Wood
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Cambridge Centre of Artificial Intelligence in Medicine, University of Cambridge, Cambridge, UK
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Francis S Collins
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joshua C Denny
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
| | - Emanuele Di Angelantonio
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Health Data Science Research Centre, Human Technopole, Milan, Italy
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
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18
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Jacobs MME, Maas RJF, Jonkman I, Negishi Y, Tielemans Zamora W, Yanginlar C, van Heck J, Matzaraki V, Martens JHA, Baltissen M, Vermeulen M, Morla-Folch J, Ranzenigo A, Wang W, Umali M, Ochando J, van der Vlag J, Hilbrands LB, Joosten LAB, Netea MG, Mulder WJM, van Leent MMT, Mhlanga MM, Teunissen AJP, Rother N, Duivenvoorden R. Trained immunity is regulated by T cell-induced CD40-TRAF6 signaling. Cell Rep 2024; 43:114664. [PMID: 39178113 DOI: 10.1016/j.celrep.2024.114664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 07/08/2024] [Accepted: 08/06/2024] [Indexed: 08/25/2024] Open
Abstract
Trained immunity is characterized by histone modifications and metabolic changes in innate immune cells following exposure to inflammatory signals, leading to heightened responsiveness to secondary stimuli. Although our understanding of the molecular regulation of trained immunity has increased, the role of adaptive immune cells herein remains largely unknown. Here, we show that T cells modulate trained immunity via cluster of differentiation 40-tissue necrosis factor receptor-associated factor 6 (CD40-TRAF6) signaling. CD40-TRAF6 inhibition modulates functional, transcriptomic, and metabolic reprogramming and modifies histone 3 lysine 4 trimethylation associated with trained immunity. Besides in vitro studies, we reveal that single-nucleotide polymorphisms in the proximity of CD40 are linked to trained immunity responses in vivo and that combining CD40-TRAF6 inhibition with cytotoxic T lymphocyte antigen 4-immunoglobulin (CTLA4-Ig)-mediated co-stimulatory blockade induces long-term graft acceptance in a murine heart transplantation model. Combined, our results reveal that trained immunity is modulated by CD40-TRAF6 signaling between myeloid and adaptive immune cells and that this can be leveraged for therapeutic purposes.
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Affiliation(s)
- Maaike M E Jacobs
- Department of Nephrology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rianne J F Maas
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Inge Jonkman
- Department of Nephrology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Yutaka Negishi
- Department of Cell Biology, Faculty of Science, Radboud University, Nijmegen, the Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Willem Tielemans Zamora
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Cansu Yanginlar
- Department of Nephrology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Julia van Heck
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Vasiliki Matzaraki
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Marijke Baltissen
- Department of Molecular Biology, Faculty of Science, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Judit Morla-Folch
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anna Ranzenigo
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - William Wang
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Martin Umali
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jordi Ochando
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Transplant Immunology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Johan van der Vlag
- Department of Nephrology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Luuk B Hilbrands
- Department of Nephrology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Medical Genetics, University of Medicine and Pharmacy, Iuliu Haţieganu, Cluj-Napoca, Romania
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Willem J M Mulder
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Mandy M T van Leent
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Musa M Mhlanga
- Department of Cell Biology, Faculty of Science, Radboud University, Nijmegen, the Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Abraham J P Teunissen
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nils Rother
- Department of Nephrology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Raphaël Duivenvoorden
- Department of Nephrology, Radboud University Medical Center, Nijmegen, the Netherlands; BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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19
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Jauhiainen MK, Pyöriä L, Viitasalo S, Aaltonen LM, Söderlund-Venermo M, Hagström J, Mäkitie AA, Perdomo MF, Sinkkonen ST. Multiple DNA Viruses and HPV Integration in Inverted Papilloma and Associated Sinonasal Carcinoma. Laryngoscope 2024. [PMID: 39171991 DOI: 10.1002/lary.31714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 08/06/2024] [Indexed: 08/23/2024]
Abstract
OBJECTIVES Sinonasal inverted papilloma (IP) has a locally destructive growth pattern, can relapse, and can undergo malignant transformation (IP-associated sinonasal squamous cell carcinoma (IP-SNSCC)). Human papillomaviruses (HPV)-6 and -16 are frequently detected in IPs. To clarify the possible roles of other DNA viruses in IPs, we explored viruses not studied in this context before. With the setting of pre- and post-malignant transformation samples, we investigated HPV genomes in depth to assess the integration of HPV into the human genome and the presence of minor intratypic variants. MATERIALS AND METHODS We analyzed 35 IP samples representing 28 individuals, of which six had IP-SNSCC. For virus screening, we applied qPCR to detect 16 different DNA viruses in three virus families, comprising herpesviruses, parvoviruses, and polyomaviruses. In addition, targeted next generation sequencing (NGS) was used for detailed HPV analysis. RESULTS We detected herpes-, parvo-, and polyomaviruses in 13/28 (46%) patients, with codetections of multiple viruses in six (21%) patients. NGS revealed HPV16 DNA in 2/6 IP-SNSCC and in their respective earlier benign IP samples, as well as in a plasma sample from one of these patients. HPV6 was detected in two IP samples without subsequent malignant transformation. We identified sequence reads containing junctions of HPV6 and HPV16 and host genome suggestive of viral integration. HPV6 and HPV16 minor intratypic variants were present across pre- and post-malignant transformation, with mostly nonsynonymous mutations. CONCLUSIONS Multiple DNA viruses were present in IPs. HPV16 was detected only in IP-SNSCCs or in tumors that later underwent malignant transformation. LEVEL OF EVIDENCE 3 Laryngoscope, 2024.
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Affiliation(s)
- Maria K Jauhiainen
- Department of Otorhinolaryngology - Head and Neck Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- The Doctoral Programme in Clinical Research, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Lari Pyöriä
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Sanna Viitasalo
- Department of Otorhinolaryngology - Head and Neck Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Leena-Maija Aaltonen
- Department of Otorhinolaryngology - Head and Neck Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Maria Söderlund-Venermo
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jaana Hagström
- Department of Pathology, University Hospital of Helsinki, Helsinki, Finland
- Department of Oral Pathology and Radiology, University of Turku, Turku, Finland
- Translational Cancer Research Medicine, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pathology, HusLab, Helsinki University Hospital, Helsinki, Finland
| | - Antti A Mäkitie
- Department of Otorhinolaryngology - Head and Neck Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Division of Ear, Nose and Throat Diseases, Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Maria F Perdomo
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Saku T Sinkkonen
- Department of Otorhinolaryngology - Head and Neck Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
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20
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Mohajeri Khorasani A, Raghibi A, Haj Mohammad Hassani B, Bolbolizadeh P, Amali A, Sadeghi M, Farshidi N, Dehghani A, Mousavi P. Decoding the Role of NEIL1 Gene in DNA Repair and Lifespan: A Literature Review with Bioinformatics Analysis. Adv Biol (Weinh) 2024:e2300708. [PMID: 39164210 DOI: 10.1002/adbi.202300708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 06/21/2024] [Indexed: 08/22/2024]
Abstract
Longevity, the length of an organism's lifespan, is impacted by environmental factors, metabolic processes, and genetic determinants. The base excision repair (BER) pathway is crucial for maintaining genomic integrity by repairing oxidatively modified base lesions. Nei-like DNA Glycosylase 1 (NEIL1), part of the BER pathway, is vital in repairing oxidative bases in G-rich DNA regions, such as telomeres and promoters. Hence, in this comprehensive review, it have undertaken a meticulous investigation of the intricate association between NEIL1 and longevity. The analysis delves into the multifaceted aspects of the NEIL1 gene, its various RNA transcripts, and the diverse protein isoforms. In addition, a combination of bioinformatic analysis is conducted to identify NEIL1 mutations, transcription factors, and epigenetic modifications, as well as its lncRNA/pseudogene/circRNA-miRNA-mRNA regulatory network. The findings suggest that the normal function of NEIL1 is a significant factor in human health and longevity, with defects in NEIL1 potentially leading to various cancers and related syndromes, Alzheimer's disease, obesity, and diabetes.
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Affiliation(s)
- Amirhossein Mohajeri Khorasani
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Student Research Committee, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Alireza Raghibi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, 1416634793, Iran
| | - Behzad Haj Mohammad Hassani
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Student Research Committee, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Pedram Bolbolizadeh
- Student Research Committee, Faculty of Para-Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Arian Amali
- School of Infection & Immunity, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Mahboubeh Sadeghi
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Student Research Committee, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Narges Farshidi
- Department of Pharmaceutics, Faculty of Pharmacy, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- USERN Office, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Aghdas Dehghani
- Endocrinology and Metabolism Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Pegah Mousavi
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
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21
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Handler JS, Li Z, Dveirin RK, Fang W, Goodarzi H, Fertig EJ, Kalhor R. Identifying a gene signature of metastatic potential by linking pre-metastatic state to ultimate metastatic fate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.14.607813. [PMID: 39185156 PMCID: PMC11343111 DOI: 10.1101/2024.08.14.607813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Identifying the key molecular pathways that enable metastasis by analyzing the eventual metastatic tumor is challenging because the state of the founder subclone likely changes following metastatic colonization. To address this challenge, we labeled primary mouse pancreatic ductal adenocarcinoma (PDAC) subclones with DNA barcodes to characterize their pre-metastatic state using ATAC-seq and RNA-seq and determine their relative in vivo metastatic potential prospectively. We identified a gene signature separating metastasis-high and metastasis-low subclones orthogonal to the normal-to-PDAC and classical-to-basal axes. The metastasis-high subclones feature activation of IL-1 pathway genes and high NF-κB and Zeb/Snail family activity and the metastasis-low subclones feature activation of neuroendocrine, motility, and Wnt pathway genes and high CDX2 and HOXA13 activity. In a functional screen, we validated novel mediators of PDAC metastasis in the IL-1 pathway, including the NF-κB targets Fos and Il23a, and beyond the IL-1 pathway including Myo1b and Tmem40. We scored human PDAC tumors for our signature of metastatic potential from mouse and found that metastases have higher scores than primary tumors. Moreover, primary tumors with higher scores are associated with worse prognosis. We also found that our metastatic potential signature is enriched in other human carcinomas, suggesting that it is conserved across epithelial malignancies. This work establishes a strategy for linking cancer cell state to future behavior, reveals novel functional regulators of PDAC metastasis, and establishes a method for scoring human carcinomas based on metastatic potential.
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Affiliation(s)
- Jesse S Handler
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zijie Li
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Rachel K Dveirin
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Weixiang Fang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hani Goodarzi
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
- Arc Institute, Palo Alto 94305, USA
| | - Elana J Fertig
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Convergence Institute, Johns Hopkins Data Science and AI Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Reza Kalhor
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Molecular Biology and Genetics, Department of Neuroscience, Department of Medicine, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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22
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Zuo Y, Liu W, Jin Y, Pan Y, Fan T, Fu X, Guo J, Tan S, He J, Yang Y, Li Z, Yang C, Peng Y. C2CDB: an advanced platform integrating comprehensive information and analysis tools of cancer-related circRNAs. BIOINFORMATICS ADVANCES 2024; 4:vbae112. [PMID: 39246384 PMCID: PMC11379471 DOI: 10.1093/bioadv/vbae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/04/2024] [Accepted: 08/14/2024] [Indexed: 09/10/2024]
Abstract
Motivation Circular RNAs (circRNAs) play important roles in gene expression and their involvement in tumorigenesis is emerging. circRNA-related database is a powerful tool for researchers to investigate circRNAs. However, existing databases lack advanced platform integrating comprehensive information and analysis tools of cancer-related circRNAs. Results We developed a comprehensive platform called CircRNA to Cancer Database (C2CDB), encompassing 318 158 cancer-related circRNAs expressed in tumors and adjacent tissues across 30 types of cancers. C2CDB provides basic details such as sequence and expression levels of circRNAs, as well as crucial insights into biological mechanisms, including miRNA binding, RNA-binding protein interaction, coding potential, base modification, mutation, and secondary structure. Moreover, C2CDB collects an extensive compilation of published literature on cancer circRNAs, extracting and presenting pivotal content encompassing biological functions, underlying mechanisms, and molecular tools in these studies. Additionally, C2CDB offers integrated tools to analyse three potential mechanisms: circRNA-miRNA ceRNA interaction, circRNA encoding, and circRNA biogenesis, facilitating investigators with convenient access to highly reliable information. To enhance clarity and organization, C2CDB has meticulously curated and integrated the previously chaotic nomenclature of circRNAs, addressing the prevailing confusion and ambiguity surrounding their designations. Availability and implementation C2CDB is freely available at http://pengyonglab.com/c2cdb.
