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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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2
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Carlisle SG, Albasha H, Michelena HI, Sabate-Rotes A, Bianco L, De Backer J, Mosquera LM, Yetman AT, Bissell MM, Andreassi MG, Foffa I, Hui DS, Caffarelli A, Kim YY, Guo D, Citro R, De Marco M, Tretter JT, McBride KL, Milewicz DM, Body SC, Prakash SK. Rare genomic copy number variants implicate new candidate genes for bicuspid aortic valve. PLoS One 2024; 19:e0304514. [PMID: 39240962 PMCID: PMC11379187 DOI: 10.1371/journal.pone.0304514] [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: 11/27/2023] [Accepted: 05/14/2024] [Indexed: 09/08/2024] Open
Abstract
Bicuspid aortic valve (BAV), the most common congenital heart defect, is a major cause of aortic valve disease requiring valve interventions and thoracic aortic aneurysms predisposing to acute aortic dissections. The spectrum of BAV ranges from early onset valve and aortic complications (EBAV) to sporadic late onset disease. Rare genomic copy number variants (CNVs) have previously been implicated in the development of BAV and thoracic aortic aneurysms. We determined the frequency and gene content of rare CNVs in EBAV probands (n = 272) using genome-wide SNP microarray analysis and three complementary CNV detection algorithms (cnvPartition, PennCNV, and QuantiSNP). Unselected control genotypes from the Database of Genotypes and Phenotypes were analyzed using identical methods. We filtered the data to select large genic CNVs that were detected by multiple algorithms. Findings were replicated in a BAV cohort with late onset sporadic disease (n = 5040). We identified 3 large and rare (< 1,1000 in controls) CNVs in EBAV probands. The burden of CNVs intersecting with genes known to cause BAV when mutated was increased in case-control analysis. CNVs intersecting with GATA4 and DSCAM were enriched in cases, recurrent in other datasets, and segregated with disease in families. In total, we identified potentially pathogenic CNVs in 9% of EBAV cases, implicating alterations of candidate genes at these loci in the pathogenesis of BAV.
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Affiliation(s)
- Steven G Carlisle
- University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Hasan Albasha
- University College Dublin School of Medicine, Dublin, Ireland
| | | | | | - Lisa Bianco
- Vall d'Hebron University Hospital, Barcelona, Spain
| | | | | | - Anji T Yetman
- University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | | | | | - Ilenia Foffa
- Consiglio Nazionale delle Richerche (CNR), Instituto di Fisiologia Clinica, Pisa, Italy
| | - Dawn S Hui
- University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Anthony Caffarelli
- Hoag Memorial Hospital Presbyterian, Newport Beach, California, United States of America
| | - Yuli Y Kim
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dongchuan Guo
- University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Rodolfo Citro
- University Hospital "San Giovanni di Dio e Ruggi d'Aragona," Salerno, Italy
| | - Margot De Marco
- Schola Medica Salernitana, University of Salerno, Baronissi, Italy
| | | | - Kim L McBride
- University of Calgary Cumming School of Medicine, Calgary, Alberta, Canada
| | - Dianna M Milewicz
- University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Simon C Body
- Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Siddharth K Prakash
- University of Texas Health Science Center at Houston, Houston, Texas, United States of America
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3
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van Lingen HJ, Suarez-Diez M, Saccenti E. Normalization of gene counts affects principal components-based exploratory analysis of RNA-sequencing data. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195058. [PMID: 39154857 DOI: 10.1016/j.bbagrm.2024.195058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/25/2024] [Accepted: 08/09/2024] [Indexed: 08/20/2024]
Abstract
Normalization of gene expression count data is an essential step of in the analysis of RNA-sequencing data. Its statistical analysis has been mostly addressed in the context of differential expression analysis, that is in the univariate setting. However, relationships among genes and samples are better explored and quantified using multivariate exploratory data analysis tools like Principal Component Analysis (PCA). In this study we investigate how normalization impacts the PCA model and its interpretation, considering twelve different widely used normalization methods that were applied on simulated and experimental data. Correlation patterns in the normalized data were explored using both summary statistics and Covariance Simultaneous Component Analysis. The impact of normalization on the PCA solution was assessed by exploring the model complexity, the quality of sample clustering in the low-dimensional PCA space and gene ranking in the model fit to normalized data. PCA models upon normalization were interpreted in the context gene enrichment pathway analysis. We found that although PCA score plots are often similar independently form the normalization used, biological interpretation of the models can depend heavily on the normalization method applied.