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Affiliation(s)
- Yuanli Zuo
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Wenrong Liu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Yang Jin
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Yitong Pan
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Ting Fan
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Xin Fu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Jiawei Guo
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Shuangyan Tan
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Juan He
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Yang Yang
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Zhang Li
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Chenyu Yang
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Yong Peng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
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23
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Thorpe HJ, Pedersen BS, Dietze M, Link N, Quinlan AR, Bonkowsky JL, Thomas A, Chow CY. Identification of CNTN2 as a genetic modifier of PIGA-CDG through pedigree analysis of a family with incomplete penetrance and functional testing in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.12.607501. [PMID: 39211166 PMCID: PMC11361168 DOI: 10.1101/2024.08.12.607501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Loss of function mutations in the X-linked PIGA gene lead to PIGA-CDG, an ultra-rare congenital disorder of glycosylation (CDG), typically presenting with seizures, hypotonia, and neurodevelopmental delay. We identified two brothers (probands) with PIGA-CDG, presenting with epilepsy and mild developmental delay. Both probands carry PIGA S132C , an ultra-rare variant predicted to be damaging. Strikingly, the maternal grandfather and a great-uncle also carry PIGA S132C , but neither presents with symptoms associated with PIGA-CDG. We hypothesized genetic modifiers may contribute to this reduced penetrance. Using whole genome sequencing and pedigree analysis, we identified possible susceptibility variants found in the probands and not in carriers and possible protective variants found in the carriers and not in the probands. Candidate variants included heterozygous, damaging variants in three genes also involved directly in GPI-anchor biosynthesis and a few genes involved in other glycosylation pathways or encoding GPI-anchored proteins. We functionally tested the predicted modifiers using a Drosophila eye-based model of PIGA-CDG. We found that loss of CNTN2 , a predicted protective modifier, rescues loss of PIGA in Drosophila eye-based model, like what we predict in the family. Further testing found that loss of CNTN2 also rescues patient-relevant phenotypes, including seizures and climbing defects in Drosophila neurological models of PIGA-CDG. By using pedigree information, genome sequencing, and in vivo testing, we identified CNTN2 as a strong candidate modifier that could explain the incomplete penetrance in this family. Identifying and studying rare disease modifier genes in human pedigrees may lead to pathways and targets that may be developed into therapies.
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24
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Lin X, Zhao R, Bin Y, Huo R, Xue G, Wu J. TIMP1 promotes thyroid cancer cell progression through macrophage phenotypic polarization via the PI3K/AKT signaling pathway. Genomics 2024; 116:110914. [PMID: 39128817 DOI: 10.1016/j.ygeno.2024.110914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/21/2024] [Accepted: 08/08/2024] [Indexed: 08/13/2024]
Abstract
Increasing evidence suggests that tissue inhibitor of metalloproteinase 1 (TIMP1) played a pivotal role in immune regulation. Our study focused on examining the expression and function of TIMP1 in humans, particularly in its regulation of tumor-associated macrophages (TAMs) in papillary thyroid carcinoma (PTC). We observed an upregulation of TIMP1 in 16 different types of malignancies, including thyroid cancer. TIMP1 shaped the inflammatory TME in PTC. Inhibiting the expression of TIMP1 has been demonstrated to reduce the malignant biological traits of PTC cells. Furthermore, reducing TIMP1 expression impeded M2 macrophage polarization as well as facilitated M1 macrophage polarization in PTC. ELISA results demonstrated that downregulated TIMP1 expression correlated with decreased levels of IL10 and TGF-β in cell supernatants. Furthermore, the supernatant from polarized macrophages in the TIMP1-silenced group inhibited the motility of wild-type PTC cells. Therefore, TIMP1 may enhance the progression of PTC by stimulating the PI3K/AKT pathway via the secretion of IL10 and TGF-β, consequently influencing M2-type polarization in TAMs.
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Affiliation(s)
- Xu Lin
- Department of Morphology Laboratory, Hebei North University, Zhangjiakou 075000, China
| | - Ruhua Zhao
- Department of Morphology Laboratory, Hebei North University, Zhangjiakou 075000, China
| | - Yu Bin
- Department of Morphology Laboratory, Hebei North University, Zhangjiakou 075000, China
| | - Ronghua Huo
- Department of Morphology Laboratory, Hebei North University, Zhangjiakou 075000, China
| | - Gang Xue
- Department of Morphology Laboratory, Hebei North University, Zhangjiakou 075000, China; Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou 075000, China.
| | - Jingfang Wu
- Department of Morphology Laboratory, Hebei North University, Zhangjiakou 075000, China.
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Khetan N, Zuckerman B, Calia GP, Chen X, Arceo XG, Weinberger LS. Quantitative comparison of single-cell RNA sequencing versus single-molecule RNA imaging for quantifying transcriptional noise. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.607289. [PMID: 39149226 PMCID: PMC11326230 DOI: 10.1101/2024.08.09.607289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Stochastic fluctuations (noise) in transcription generate substantial cell-to-cell variability. However, how best to quantify genome-wide noise, remains unclear. Here we utilize a small-molecule perturbation (IdU) to amplify noise and assess noise quantification from numerous scRNA-seq algorithms on human and mouse datasets, and then compare to noise quantification from single-molecule RNA FISH (smFISH) for a panel of representative genes. We find that various scRNA-seq analyses report amplified noise, without altered mean-expression levels, for ~90% of genes and that smFISH analysis verifies noise amplification for the vast majority of genes tested. Collectively, the analyses suggest that most scRNA-seq algorithms are appropriate for quantifying noise including a simple normalization approach, although all of these systematically underestimate noise compared to smFISH. From a practical standpoint, this analysis argues that IdU is a globally penetrant noise-enhancer molecule-amplifying noise without altering mean-expression levels-which could enable investigations of the physiological impacts of transcriptional noise.
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Affiliation(s)
- Neha Khetan
- Gladstone|UCSF Center for Cell Circuitry, University of California, San Francisco, CA 94158
| | - Binyamin Zuckerman
- Gladstone|UCSF Center for Cell Circuitry, University of California, San Francisco, CA 94158
| | - Giuliana P. Calia
- Gladstone|UCSF Center for Cell Circuitry, University of California, San Francisco, CA 94158
| | - Xinyue Chen
- Gladstone|UCSF Center for Cell Circuitry, University of California, San Francisco, CA 94158
| | - Ximena Garcia Arceo
- Gladstone|UCSF Center for Cell Circuitry, University of California, San Francisco, CA 94158
| | - Leor S. Weinberger
- Gladstone|UCSF Center for Cell Circuitry, University of California, San Francisco, CA 94158
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
- Lead contact
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Witmer NH, McLendon JM, Stein CS, Yoon JY, Berezhnaya E, Elrod JW, London BL, Boudreau RL. Upstream alternative polyadenylation in SCN5A produces a short transcript isoform encoding a mitochondria-localized NaV1.5 N-terminal fragment that influences cardiomyocyte respiration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.607406. [PMID: 39211120 PMCID: PMC11360925 DOI: 10.1101/2024.08.09.607406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
SCN5A encodes the cardiac voltage-gated Na+ channel, NaV1.5, that initiates action potentials. SCN5A gene variants cause arrhythmias and increased heart failure risk. Mechanisms controlling NaV1.5 expression and activity are not fully understood. We recently found a well-conserved alternative polyadenylation (APA) signal downstream of the first SCN5A coding exon. This yields a SCN5A-short transcript isoform expressed in several species (e.g. human, pig, and cat), though rodents lack this upstream APA. Reanalysis of transcriptome-wide cardiac APA-seq and mRNA-seq data shows reductions in both upstream APA usage and short/full-length SCN5A mRNA ratios in failing hearts. Knock-in of the human SCN5A APA sequence into mice is sufficient to enable expression of SCN5A -short transcript, while significantly decreasing expression of full-length SCN5A mRNA. Notably, SCN5A -short transcript encodes a novel protein (NaV1.5-NT), composed of an N-terminus identical to NaV1.5 and a unique C-terminus derived from intronic sequence. AAV9 constructs were able to achieve stable NaV1.5-NT expression in mouse hearts, and western blot of human heart tissues showed bands co-migrating with NaV1.5-NT transgene-derived bands. NaV1.5-NT is predicted to contain a mitochondrial targeting sequence and localizes to mitochondria in cultured cardiomyocytes and in mouse hearts. NaV1.5-NT expression in cardiomyocytes led to elevations in basal oxygen consumption rate, ATP production, and mitochondrial ROS, while depleting NADH supply. Native PAGE analyses of mitochondria lysates revealed that NaV1.5-NT expression resulted in increased levels of disassembled complex V subunits and accumulation of complex I-containing supercomplexes. Overall, we discovered that APA-mediated regulation of SCN5A produces a short transcript encoding NaV1.5-NT. Our data support that NaV1.5-NT plays a multifaceted role in influencing mitochondrial physiology: 1) by increasing basal respiration likely through promoting complex V conformations that enhance proton leak, and 2) by increasing overall respiratory efficiency and NADH consumption by enhancing formation and/or stability of complex I-containing respiratory supercomplexes, though the specific molecular mechanisms underlying each of these remain unresolved.
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Lipowicz JM, Malińska A, Nowicki M, Rawłuszko-Wieczorek AA. Genes Co-Expressed with ESR2 Influence Clinical Outcomes in Cancer Patients: TCGA Data Analysis. Int J Mol Sci 2024; 25:8707. [PMID: 39201394 PMCID: PMC11354723 DOI: 10.3390/ijms25168707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/02/2024] [Accepted: 08/07/2024] [Indexed: 09/02/2024] Open
Abstract
ERβ has been assigned a tumor suppressor role in many cancer types. However, as conflicting findings emerge, ERβ's tissue-specific expression and functional role have remained elusive. There remains a notable gap in compact and comprehensive analyses of ESR2 mRNA expression levels across diverse tumor types coupled with an exploration of its potential gene network. In this study, we aim to address these gaps by presenting a comprehensive analysis of ESR2 transcriptomic data. We distinguished cancer types with significant changes in ESR2 expression levels compared to corresponding healthy tissue and concluded that ESR2 influences patient survival. Gene Set Enrichment Analysis (GSEA) distinguished molecular pathways affected by ESR2, including oxidative phosphorylation and epithelial-mesenchymal transition. Finally, we investigated genes displaying similar expression patterns as ESR2 in tumor tissues, identifying potential co-expressed genes that may exert a synergistic effect on clinical outcomes, with significant results, including the expression of ACIN1, SYNE2, TNFRSF13C, and MDM4. Collectively, our results highlight the significant influence of ESR2 mRNA expression on the transcriptomic landscape and the overall metabolism of cancerous cells across various tumor types.
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Affiliation(s)
- Julia Maria Lipowicz
- Department of Histology and Embryology, Doctoral School, Poznan University of Medical Sciences, Święcickiego 6 Street, 60-781 Poznań, Poland;
| | - Agnieszka Malińska
- Department of Histology and Embryology, Poznan University of Medical Sciences, Święcickiego 6 Street, 60-781 Poznań, Poland
| | - Michał Nowicki
- Department of Histology and Embryology, Poznan University of Medical Sciences, Święcickiego 6 Street, 60-781 Poznań, Poland
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Rots D, Choufani S, Faundes V, Dingemans AJM, Joss S, Foulds N, Jones EA, Stewart S, Vasudevan P, Dabir T, Park SM, Jewell R, Brown N, Pais L, Jacquemont S, Jizi K, Ravenswaaij-Arts CMAV, Kroes HY, Stumpel CTRM, Ockeloen CW, Diets IJ, Nizon M, Vincent M, Cogné B, Besnard T, Kambouris M, Anderson E, Zackai EH, McDougall C, Donoghue S, O'Donnell-Luria A, Valivullah Z, O'Leary M, Srivastava S, Byers H, Leslie N, Mazzola S, Tiller GE, Vera M, Shen JJ, Boles R, Jain V, Brischoux-Boucher E, Kinning E, Simpson BN, Giltay JC, Harris J, Keren B, Guimier A, Marijon P, Vries BBAD, Motter CS, Mendelsohn BA, Coffino S, Gerkes EH, Afenjar A, Visconti P, Bacchelli E, Maestrini E, Delahaye-Duriez A, Gooch C, Hendriks Y, Adams H, Thauvin-Robinet C, Josephi-Taylor S, Bertoli M, Parker MJ, Rutten JW, Caluseriu O, Vernon HJ, Kaziyev J, Zhu J, Kremen J, Frazier Z, Osika H, Breault D, Nair S, Lewis SME, Ceroni F, Viggiano M, Posar A, Brittain H, Giovanna T, Giulia G, Quteineh L, Ha-Vinh Leuchter R, Zonneveld-Huijssoon E, Mellado C, Marey I, Coudert A, Aracena Alvarez MI, Kennis MGP, Bouman A, Roifman M, Amorós Rodríguez MI, Ortigoza-Escobar JD, Vernimmen V, Sinnema M, Pfundt R, Brunner HG, Vissers LELM, Kleefstra T, Weksberg R, Banka S. Pathogenic variants in KMT2C result in a neurodevelopmental disorder distinct from Kleefstra and Kabuki syndromes. Am J Hum Genet 2024; 111:1626-1642. [PMID: 39013459 PMCID: PMC11339626 DOI: 10.1016/j.ajhg.2024.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/08/2024] [Accepted: 06/19/2024] [Indexed: 07/18/2024] Open
Abstract
Trithorax-related H3K4 methyltransferases, KMT2C and KMT2D, are critical epigenetic modifiers. Haploinsufficiency of KMT2C was only recently recognized as a cause of neurodevelopmental disorder (NDD), so the clinical and molecular spectrums of the KMT2C-related NDD (now designated as Kleefstra syndrome 2) are largely unknown. We ascertained 98 individuals with rare KMT2C variants, including 75 with protein-truncating variants (PTVs). Notably, ∼15% of KMT2C PTVs were inherited. Although the most highly expressed KMT2C transcript consists of only the last four exons, pathogenic PTVs were found in almost all the exons of this large gene. KMT2C variant interpretation can be challenging due to segmental duplications and clonal hematopoesis-induced artifacts. Using samples from 27 affected individuals, divided into discovery and validation cohorts, we generated a moderate strength disorder-specific KMT2C DNA methylation (DNAm) signature and demonstrate its utility in classifying non-truncating variants. Based on 81 individuals with pathogenic/likely pathogenic variants, we demonstrate that the KMT2C-related NDD is characterized by developmental delay, intellectual disability, behavioral and psychiatric problems, hypotonia, seizures, short stature, and other comorbidities. The facial module of PhenoScore, applied to photographs of 34 affected individuals, reveals that the KMT2C-related facial gestalt is significantly different from the general NDD population. Finally, using PhenoScore and DNAm signatures, we demonstrate that the KMT2C-related NDD is clinically and epigenetically distinct from Kleefstra and Kabuki syndromes. Overall, we define the clinical features, molecular spectrum, and DNAm signature of the KMT2C-related NDD and demonstrate they are distinct from Kleefstra and Kabuki syndromes highlighting the need to rename this condition.
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Affiliation(s)
- Dmitrijs Rots
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands; Genetics Laboratory, Children's Clinical University Hospital, Riga, Latvia
| | - Sanaa Choufani
- Genetics and Genome Biology Program, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Victor Faundes
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de Los Alimentos (INTA), Universidad de Chile, Santiago, Chile; Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | | | - Shelagh Joss
- West of Scotland Centre for Genomic Medicine, Queen Elizabeth University Hospital, Glasgow, UK
| | - Nicola Foulds
- Wessex Clinical Genetics Services, University Hospital Southampton NHS Foundation Trust, Southampton SO16 5YA, UK
| | - Elizabeth A Jones
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Sarah Stewart
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Pradeep Vasudevan
- Department of Clinical Genetics, University Hospitals of Leicester, Leicester Royal Infirmary, Leicester LE1 7RH, UK
| | - Tabib Dabir
- Northern Ireland Regional Genetics Centre, Belfast City Hospital, Belfast, UK
| | - Soo-Mi Park
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Rosalyn Jewell
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Natasha Brown
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, Royal Children's Hospital, The University of Melbourne, Melbourne, VIC, Australia
| | - Lynn Pais
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Khadijé Jizi
- Service de Génétique Médicale, CHU Ste-Justine, Montréal, QC, Canada
| | | | - Hester Y Kroes
- Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Constance T R M Stumpel
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands; GROW-School for Oncology and Reproduction, Maastricht, the Netherlands
| | - Charlotte W Ockeloen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Illja J Diets
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Mathilde Nizon
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Marie Vincent
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Benjamin Cogné
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Thomas Besnard
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Marios Kambouris
- Division of Genetics, Department of Pathology and Laboratory Medicine Department, Sidra Medicine, Doha, Qatar
| | - Emily Anderson
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Elaine H Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Carey McDougall
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah Donoghue
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Anne O'Donnell-Luria
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zaheer Valivullah
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Melanie O'Leary
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | | | - Heather Byers
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Nancy Leslie
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Sarah Mazzola
- Center for Personalized Genetic Healthcare, Cleveland Clinic, Cleveland, OH, USA
| | - George E Tiller
- Department of Genetics, Kaiser Permanente, Los Angeles, CA, USA
| | - Moin Vera
- Department of Genetics, Kaiser Permanente, Los Angeles, CA, USA
| | - Joseph J Shen
- Division of Genetics, Department of Pediatrics, UCSF Fresno, Fresno, CA, USA; Division of Genomic Medicine, Department of Pediatrics, University of California Davis, Sacramento, CA, USA
| | | | - Vani Jain
- All Wales Medical Genomics Service, Wales Genomic Health Centre, Cardiff Edge Business Park, Longwood Drive, Whitchurch, Cardiff CF14 7YU, UK
| | | | - Esther Kinning
- Clinical Genetics, Birmingham Women's and Children's, Birmingham, UK
| | - Brittany N Simpson
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Jacques C Giltay
- Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jacqueline Harris
- Kennedy Krieger Institute, Baltimore, MD, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Boris Keren
- Department of Genetics, APHP Sorbonne University, Paris, France
| | - Anne Guimier
- Service de Médecine Genomique des Maladies Rares, CRMR Anomalies Du Développement, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Pierre Marijon
- Laboratoire de Biologie Médicale Multisites Seqoia FMG2025, 75014 Paris, France
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | | | - Samantha Coffino
- Department of Pediatric Neurology, Kaiser Permanente, Oakland, CA, USA
| | - Erica H Gerkes
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Afenjar
- APHP Sorbonne Université, Centre de Référence Malformations et Maladies Congénitales Du Cervelet et Déficiences Intellectuelles de Causes Rares, Département de Génétique et Embryologie Médicale, Hôpital Trousseau, Paris, France
| | - Paola Visconti
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, UOSI Disturbi Dello Spettro Autistico, Bologna, Italy
| | - Elena Bacchelli
- Pharmacy and Biotechnology Department, University of Bologna, Bologna, Italy
| | - Elena Maestrini
- Pharmacy and Biotechnology Department, University of Bologna, Bologna, Italy
| | | | - Catherine Gooch
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - Yvonne Hendriks
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Hieab Adams
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands
| | - Christel Thauvin-Robinet
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France; Centre de Référence Déficiences Intellectuelles de Causes Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Sarah Josephi-Taylor
- Department of Clinical Genetics, The Children's Hospital at Westmead, Sydney, NSW, Australia; Discipline of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Marta Bertoli
- Northern Genetics Service, Newcastle Upon Tyne NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Michael J Parker
- Department of Clinical Genetics, Sheffield Children's Hospital, Sheffield, UK
| | - Julie W Rutten
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Oana Caluseriu
- Department of Medical Genetics, University of Alberta, Edmonton, Canada
| | - Hilary J Vernon
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jonah Kaziyev
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jia Zhu
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jessica Kremen
- Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zoe Frazier
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hailey Osika
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - David Breault
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sreelata Nair
- Department of Fetal Medicine, Lifeline Super Specialty Hospital, Kerala, India
| | - Suzanne M E Lewis
- Department of Medical Genetics, BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Fabiola Ceroni
- Pharmacy and Biotechnology Department, University of Bologna, Bologna, Italy; Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Marta Viggiano
- Pharmacy and Biotechnology Department, University of Bologna, Bologna, Italy
| | - Annio Posar
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, UOSI Disturbi Dello Spettro Autistico, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Helen Brittain
- Department of Clinical Genetics, Birmingham Women's & Children's NHS Trust, Birmingham, UK
| | - Traficante Giovanna
- Medical Genetics Unit, Meyer Children's Hospital IRCCS Florence, Florence, Italy
| | - Gori Giulia
- Medical Genetics Unit,Meyer Children's Hospital IRCCS, Florence, Italy
| | - Lina Quteineh
- Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Russia Ha-Vinh Leuchter
- Division of Development and Growth, Department of Pediatrics, University of Geneva, Geneva, Switzerland
| | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cecilia Mellado
- Sección de Genética y Errores Congénitos Del Metabolismo, División de Pediatría, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | | | - Mariana Inés Aracena Alvarez
- Unit of Genetics and Metabolic Diseases, Division of Pediatrics, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Milou G P Kennis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Arianne Bouman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Maian Roifman
- The Prenatal Diagnosis and Medical Genetics Program, Division of Maternal Fetal Medicine, Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Canada
| | | | - Juan Dario Ortigoza-Escobar
- Movement Disorders Unit, Institut de Recerca Sant Joan de Déu, CIBERER-ISCIII and European Reference Network for Rare Neurological Diseases (ERN-RND), Barcelona, Spain
| | - Vivian Vernimmen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands; GROW-School for Oncology and Reproduction, Maastricht, the Netherlands
| | - Margje Sinnema
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands; Center of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, the Netherlands.
| | - Rosanna Weksberg
- Genetics and Genome Biology Program, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Division of Clinical and Metabolic Genetics, Department of Pediatrics, the Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada.
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
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Flores CC, Pasetto NA, Wang H, Dimitrov AG, Davis JF, Jiang Z, Davis CJ, Gerstner JR. Sleep and diurnal alternative polyadenylation sites associated with human APA-linked brain disorders. RESEARCH SQUARE 2024:rs.3.rs-4707772. [PMID: 39149473 PMCID: PMC11326403 DOI: 10.21203/rs.3.rs-4707772/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Disruption of sleep and circadian rhythms are a comorbid feature of many pathologies, and can negatively influence many health conditions, including neurodegenerative disease, metabolic illness, cancer, and various neurological disorders. Genetic association studies linking sleep and circadian disturbances with disease susceptibility have mainly focused on changes in gene expression due to mutations, such as single-nucleotide polymorphisms. The interaction between sleep and/or circadian rhythms with the use of Alternative Polyadenylation (APA) has been largely undescribed, particularly in the context of other disorders. APA is a process that generates various transcript isoforms of the same gene affecting its mRNA translation, stability, localization, and subsequent function. Here we identified unique APAs expressed in rat brain over time-of-day, immediately following sleep deprivation, and the subsequent recovery period. From these data, we performed a secondary analysis of these sleep- or time-of-day associated PASs with recently described APA-linked human brain disorder susceptibility genes.
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Chatterjee S, Ghosh S, Sin Z, Davis E, Preval LV, Tran N, Bammidi S, Gautam P, Hose S, Sergeev Y, Flores-Bellver M, Aldiri I, Sinha D, Guha P. βA3/A1-crystallin is an epigenetic regulator of histone deacetylase 3 (HDAC3) in the retinal pigmented epithelial (RPE) cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.06.606634. [PMID: 39211129 PMCID: PMC11361014 DOI: 10.1101/2024.08.06.606634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The retinal pigmented epithelial (RPE) cells maintain retinal homeostasis, and alterations in their function contribute to non-exudative age-related macular degeneration (AMD) 1,2 . Here, we explore the intricate relationship between RPE cells, epigenetic modifications, and the development of AMD. Importantly, the study reveals a substantial decrease in histone deacetylase 3 (HDAC3) activity and elevated histone acetylation in the RPE of human AMD donor eyes. To investigate epigenetic mechanisms in AMD development, we used a mouse model with RPE-specific Cryba1 knockout 3-5 , revealing that the loss of βA3/A1-crystallin selectively reduces HDAC3 activity, resulting in increased histone acetylation. βA3/A1-crystallin activates HDAC3 by facilitating its interaction with the casein kinase II (CK2) and phosphorylating HDAC3, as well as by regulating intracellular InsP6 (phytic acid) levels, required for activating HDAC3. These findings highlight a novel function of βA3/A1-crystallin as an epigenetic regulator of HDAC3 in the RPE cells and provide insights into potential therapeutic strategies in non-exudative AMD.
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Li L, Li D, Jin J, Xu F, He N, Ren Y, Wang X, Tian L, Chen B, Li X, Chen Z, Zhang L, Qiao L, Wang L, Wang J. FOSL1-mediated LINC01566 negatively regulates CD4 + T-cell activation in myasthenia gravis. J Neuroinflammation 2024; 21:197. [PMID: 39113081 PMCID: PMC11308467 DOI: 10.1186/s12974-024-03194-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Myasthenia gravis (MG) is an autoimmune disease characterized by pathogenic antibodies that target structures of the neuromuscular junction. The evidence suggests that the regulation of long noncoding RNAs (lncRNAs) that is mediated by transcription factors (TFs) plays a key role in the pathophysiology of MG. Nevertheless, the detailed molecular mechanisms of lncRNAs in MG remain largely undetermined. METHODS Using microarray analysis, we analyzed the lncRNA levels in MG. By bioinformatics analysis, LINC01566 was found to potentially play an important role in MG. First, qRT‒PCR was performed to verify the LINC1566 expressions in MG patients. Then, fluorescence in situ hybridization was conducted to determine the localization of LINC01566 in CD4 + T cells. Finally, the impact of LINC01566 knockdown or overexpression on CD4 + T-cell function was also analyzed using flow cytometry and CCK-8 assay. A dual-luciferase reporter assay was used to validate the binding of the TF FOSL1 to the LINC01566 promoter. RESULTS Based on the lncRNA microarray and differential expression analyses, we identified 563 differentially expressed (DE) lncRNAs, 450 DE mRNAs and 19 DE TFs in MG. We then constructed a lncRNA-TF-mRNA network. Through network analysis, we found that LINC01566 may play a crucial role in MG by regulating T-cell-related pathways. Further experiments indicated that LINC01566 is expressed at low levels in MG patients. Functionally, LINC01566 is primarily distributed in the nucleus and can facilitate CD4 + T-cell apoptosis and inhibit cell proliferation. Mechanistically, we hypothesized that LINC01566 may negatively regulate the expressions of DUSP3, CCR2, FADD, SIRPB1, LGALS3 and SIRPB1, which are involved in the T-cell activation pathway, to further influence the cellular proliferation and apoptosis in MG. Moreover, we found that the effect of LINC01566 on CD4 + T cells in MG was mediated by the TF FOSL1, and in vitro experiments indicated that FOSL1 can bind to the promoter region of LINC01566. CONCLUSIONS In summary, our research revealed the protective roles of LINC01566 in clinical samples and cellular experiments, illustrating the potential roles and mechanism by which FOSL1/LINC01566 negatively regulates CD4 + T-cell activation in MG.
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Affiliation(s)
- Lifang Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Danyang Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Jingnan Jin
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Fanfan Xu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Ni He
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Yingjie Ren
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Xiaokun Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Liting Tian
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Biying Chen
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Xiaoju Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Zihong Chen
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Lanxin Zhang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Lukuan Qiao
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China.
| | - Jianjian Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China.
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Zhao Y, Feng Y, Sun F, Li L, Chen J, Song Y, Zhu W, Hu X, Li Z, Kong F, Du Y, Kong X. Optimized rAAV8 targeting acinar KLF4 ameliorates fibrosis in chronic pancreatitis via exosomes-enriched let-7s suppressing pancreatic stellate cells activation. Mol Ther 2024; 32:2624-2640. [PMID: 38956871 PMCID: PMC11405174 DOI: 10.1016/j.ymthe.2024.06.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 05/14/2024] [Accepted: 06/20/2024] [Indexed: 07/04/2024] Open
Abstract
Chronic pancreatitis (CP) is marked by progressive fibrosis and the activation of pancreatic stellate cells (PSCs), accompanied by the destruction of pancreatic parenchyma, leading to the loss of acinar cells (ACs). Few research studies have explored the mechanism by which damaged ACs (DACs) contribute to PSCs activation and pancreatic fibrosis. Currently, there are no effective drugs for curing CP or limiting the progression of pancreatic fibrosis. In this research, co-culture with intact acinar cells (IACs) suppressed PSC activation, while co-culture with DACs did the opposite. Krüppel-like factor 4 (KLF4) was significantly upregulated in DACs and was established as the key molecule that switches ACs from PSCs-suppressor to PSCs-activator. We revealed the exosomes of IACs contributed to the anti-activated function of IACs-CS on PSCs. MiRNome profiling showed that let-7 family is significantly enriched in IAC-derived exosomes (>30% miRNome), which partially mediates IACs' suppressive impacts on PSCs. Furthermore, it has been observed that the enrichment of let-7 in exosomes was influenced by the expression level of KLF4. Mechanistic studies demonstrated that KLF4 in ACs upregulated Lin28A, thereby decreasing let-7 levels in AC-derived exosomes, and thus promoting PSCs activation. We utilized an adeno-associated virus specifically targeting KLF4 in ACs (shKLF4-pAAV) to suppress PSCs activation in CP, resulting in reduced pancreatic fibrosis. IAC-derived exosomes hold potential as potent weapons against PSCs activation via let-7s, while activated KLF4/Lin28A signaling in DACs diminished such functions. ShKLF4-pAAV holds promise as a novel therapeutic approach for CP.
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Affiliation(s)
- Yating Zhao
- Department of Gastroenterology, Shanghai Institute of Pancreatic Diseases, Changhai Hospital, National Key Laboratory of Immunity and Inflammation, Naval Medical University, Shanghai, 200433, China
| | - Yongpu Feng
- Department of Gastroenterology, Shanghai Institute of Pancreatic Diseases, Changhai Hospital, National Key Laboratory of Immunity and Inflammation, Naval Medical University, Shanghai, 200433, China
| | - Fengyuan Sun
- Department of Gastroenterology, Shanghai Institute of Pancreatic Diseases, Changhai Hospital, National Key Laboratory of Immunity and Inflammation, Naval Medical University, Shanghai, 200433, China
| | - Lei Li
- Digestive Endoscopy Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Jiayu Chen
- Department of Gastroenterology, Shanghai Institute of Pancreatic Diseases, Changhai Hospital, National Key Laboratory of Immunity and Inflammation, Naval Medical University, Shanghai, 200433, China
| | - Yingxiao Song
- Department of Gastroenterology, Shanghai Institute of Pancreatic Diseases, Changhai Hospital, National Key Laboratory of Immunity and Inflammation, Naval Medical University, Shanghai, 200433, China
| | - Wenbo Zhu
- Department of Gastroenterology, Shanghai Institute of Pancreatic Diseases, Changhai Hospital, National Key Laboratory of Immunity and Inflammation, Naval Medical University, Shanghai, 200433, China
| | - Xiulin Hu
- Department of Gastroenterology, Shanghai Institute of Pancreatic Diseases, Changhai Hospital, National Key Laboratory of Immunity and Inflammation, Naval Medical University, Shanghai, 200433, China
| | - Zhaoshen Li
- Department of Gastroenterology, Shanghai Institute of Pancreatic Diseases, Changhai Hospital, National Key Laboratory of Immunity and Inflammation, Naval Medical University, Shanghai, 200433, China.
| | - Fanyang Kong
- Department of Gastroenterology, Shanghai Institute of Pancreatic Diseases, Changhai Hospital, National Key Laboratory of Immunity and Inflammation, Naval Medical University, Shanghai, 200433, China.
| | - Yiqi Du
- Department of Gastroenterology, Shanghai Institute of Pancreatic Diseases, Changhai Hospital, National Key Laboratory of Immunity and Inflammation, Naval Medical University, Shanghai, 200433, China.
| | - Xiangyu Kong
- Department of Gastroenterology, Shanghai Institute of Pancreatic Diseases, Changhai Hospital, National Key Laboratory of Immunity and Inflammation, Naval Medical University, Shanghai, 200433, China.
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Gable SM, Bushroe NA, Mendez JM, Wilson A, Pinto BJ, Gamble T, Tollis M. Differential Conservation and Loss of Chicken Repeat 1 (CR1) Retrotransposons in Squamates Reveal Lineage-Specific Genome Dynamics Across Reptiles. Genome Biol Evol 2024; 16:evae157. [PMID: 39031594 PMCID: PMC11303007 DOI: 10.1093/gbe/evae157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/22/2024] Open
Abstract
Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniote vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; including ∼11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific genome dynamics have evolved over the course of squamate evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the chicken repeat 1 (CR1) retrotransposon, a TE family found in most tetrapod genomes which is the dominant TE in most reptiles. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.
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Affiliation(s)
- Simone M Gable
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Nicholas A Bushroe
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Jasmine M Mendez
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Adam Wilson
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Brendan J Pinto
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
| | - Tony Gamble
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
- Bell Museum of Natural History, University of Minnesota, St. Paul, MN, USA
| | - Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
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Boughalem A, Ciorna-Monferrato V, Sloboda N, Guegan A, Page F, Zimmer S, Benazra M, Kleinfinger P, Lohmann L, Valduga M, Receveur A, Martin F, Trost D. Optical genome mapping identifies a homozygous deletion in the non-coding region of the SCN9A gene in individuals from the same family with congenital insensitivity to pain. Front Genet 2024; 15:1375770. [PMID: 39156962 PMCID: PMC11327051 DOI: 10.3389/fgene.2024.1375770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 07/18/2024] [Indexed: 08/20/2024] Open
Abstract
We report an index patient with complete insensitivity to pain and a history of painless fractures, joint hypermobility, and behavioral problems. The index patient descends from a family with notable cases among his maternal relatives, including his aunt and his mother's first cousin, both of whom suffer from congenital insensitivity to pain. The patient had normal results for prior genetic testing: fragile-X syndrome testing, chromosomal microarray analysis, and exome sequencing. Optical genome mapping detected a homozygous deletion affecting the noncoding 5' untranslated region (UTR) and the first non-coding exon of the SCN9A gene in all affected family members, compatible with recessive disease transmission. Pathogenic homozygous loss-of-function variants in the SCN9A gene are associated with impaired pain sensation in humans. Optical genome mapping can thus detect pathogenic structural variants in patients without molecular etiology by standard diagnostic procedures and is a more accessible diagnostic tool than short-read or long-read whole-genome sequencing.
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Affiliation(s)
- Aïcha Boughalem
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Viorica Ciorna-Monferrato
- Génétique Médicale et Oncogénétique, Hôpital Femme Mère Enfant, CHR Metz-Thionville, site de Mercy, 1, Allée du Château, Metz Cedex, France
| | - Natacha Sloboda
- Génétique Médicale et Oncogénétique, Hôpital Femme Mère Enfant, CHR Metz-Thionville, site de Mercy, 1, Allée du Château, Metz Cedex, France
| | - Amélie Guegan
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - François Page
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Sophie Zimmer
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Marion Benazra
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Pascale Kleinfinger
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Laurence Lohmann
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Mylène Valduga
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Aline Receveur
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Fernando Martin
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Detlef Trost
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
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35
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Luo H, Tang L, Zeng M, Yin R, Ding P, Luo L, Li M. BertSNR: an interpretable deep learning framework for single-nucleotide resolution identification of transcription factor binding sites based on DNA language model. Bioinformatics 2024; 40:btae461. [PMID: 39107889 PMCID: PMC11310455 DOI: 10.1093/bioinformatics/btae461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/07/2024] [Indexed: 08/10/2024] Open
Abstract
MOTIVATION Transcription factors are pivotal in the regulation of gene expression, and accurate identification of transcription factor binding sites (TFBSs) at high resolution is crucial for understanding the mechanisms underlying gene regulation. The task of identifying TFBSs from DNA sequences is a significant challenge in the field of computational biology today. To address this challenge, a variety of computational approaches have been developed. However, these methods face limitations in their ability to achieve high-resolution identification and often lack interpretability. RESULTS We propose BertSNR, an interpretable deep learning framework for identifying TFBSs at single-nucleotide resolution. BertSNR integrates sequence-level and token-level information by multi-task learning based on pre-trained DNA language models. Benchmarking comparisons show that our BertSNR outperforms the existing state-of-the-art methods in TFBS predictions. Importantly, we enhanced the interpretability of the model through attentional weight visualization and motif analysis, and discovered the subtle relationship between attention weight and motif. Moreover, BertSNR effectively identifies TFBSs in promoter regions, facilitating the study of intricate gene regulation. AVAILABILITY AND IMPLEMENTATION The BertSNR source code can be found at https://github.com/lhy0322/BertSNR.
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Affiliation(s)
- Hanyu Luo
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
- School of Computer Science, University of South China, Hengyang, Hunan 421001, China
| | - Li Tang
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Min Zeng
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Rui Yin
- Department of Health Outcome and Biomedical Informatics, University of Florida, Gainesville, FL 32611, United States
| | - Pingjian Ding
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Lingyun Luo
- School of Computer Science, University of South China, Hengyang, Hunan 421001, China
| | - Min Li
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
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36
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Ding P, Wu H, Wu J, Li T, He J, Ju Y, Liu Y, Li F, Deng H, Gu R, Zhang L, Guo H, Tian Y, Yang P, Meng N, Li X, Guo Z, Meng L, Zhao Q. N6-methyladenosine modified circPAK2 promotes lymph node metastasis via targeting IGF2BPs/VEGFA signaling in gastric cancer. Oncogene 2024; 43:2548-2563. [PMID: 39014193 DOI: 10.1038/s41388-024-03099-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 07/18/2024]
Abstract
Circular RNAs (circRNAs) have emerged as key regulators of cancer occurrence and progression, as well as promising biomarkers for cancer diagnosis and prognosis. However, the potential mechanisms of circRNAs implicated in lymph node (LN) metastasis of gastric cancer remain unclear. Herein, we identify a novel N6-methyladenosine (m6A) modified circRNA, circPAK2, which is significantly upregulated in gastric cancer tissues and metastatic LN tissues. Functionally, circPAK2 enhances the migration, invasion, lymphangiogenesis, angiogenesis, epithelial-mesenchymal transition (EMT), and metastasis of gastric cancer in vitro and in vivo. Mechanistically, circPAK2 is exported by YTH domain-containing protein 1 (YTHDC1) from the nucleus to the cytoplasm in an m6A methylation-dependent manner. Moreover, increased cytoplasmic circPAK2 interacts with Insulin-Like Growth Factor 2 mRNA-Binding Proteins (IGF2BPs) and forms a circPAK2/IGF2BPs/VEGFA complex to stabilize VEGFA mRNA, which contributes to gastric cancer vasculature formation and aggressiveness. Clinically, high circPAK2 expression is positively associated with LN metastasis and poor prognosis in gastric cancer. This study highlights m6A-modified circPAK2 as a key regulator of LN metastasis of gastric cancer, thus supporting circPAK2 as a promising therapeutic target and prognostic biomarker for gastric cancer.
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Affiliation(s)
- Ping'an Ding
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, Hebei, China
- Big data analysis and mining application for precise diagnosis and treatment of gastric cancer Hebei Provincial Engineering Research Center, Shijiazhuang, Hebei, China
| | - Haotian Wu
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, Hebei, China
- Big data analysis and mining application for precise diagnosis and treatment of gastric cancer Hebei Provincial Engineering Research Center, Shijiazhuang, Hebei, China
| | - Jiaxiang Wu
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, Hebei, China
- Big data analysis and mining application for precise diagnosis and treatment of gastric cancer Hebei Provincial Engineering Research Center, Shijiazhuang, Hebei, China
| | - Tongkun Li
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, Hebei, China
- Big data analysis and mining application for precise diagnosis and treatment of gastric cancer Hebei Provincial Engineering Research Center, Shijiazhuang, Hebei, China
| | - Jinchen He
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, Hebei, China
- Big data analysis and mining application for precise diagnosis and treatment of gastric cancer Hebei Provincial Engineering Research Center, Shijiazhuang, Hebei, China
| | - Yingchao Ju
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, Hebei, China
- Big data analysis and mining application for precise diagnosis and treatment of gastric cancer Hebei Provincial Engineering Research Center, Shijiazhuang, Hebei, China
- Animal Center of the Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yueping Liu
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, Hebei, China
- Big data analysis and mining application for precise diagnosis and treatment of gastric cancer Hebei Provincial Engineering Research Center, Shijiazhuang, Hebei, China
- Department of Pathology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Fang Li
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, Hebei, China
- Big data analysis and mining application for precise diagnosis and treatment of gastric cancer Hebei Provincial Engineering Research Center, Shijiazhuang, Hebei, China
- Department of Pathology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Huiyan Deng
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, Hebei, China
- Big data analysis and mining application for precise diagnosis and treatment of gastric cancer Hebei Provincial Engineering Research Center, Shijiazhuang, Hebei, China
- Department of Pathology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Renjun Gu
- School of Chinese Medicine & School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- Department of Gastroenterology and Hepatology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Lilong Zhang
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Honghai Guo
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, Hebei, China
- Big data analysis and mining application for precise diagnosis and treatment of gastric cancer Hebei Provincial Engineering Research Center, Shijiazhuang, Hebei, China
| | - Yuan Tian
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, Hebei, China
- Big data analysis and mining application for precise diagnosis and treatment of gastric cancer Hebei Provincial Engineering Research Center, Shijiazhuang, Hebei, China
| | - Peigang Yang
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, Hebei, China
- Big data analysis and mining application for precise diagnosis and treatment of gastric cancer Hebei Provincial Engineering Research Center, Shijiazhuang, Hebei, China
| | - Ning Meng
- Department of General Surgery, Shijiazhuang People's Hospital, Shijiazhuang, Hebei, China
| | - Xiaolong Li
- Department of General Surgery, Baoding Central Hospital, Baoding, Hebei, China
| | - Zhenjiang Guo
- General Surgery Department, Hengshui People's Hospital, Hengshui, Hebei, China
| | - Lingjiao Meng
- Research Center and Tumor Research Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China.
| | - Qun Zhao
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China.
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, Hebei, China.
- Big data analysis and mining application for precise diagnosis and treatment of gastric cancer Hebei Provincial Engineering Research Center, Shijiazhuang, Hebei, China.
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37
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Nguyen AK, Schall PZ, Kidd JM. A map of canine sequence variation relative to a Greenland wolf outgroup. Mamm Genome 2024:10.1007/s00335-024-10056-1. [PMID: 39088040 DOI: 10.1007/s00335-024-10056-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 07/25/2024] [Indexed: 08/02/2024]
Abstract
For over 15 years, canine genetics research relied on a reference assembly from a Boxer breed dog named Tasha (i.e., canFam3.1). Recent advances in long-read sequencing and genome assembly have led to the development of numerous high-quality assemblies from diverse canines. These assemblies represent notable improvements in completeness, contiguity, and the representation of gene promoters and gene models. Although genome graph and pan-genome approaches have promise, most genetic analyses in canines rely upon the mapping of Illumina sequencing reads to a single reference. The Dog10K consortium, and others, have generated deep catalogs of genetic variation through an alignment of Illumina sequencing reads to a reference genome obtained from a German Shepherd Dog named Mischka (i.e., canFam4, UU_Cfam_GSD_1.0). However, alignment to a breed-derived genome may introduce bias in genotype calling across samples. Since the use of an outgroup reference genome may remove this effect, we have reprocessed 1929 samples analyzed by the Dog10K consortium using a Greenland wolf (mCanLor1.2) as the reference. We efficiently performed remapping and variant calling using a GPU-implementation of common analysis tools. The resulting call set removes the variability in genetic differences seen across samples and breed relationships revealed by principal component analysis are not affected by the choice of reference genome. Using this sequence data, we inferred the history of population sizes and found that village dog populations experienced a 9-13 fold reduction in historic effective population size relative to wolves.
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Affiliation(s)
- Anthony K Nguyen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Peter Z Schall
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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38
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Yoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov D, Pickett BD, Safonova Y, Montinaro F, Luo Y, Malukiewicz J, Storer JM, Lin J, Sequeira AN, Mangan RJ, Hickey G, Anez GM, Balachandran P, Bankevich A, Beck CR, Biddanda A, Borchers M, Bouffard GG, Brannan E, Brooks SY, Carbone L, Carrel L, Chan AP, Crawford J, Diekhans M, Engelbrecht E, Feschotte C, Formenti G, Garcia GH, de Gennaro L, Gilbert D, Green RE, Guarracino A, Gupta I, Haddad D, Han J, Harris RS, Hartley GA, Harvey WT, Hiller M, Hoekzema K, Houck ML, Jeong H, Kamali K, Kellis M, Kille B, Lee C, Lee Y, Lees W, Lewis AP, Li Q, Loftus M, Loh YHE, Loucks H, Ma J, Mao Y, Martinez JFI, Masterson P, McCoy RC, McGrath B, McKinney S, Meyer BS, Miga KH, Mohanty SK, Munson KM, Pal K, Pennell M, Pevzner PA, Porubsky D, Potapova T, Ringeling FR, Rocha JL, Ryder OA, Sacco S, Saha S, Sasaki T, Schatz MC, Schork NJ, Shanks C, Smeds L, Son DR, Steiner C, Sweeten AP, Tassia MG, Thibaud-Nissen F, Torres-González E, Trivedi M, Wei W, Wertz J, Yang M, Zhang P, Zhang S, Zhang Y, Zhang Z, Zhao SA, Zhu Y, Jarvis ED, Gerton JL, Rivas-González I, Paten B, Szpiech ZA, Huber CD, Lenz TL, Konkel MK, Yi SV, Canzar S, Watson CT, Sudmant PH, Molloy E, Garrison E, Lowe CB, Ventura M, O’Neill RJ, Koren S, Makova KD, Phillippy AM, Eichler EE. Complete sequencing of ape genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.31.605654. [PMID: 39131277 PMCID: PMC11312596 DOI: 10.1101/2024.07.31.605654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, providing more in-depth evolutionary insights. Comparative analyses, including human, allow us to investigate the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference. This includes newly minted gene families within lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes, and subterminal heterochromatin. This resource should serve as a definitive baseline for all future evolutionary studies of humans and our closest living ape relatives.
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Affiliation(s)
- DongAhn Yoo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Arang Rhie
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Prajna Hebbar
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Francesca Antonacci
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy
| | - Glennis A. Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Department of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Steven J. Solar
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dmitry Antipov
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brandon D. Pickett
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yana Safonova
- Computer Science and Engineering Department, Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA
| | - Francesco Montinaro
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Yanting Luo
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Joanna Malukiewicz
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Jessica M. Storer
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Jiadong Lin
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Abigail N. Sequeira
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Riley J. Mangan
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Genetics Training Program, Harvard Medical School, Boston, MA 02115, USA
| | - Glenn Hickey
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | | | | | - Anton Bankevich
- Computer Science and Engineering Department, Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA
| | - Christine R. Beck
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Arjun Biddanda
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Matthew Borchers
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Gerard G. Bouffard
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emry Brannan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Shelise Y. Brooks
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lucia Carbone
- Department of Medicine, KCVI, Oregon Health Sciences University, Portland, OR, USA
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA
| | - Laura Carrel
- PSU Medical School, Penn State University School of Medicine, Hershey, PA, USA
| | - Agnes P. Chan
- The Translational Genomics Research Institute, a part of the City of Hope National Medical Center, Phoenix, AZ, USA
| | - Juyun Crawford
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Eric Engelbrecht
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Cedric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10021, USA
| | - Gage H. Garcia
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Luciana de Gennaro
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy
| | - David Gilbert
- San Diego Biomedical Research Institute, San Diego, CA, USA
| | | | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Ishaan Gupta
- Department of Computer Science and Engineering, University of California San Diego, CA, USA
| | - Diana Haddad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Junmin Han
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Robert S. Harris
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Gabrielle A. Hartley
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - William T. Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Research Institute, Goethe University, Frankfurt, Germany
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marlys L. Houck
- San Diego Zoo Wildlife Alliance, Escondido, CA, 92027-7000, USA
| | - Hyeonsoo Jeong
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Kaivan Kamali
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bryce Kille
- Department of Computer Science, Rice University, Houston, TX 77005, USA
| | - Chul Lee
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Youngho Lee
- Laboratory of bioinformatics and population genetics, Interdisciplinary program in bioinformatics, Seoul National University, Republic of Korea
| | - William Lees
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Alexandra P. Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Qiuhui Li
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Mark Loftus
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC, USA
- Center for Human Genetics, Clemson University, Greenwood, SC, USA
| | - Yong Hwee Eddie Loh
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Hailey Loucks
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Jian Ma
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, PA, USA
| | - Yafei Mao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- Center for Genomic Research, International Institutes of Medicine, Fourth Affiliated Hospital, Zhejiang University, Yiwu, Zhejiang, China
- Shanghai Jiao Tong University Chongqing Research Institute, Chongqing, China
| | - Juan F. I. Martinez
- Computer Science and Engineering Department, Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA
| | - Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Rajiv C. McCoy
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Barbara McGrath
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Sean McKinney
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Britta S. Meyer
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Saswat K. Mohanty
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Katherine M. Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Karol Pal
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Pavel A. Pevzner
- Department of Computer Science and Engineering, University of California San Diego, CA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Tamara Potapova
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Francisca R. Ringeling
- Faculty of Informatics and Data Science, University of Regensburg, 93053 Regensburg, Germany
| | - Joana L. Rocha
- Department of Integrative Biology, University of California, Berkeley, Berkeley, USA
| | - Oliver A. Ryder
- San Diego Zoo Wildlife Alliance, Escondido, CA, 92027-7000, USA
| | - Samuel Sacco
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Swati Saha
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Takayo Sasaki
- San Diego Biomedical Research Institute, San Diego, CA, USA
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Nicholas J. Schork
- The Translational Genomics Research Institute, a part of the City of Hope National Medical Center, Phoenix, AZ, USA
| | - Cole Shanks
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Linnéa Smeds
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Dongmin R. Son
- Department of Ecology, Evolution and Marine Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Cynthia Steiner
- San Diego Zoo Wildlife Alliance, Escondido, CA, 92027-7000, USA
| | - Alexander P. Sweeten
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael G. Tassia
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | | | - Mihir Trivedi
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Wenjie Wei
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- National Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Julie Wertz
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Muyu Yang
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, PA, USA
| | - Panpan Zhang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Shilong Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Zhang
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, PA, USA
| | - Zhenmiao Zhang
- Department of Computer Science and Engineering, University of California San Diego, CA, USA
| | - Sarah A. Zhao
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yixin Zhu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Erich D. Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Iker Rivas-González
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Zachary A. Szpiech
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Christian D. Huber
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Tobias L. Lenz
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Miriam K. Konkel
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC, USA
- Center for Human Genetics, Clemson University, Greenwood, SC, USA
| | - Soojin V. Yi
- Department of Ecology, Evolution and Marine Biology, Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Stefan Canzar
- Faculty of Informatics and Data Science, University of Regensburg, 93053 Regensburg, Germany
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Peter H. Sudmant
- Department of Integrative Biology, University of California, Berkeley, Berkeley, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, USA
| | - Erin Molloy
- Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Craig B. Lowe
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Mario Ventura
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy
| | - Rachel J. O’Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
- Departments of Molecular and Cell Biology, UConn Storrs, CT, USA
| | - Sergey Koren
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kateryna D. Makova
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Adam M. Phillippy
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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39
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Du N, Yi L, Wang J, Lei Y, Bo X, Guo F, Wang R, Chai J, Liu G. High expression of YEATS2 as a predictive factor of poor prognosis in patients with hepatocellular carcinoma. Sci Rep 2024; 14:17246. [PMID: 39060453 PMCID: PMC11282058 DOI: 10.1038/s41598-024-68348-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/23/2024] [Indexed: 07/28/2024] Open
Abstract
YEATS domain containing 2 (YEATS2), it may function as a proto-oncogene. This study aims to investigate if YEATS2 correlates with prognosis in hepatocellular carcinoma. The prognostic landscape of YEATS2 and its relationship with expression in hepatocellular carcinoma were deciphered with public databases, RT-qPCR and western-blot in tissue samples. The expression profiling and prognostic value of YEATS2 were explored using UALCAN, TIMER, OncoLnc database. Transcription and survival analyses of YEATS2 in hepatocellular carcinoma were investigated with cBioPortal database. The STRING database was explored to identify molecular functions and signaling pathways downstream of YEATS2. YEATS2 expression was significantly higher in hepatocellular carcinoma compared with adjacent non-malignant tissues. Promoter methylation of YEATS2 exhibited different patterns in hepatocellular carcinoma. High expression of YEATS2 was associated with poorer survival. Mechanistically, YEATS2 was involved in mediating multiple biological processes including morphogenesis and migration.
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Affiliation(s)
- Ning Du
- Department of Hepatobiliary Surgery, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Lili Yi
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Jiamu Wang
- Department of Hepatobiliary Surgery, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Yongqiang Lei
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Xiaohui Bo
- Department of Hepatobiliary Surgery, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Fangjie Guo
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Ruhao Wang
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Jian Chai
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, 252000, China.
| | - Guijie Liu
- Department of Hepatobiliary Surgery, Liaocheng People's Hospital, Liaocheng, 252000, China.
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40
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Ungar RA, Goddard PC, Jensen TD, Degalez F, Smith KS, Jin CA, Bonner DE, Bernstein JA, Wheeler MT, Montgomery SB. Impact of genome build on RNA-seq interpretation and diagnostics. Am J Hum Genet 2024; 111:1282-1300. [PMID: 38834072 PMCID: PMC11267525 DOI: 10.1016/j.ajhg.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/04/2024] [Accepted: 05/06/2024] [Indexed: 06/06/2024] Open
Abstract
Transcriptomics is a powerful tool for unraveling the molecular effects of genetic variants and disease diagnosis. Prior studies have demonstrated that choice of genome build impacts variant interpretation and diagnostic yield for genomic analyses. To identify the extent genome build also impacts transcriptomics analyses, we studied the effect of the hg19, hg38, and CHM13 genome builds on expression quantification and outlier detection in 386 rare disease and familial control samples from both the Undiagnosed Diseases Network and Genomics Research to Elucidate the Genetics of Rare Disease Consortium. Across six routinely collected biospecimens, 61% of quantified genes were not influenced by genome build. However, we identified 1,492 genes with build-dependent quantification, 3,377 genes with build-exclusive expression, and 9,077 genes with annotation-specific expression across six routinely collected biospecimens, including 566 clinically relevant and 512 known OMIM genes. Further, we demonstrate that between builds for a given gene, a larger difference in quantification is well correlated with a larger change in expression outlier calling. Combined, we provide a database of genes impacted by build choice and recommend that transcriptomics-guided analyses and diagnoses are cross referenced with these data for robustness.
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Affiliation(s)
- Rachel A Ungar
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Pagé C Goddard
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Tanner D Jensen
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Kevin S Smith
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Christopher A Jin
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Devon E Bonner
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA, USA; Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Jonathan A Bernstein
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Matthew T Wheeler
- Department of Cardiovascular Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Stephen B Montgomery
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
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41
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Mangum KD, Li Q, Bauer TM, Wolf SJ, Shadiow J, Moon JY, Barrett EC, Joshi AD, Ahmed Z, Wasikowski R, Boyer K, Obi AT, Davis FM, Chang L, Tsoi LC, Gudjonsson J, Gallagher KA. Epigenetic Alteration of Smooth Muscle Cells Regulates Endothelin-Dependent Blood Pressure and Hypertensive Arterial Remodeling. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.09.24310178. [PMID: 39040193 PMCID: PMC11261912 DOI: 10.1101/2024.07.09.24310178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Long-standing hypertension (HTN) affects multiple organ systems and leads to pathologic arterial remodeling, which is driven largely by smooth muscle cell (SMC) plasticity. Although genome wide association studies (GWAS) have identified numerous variants associated with changes in blood pressure in humans, only a small percentage of these variants actually cause HTN. In order to identify relevant genes important in SMC function in HTN, we screened three separate human GWAS and Mendelian randomization studies to identify SNPs located within non-coding gene regions, focusing on genes encoding epigenetic enzymes, as these have been recently identified to control SMC fate in cardiovascular disease. We identified SNPs rs62059712 and rs74480102 in the promoter of the human JMJD3 gene and show that the minor C allele increases JMJD3 transcription in SMCs via increased SP1 binding to the JMJD3 promoter. Using our novel SMC-specific Jmjd3-deficient murine model ( Jmjd3 flox/flox Myh11 CreERT ), we show that loss of Jmjd3 in SMCs results in HTN, mechanistically, due to decreased EDNRB expression and a compensatory increase in EDNRA expression. As a translational corollary, through single cell RNA-sequencing (scRNA-seq) of human arteries, we found strong correlation between JMJD3 and EDNRB expression in SMCs. Further, we identified that JMJD3 is required for SMC-specific gene expression, and loss of JMJD3 in SMCs in the setting of HTN results in increased arterial remodeling by promoting the SMC synthetic phenotype. Our findings link a HTN-associated human DNA variant with regulation of SMC plasticity, revealing therapeutic targets that may be used in the screening and/or personalized treatment of HTN.
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42
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Wan CY, Davis J, Chauhan M, Gleeson J, Prawer YJ, De Paoli-Iseppi R, Wells C, Choi J, Clark M. IsoVis - a webserver for visualization and annotation of alternative RNA isoforms. Nucleic Acids Res 2024; 52:W341-W347. [PMID: 38709877 PMCID: PMC11223830 DOI: 10.1093/nar/gkae343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/28/2024] [Accepted: 04/18/2024] [Indexed: 05/08/2024] Open
Abstract
Genes commonly express multiple RNA products (RNA isoforms), which differ in exonic content and can have different functions. Making sense of the plethora of known and novel RNA isoforms being identified by transcriptomic approaches requires a user-friendly way to visualize gene isoforms and how they differ in exonic content, expression levels and potential functions. Here we introduce IsoVis, a freely available webserver that accepts user-supplied transcriptomic data and visualizes the expressed isoforms in a clear, intuitive manner. IsoVis contains numerous features, including the ability to visualize all RNA isoforms of a gene and their expression levels; the annotation of known isoforms from external databases; mapping of protein domains and features to exons, allowing changes to protein sequence and function between isoforms to be established; and extensive species compatibility. Datasets visualised on IsoVis remain private to the user, allowing analysis of sensitive data. IsoVis visualisations can be downloaded to create publication-ready figures. The IsoVis webserver enables researchers to perform isoform analyses without requiring programming skills, is free to use, and available at https://isomix.org/isovis/.
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Affiliation(s)
- Ching Yin Wan
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Jack Davis
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Manveer Chauhan
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Josie Gleeson
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Yair D J Prawer
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Ricardo De Paoli-Iseppi
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Christine A Wells
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Jarny Choi
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Michael B Clark
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
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43
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Coetzee SG, Hazelett DJ. MotifbreakR v2: extended capability and database integration. ARXIV 2024:arXiv:2407.03441v1. [PMID: 39010878 PMCID: PMC11247919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
MotifbreakR is a software tool that scans genetic variants against position weight matrices of transcription factors (TF) to determine the potential for the disruption of TF binding at the site of the variant. It leverages the Bioconductor suite of software packages and annotations to operate across a diverse array of genomes and motif databases. Initially developed to interrogate the effect of single nucleotide variants (common and rare SNVs) on potential TF binding sites, in motifbreakR v2, we have updated the functionality. New features include the ability to query other types of more complex genetic variants, such as short insertions and deletions (indels). This function allows modeling a more extensive array of variants that may have more significant effects on TF binding. Additionally, while TF binding is based partly on sequence preference, predictions of TF binding based on sequence preference alone can indicate many more potential binding events than observed. Adding information from DNA-binding sequencing datasets lends confidence to motif disruption prediction by demonstrating TF binding in cell lines and tissue types. Therefore, motifbreakR implements querying the ReMap2022 database for evidence that a TF matching the disrupted motif binds over the disrupting variant. Finally, in motifbreakR, in addition to the existing interface, we have implemented an R/Shiny graphical user interface to simplify and enhance access to researchers with different skill sets.
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Affiliation(s)
- Simon G Coetzee
- Department of Computational Biomedicine at Cedars-Sinai Medical Center
| | - Dennis J Hazelett
- Department of Computational Biomedicine at Cedars-Sinai Medical Center
- Cancer Prevention and Control - Samuel Oschin Cancer Center, Cedars-Sinai
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44
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Wang X, Lian Q, Dong H, Xu S, Su Y, Wu X. Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae014. [PMID: 39049508 DOI: 10.1093/gpbjnl/qzae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/20/2023] [Accepted: 06/25/2023] [Indexed: 07/27/2024]
Abstract
Gene set scoring (GSS) has been routinely conducted for gene expression analysis of bulk or single-cell RNA sequencing (RNA-seq) data, which helps to decipher single-cell heterogeneity and cell type-specific variability by incorporating prior knowledge from functional gene sets. Single-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) is a powerful technique for interrogating single-cell chromatin-based gene regulation, and genes or gene sets with dynamic regulatory potentials can be regarded as cell type-specific markers as if in single-cell RNA-seq (scRNA-seq). However, there are few GSS tools specifically designed for scATAC-seq, and the applicability and performance of RNA-seq GSS tools on scATAC-seq data remain to be investigated. Here, we systematically benchmarked ten GSS tools, including four bulk RNA-seq tools, five scRNA-seq tools, and one scATAC-seq method. First, using matched scATAC-seq and scRNA-seq datasets, we found that the performance of GSS tools on scATAC-seq data was comparable to that on scRNA-seq, suggesting their applicability to scATAC-seq. Then, the performance of different GSS tools was extensively evaluated using up to ten scATAC-seq datasets. Moreover, we evaluated the impact of gene activity conversion, dropout imputation, and gene set collections on the results of GSS. Results show that dropout imputation can significantly promote the performance of almost all GSS tools, while the impact of gene activity conversion methods or gene set collections on GSS performance is more dependent on GSS tools or datasets. Finally, we provided practical guidelines for choosing appropriate preprocessing methods and GSS tools in different application scenarios.
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Affiliation(s)
- Xi Wang
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China
- Department of Automation, Xiamen University, Xiamen 361005, China
| | - Qiwei Lian
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China
- Department of Automation, Xiamen University, Xiamen 361005, China
| | - Haoyu Dong
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China
| | - Shuo Xu
- Department of Automation, Xiamen University, Xiamen 361005, China
| | - Yaru Su
- College of Mathematics and Computer Science, Fuzhou University, Fuzhou 350116, China
| | - Xiaohui Wu
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China
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45
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Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez Martinez JM, Hunt T, Lagarde J, Liang CE, Li H, Meade MJ, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Çelik MH, Chen Y, Du MRM, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Li JL, Lienhard M, Mikheenko A, Mulligan D, Nip KM, Pertea M, Ritchie ME, Sim AD, Tang AD, Wan YK, Wang C, Wong BY, Yang C, Barnes I, Berry AE, Capella-Gutierrez S, Cousineau A, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Götz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Ren X, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Smith ML, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Maehr R, Shen Y, Tilgner HU, Wold BJ, Vollmers C, Frankish A, Au KF, Sheynkman GM, Mortazavi A, Conesa A, Brooks AN. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nat Methods 2024; 21:1349-1363. [PMID: 38849569 DOI: 10.1038/s41592-024-02298-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 05/03/2024] [Indexed: 06/09/2024]
Abstract
The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the consortium generated over 427 million long-read sequences from complementary DNA and direct RNA datasets, encompassing human, mouse and manatee species. Developers utilized these data to address challenges in transcript isoform detection, quantification and de novo transcript detection. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. Incorporating additional orthogonal data and replicate samples is advised when aiming to detect rare and novel transcripts or using reference-free approaches. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.
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Affiliation(s)
| | - Dingjie Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Fairlie Reese
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Sílvia Carbonell-Sala
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Brian Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jane E Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK
| | - Maite De María
- Department of Physiological Sciences, College of Veterinary Medicine, Gainesville, FL, USA
- Cherokee Nation System Solutions, contractor to the US Geological Survey-Wetland and Aquatic Research Center, Gainesville, FL, USA
| | - Matthew S Adams
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Gabriela Balderrama-Gutierrez
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
| | - Amit K Behera
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jose M Gonzalez Martinez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK
| | - Julien Lagarde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Flomics Biotech, SL, Barcelona, Spain
| | - Cindy E Liang
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Haoran Li
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Marcus Jerryd Meade
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - David A Moraga Amador
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Andrey D Prjibelski
- Department of Computer Science, University of Helsinki, Helsinki, Finland
- Center for Bioinformatics and Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Hamed Bostan
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Ashley M Brooks
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Muhammed Hasan Çelik
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
| | - Ying Chen
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mei R M Du
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Colette Felton
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jonathan Göke
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore
| | - Saber Hafezqorani
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Ralf Herwig
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Hideya Kawaji
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Joseph Lee
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jian-Liang Li
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Matthias Lienhard
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Alla Mikheenko
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Dennis Mulligan
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Mihaela Pertea
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Matthew E Ritchie
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Andre D Sim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Alison D Tang
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Yuk Kei Wan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Changqing Wang
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Brandon Y Wong
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Chen Yang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - If Barnes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK
| | - Andrew E Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK
| | | | - Alyssa Cousineau
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Namrita Dhillon
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - Luis Ferrández-Peral
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | - Natàlia Garcia-Reyero
- Energy, Installations & Environment, Office of the Assistant Secretary of Defense, Washington, DC, USA
| | | | | | | | | | | | | | - Jorge Mestre-Tomás
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK
| | - Nedka G Panayotova
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Alejandro Paniagua
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | | | - Xingjie Ren
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Eric Rouchka
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, KY, USA
| | - Brandon Saint-John
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Enrique Sapena
- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Leon Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Melissa Laird Smith
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, KY, USA
| | - Marie-Marthe Suner
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK
| | - Hazuki Takahashi
- Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan
| | | | - Piero Carninci
- Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan
- Human Technopole, Milano, Italy
| | - Nancy D Denslow
- Department of Physiological Sciences, College of Veterinary Medicine, Gainesville, FL, USA
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, University of Florida, Gainesville, FL, USA
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Margaret E Hunter
- US Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, USA
| | - Rene Maehr
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Yin Shen
- Institute for Human Genetics, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Hagen U Tilgner
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York City, NY, USA
| | - Barbara J Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK.
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
| | - Gloria M Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.
- UVA Cancer Center, University of Virginia, Charlottesville, VA, USA.
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA.
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA.
| | - Angela N Brooks
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
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Albury CL, Sutherland HG, Lam AWY, Tran NK, Lea RA, Haupt LM, Griffiths LR. Identification of Polymorphisms in EAAT1 Glutamate Transporter Gene SLC1A3 Associated with Reduced Migraine Risk. Genes (Basel) 2024; 15:797. [PMID: 38927733 PMCID: PMC11202508 DOI: 10.3390/genes15060797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Dysfunction in ion channels or processes involved in maintaining ionic homeostasis is thought to lower the threshold for cortical spreading depression (CSD), and plays a role in susceptibility to associated neurological disorders, including pathogenesis of a migraine. Rare pathogenic variants in specific ion channels have been implicated in monogenic migraine subtypes. In this study, we further examined the channelopathic nature of a migraine through the analysis of common genetic variants in three selected ion channel or transporter genes: SLC4A4, SLC1A3, and CHRNA4. Using the Agena MassARRAY platform, 28 single-nucleotide polymorphisms (SNPs) across the three candidate genes were genotyped in a case-control cohort comprised of 182 migraine cases and 179 matched controls. Initial results identified significant associations between migraine and rs3776578 (p = 0.04) and rs16903247 (p = 0.05) genotypes within the SLC1A3 gene, which encodes the EAAT1 glutamate transporter. These SNPs were subsequently genotyped in an independent cohort of 258 migraine cases and 290 controls using a high-resolution melt assay, and association testing supported the replication of initial findings-rs3776578 (p = 0.0041) and rs16903247 (p = 0.0127). The polymorphisms are in linkage disequilibrium and localise within a putative intronic enhancer region of SLC1A3. The minor alleles of both SNPs show a protective effect on migraine risk, which may be conferred via influencing the expression of SLC1A3.
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Affiliation(s)
- Cassie L. Albury
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, QLD 4059, Australia; (C.L.A.); (H.G.S.); (A.W.Y.L.); (N.K.T.); (R.A.L.)
| | - Heidi G. Sutherland
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, QLD 4059, Australia; (C.L.A.); (H.G.S.); (A.W.Y.L.); (N.K.T.); (R.A.L.)
| | - Alexis W. Y. Lam
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, QLD 4059, Australia; (C.L.A.); (H.G.S.); (A.W.Y.L.); (N.K.T.); (R.A.L.)
| | - Ngan K. Tran
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, QLD 4059, Australia; (C.L.A.); (H.G.S.); (A.W.Y.L.); (N.K.T.); (R.A.L.)
| | - Rod A. Lea
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, QLD 4059, Australia; (C.L.A.); (H.G.S.); (A.W.Y.L.); (N.K.T.); (R.A.L.)
| | - Larisa M. Haupt
- Stem Cell and Neurogenesis Group, Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD 4059, Australia;
- ARC Training Centre for Cell and Tissue Engineering Technologies, Queensland University of Technology(QUT), Kelvin Grove, QLD 4059, Australia
- Max Planck Queensland Centre for the Materials Science of Extracellular Matrices, Kelvin Grove, QLD 4059, Australia
- Centre for Biomedical Technologies, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, QLD 4059, Australia
| | - Lyn R. Griffiths
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, QLD 4059, Australia; (C.L.A.); (H.G.S.); (A.W.Y.L.); (N.K.T.); (R.A.L.)
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47
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Kocher AA, Dutrow EV, Uebbing S, Yim KM, Rosales Larios MF, Baumgartner M, Nottoli T, Noonan JP. CpG island turnover events predict evolutionary changes in enhancer activity. Genome Biol 2024; 25:156. [PMID: 38872220 PMCID: PMC11170920 DOI: 10.1186/s13059-024-03300-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/04/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND Genetic changes that modify the function of transcriptional enhancers have been linked to the evolution of biological diversity across species. Multiple studies have focused on the role of nucleotide substitutions, transposition, and insertions and deletions in altering enhancer function. CpG islands (CGIs) have recently been shown to influence enhancer activity, and here we test how their turnover across species contributes to enhancer evolution. RESULTS We integrate maps of CGIs and enhancer activity-associated histone modifications obtained from multiple tissues in nine mammalian species and find that CGI content in enhancers is strongly associated with increased histone modification levels. CGIs show widespread turnover across species and species-specific CGIs are strongly enriched for enhancers exhibiting species-specific activity across all tissues and species. Genes associated with enhancers with species-specific CGIs show concordant biases in their expression, supporting that CGI turnover contributes to gene regulatory innovation. Our results also implicate CGI turnover in the evolution of Human Gain Enhancers (HGEs), which show increased activity in human embryonic development and may have contributed to the evolution of uniquely human traits. Using a humanized mouse model, we show that a highly conserved HGE with a large CGI absent from the mouse ortholog shows increased activity at the human CGI in the humanized mouse diencephalon. CONCLUSIONS Collectively, our results point to CGI turnover as a mechanism driving gene regulatory changes potentially underlying trait evolution in mammals.
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Affiliation(s)
- Acadia A Kocher
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
- Division of Molecular Genetics and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Emily V Dutrow
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
- Zoetis, Inc, 333 Portage St, Kalamazoo, MI, 49007, USA
| | - Severin Uebbing
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Kristina M Yim
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
| | | | | | - Timothy Nottoli
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
- Yale Genome Editing Center, Yale School of Medicine, New Haven, CT, 06510, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA.
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA.
- Wu Tsai Institute, Yale University, New Haven, CT, 06510, USA.
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48
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Ochi S, Manabe S, Kikkawa T, Ebrahimiazar S, Kimura R, Yoshizaki K, Osumi N. A Transcriptomic Dataset of Embryonic Murine Telencephalon. Sci Data 2024; 11:586. [PMID: 38839806 PMCID: PMC11153524 DOI: 10.1038/s41597-024-03421-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 05/24/2024] [Indexed: 06/07/2024] Open
Abstract
Sex bias is known in the prevalence/pathology of neurodevelopmental disorders. Sex-dependent differences of the certain brain areas are known to emerge perinatally through the exposure to sex hormones, while gene expression patterns in the rodent embryonic brain does not seem to be completely the same between male and female. To investigate potential sex differences in gene expression and cortical organization during the embryonic period in mice, we conducted a comprehensive analysis of gene expression for the telencephalon at embryonic day (E) 11.5 (a peak of neural stem cell expansion) and E14.5 (a peak of neurogenesis) using bulk RNA-seq data. As a result, our data showed the existence of notable sex differences in gene expression patterns not obviously at E11.5, but clearly at E14.5 when neurogenesis has become its peak. These data can be useful for exploring potential contribution of genes exhibiting sex differences to the divergence in brain development. Additionally, our data underscore the significance of studying the embryonic period to gain a deeper understanding of sex differences in brain development.
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Affiliation(s)
- Shohei Ochi
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Shyu Manabe
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Takako Kikkawa
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Sara Ebrahimiazar
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Ryuichi Kimura
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Kaichi Yoshizaki
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
- Kobe University Graduate School of Medicine, Department of Future Medical Sciences, Division of Integrated Analysis of Bioresource and Health Care, Kobe, 650-0047, Japan
- Kobe University Hospital, Bioresource Center, Kobe, 650-0047, Japan
| | - Noriko Osumi
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan.
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49
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Steux C, Szpiech ZA. The Maintenance of Deleterious Variation in Wild Chinese Rhesus Macaques. Genome Biol Evol 2024; 16:evae115. [PMID: 38795368 PMCID: PMC11157460 DOI: 10.1093/gbe/evae115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 04/25/2024] [Accepted: 05/22/2024] [Indexed: 05/27/2024] Open
Abstract
Understanding how deleterious variation is shaped and maintained in natural populations is important in conservation and evolutionary biology, as decreased fitness caused by these deleterious mutations can potentially lead to an increase in extinction risk. It is known that demographic processes can influence these patterns. For example, population bottlenecks and inbreeding increase the probability of inheriting identical-by-descent haplotypes from a recent common ancestor, creating long tracts of homozygous genotypes called runs of homozygosity (ROH), which have been associated with an accumulation of mildly deleterious homozygotes. Counterintuitively, positive selection can also maintain deleterious variants in a population through genetic hitchhiking. Here, we analyze the whole genomes of 79 wild Chinese rhesus macaques across five subspecies and characterize patterns of deleterious variation with respect to ROH and signals of recent positive selection. We show that the fraction of homozygotes occurring in long ROH is significantly higher for deleterious homozygotes than tolerated ones, whereas this trend is not observed for short and medium ROH. This confirms that inbreeding, by generating these long tracts of homozygosity, is the main driver of the high burden of homozygous deleterious alleles in wild macaque populations. Furthermore, we show evidence that homozygous LOF variants are being purged. Next, we identify seven deleterious variants at high frequency in regions putatively under selection near genes involved with olfaction and other processes. Our results shed light on how evolutionary processes can shape the distribution of deleterious variation in wild nonhuman primates.
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Affiliation(s)
- Camille Steux
- Department of Biology, Pennsylvania State University, University Park, USA
- Centre de Recherche sur la Biodiversité et l’Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3—Paul Sabatier (UT3), Toulouse, France
| | - Zachary A Szpiech
- Department of Biology, Pennsylvania State University, University Park, USA
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, USA
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50
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Parsons BL, Beal MA, Dearfield KL, Douglas GR, Gi M, Gollapudi BB, Heflich RH, Horibata K, Kenyon M, Long AS, Lovell DP, Lynch AM, Myers MB, Pfuhler S, Vespa A, Zeller A, Johnson GE, White PA. Severity of effect considerations regarding the use of mutation as a toxicological endpoint for risk assessment: A report from the 8th International Workshop on Genotoxicity Testing (IWGT). ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024. [PMID: 38828778 DOI: 10.1002/em.22599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/13/2024] [Accepted: 04/15/2024] [Indexed: 06/05/2024]
Abstract
Exposure levels without appreciable human health risk may be determined by dividing a point of departure on a dose-response curve (e.g., benchmark dose) by a composite adjustment factor (AF). An "effect severity" AF (ESAF) is employed in some regulatory contexts. An ESAF of 10 may be incorporated in the derivation of a health-based guidance value (HBGV) when a "severe" toxicological endpoint, such as teratogenicity, irreversible reproductive effects, neurotoxicity, or cancer was observed in the reference study. Although mutation data have been used historically for hazard identification, this endpoint is suitable for quantitative dose-response modeling and risk assessment. As part of the 8th International Workshops on Genotoxicity Testing, a sub-group of the Quantitative Analysis Work Group (WG) explored how the concept of effect severity could be applied to mutation. To approach this question, the WG reviewed the prevailing regulatory guidance on how an ESAF is incorporated into risk assessments, evaluated current knowledge of associations between germline or somatic mutation and severe disease risk, and mined available data on the fraction of human germline mutations expected to cause severe disease. Based on this review and given that mutations are irreversible and some cause severe human disease, in regulatory settings where an ESAF is used, a majority of the WG recommends applying an ESAF value between 2 and 10 when deriving a HBGV from mutation data. This recommendation may need to be revisited in the future if direct measurement of disease-causing mutations by error-corrected next generation sequencing clarifies selection of ESAF values.
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Affiliation(s)
- Barbara L Parsons
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Marc A Beal
- Bureau of Chemical Safety, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Kerry L Dearfield
- U.S. Environmental Protection Agency and U.S. Department of Agriculture, Washington, DC, USA
| | - George R Douglas
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Min Gi
- Department of Environmental Risk Assessment, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | | | - Robert H Heflich
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Michelle Kenyon
- Portfolio and Regulatory Strategy, Drug Safety Research and Development, Pfizer, Groton, Connecticut, USA
| | - Alexandra S Long
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - David P Lovell
- Population Health Research Institute, St George's Medical School, University of London, London, UK
| | | | - Meagan B Myers
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Alisa Vespa
- Pharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Andreas Zeller
- Pharmaceutical Sciences, pRED Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
| | - George E Johnson
- Swansea University Medical School, Swansea University, Swansea, Wales, UK
| | - Paul A White
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
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