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Affiliation(s)
- Henk J van Lingen
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, the Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, the Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, the Netherlands.
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4
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DeGroat W, Inoue F, Ashuach T, Yosef N, Ahituv N, Kreimer A. Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation. Genome Biol 2024; 25:221. [PMID: 39143563 PMCID: PMC11323586 DOI: 10.1186/s13059-024-03365-w] [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: 11/17/2023] [Accepted: 08/01/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Increasing evidence suggests that a substantial proportion of disease-associated mutations occur in enhancers, regions of non-coding DNA essential to gene regulation. Understanding the structures and mechanisms of the regulatory programs this variation affects can shed light on the apparatuses of human diseases. RESULTS We collect epigenetic and gene expression datasets from seven early time points during neural differentiation. Focusing on this model system, we construct networks of enhancer-promoter interactions, each at an individual stage of neural induction. These networks serve as the base for a rich series of analyses, through which we demonstrate their temporal dynamics and enrichment for various disease-associated variants. We apply the Girvan-Newman clustering algorithm to these networks to reveal biologically relevant substructures of regulation. Additionally, we demonstrate methods to validate predicted enhancer-promoter interactions using transcription factor overexpression and massively parallel reporter assays. CONCLUSIONS Our findings suggest a generalizable framework for exploring gene regulatory programs and their dynamics across developmental processes; this includes a comprehensive approach to studying the effects of disease-associated variation on transcriptional networks. The techniques applied to our networks have been published alongside our findings as a computational tool, E-P-INAnalyzer. Our procedure can be utilized across different cellular contexts and disorders.
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Affiliation(s)
- William DeGroat
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, 679 Hoes Lane West, Piscataway, NJ, 08854, USA
| | - Fumitaka Inoue
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Tal Ashuach
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, 387 Soda Hall, Berkeley, CA, 94720, USA
| | - Nir Yosef
- Department of Systems Immunology, Weizmann Institute of Science, 234 Herzl Street, Rehovot, 7610001, Israel
- Chan-Zuckerberg Biohub, 499 Illinois St, San Francisco, CA, 94158, USA
- Department of Systems Immunology, Ragon Institute of MGH, MIT, and Harvard Institute of Science, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, 513 Parnassus Ave, San Francisco, CA, 94143, USA
- Institute for Human Genetics, University of California, 513 Parnassus Ave, San Francisco, CA, 94143, USA
| | - Anat Kreimer
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, 679 Hoes Lane West, Piscataway, NJ, 08854, USA.
- Department of Biochemistry and Molecular Biology, Rutgers, The State University of New Jersey, 604 Allison Road, Piscataway, NJ, 08854, USA.
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5
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Bond A, Fiaz S, Rollins K, Nario JEQ, Snyder ET, Atkins DJ, Rosen SJ, Granados A, Dey SS, Wilson MZ, Morrissey MA. Prior Fc receptor activation primes macrophages for increased sensitivity to IgG via long-term and short-term mechanisms. Dev Cell 2024:S1534-5807(24)00457-X. [PMID: 39137774 DOI: 10.1016/j.devcel.2024.07.017] [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: 11/14/2023] [Revised: 04/17/2024] [Accepted: 07/16/2024] [Indexed: 08/15/2024]
Abstract
Macrophages measure the "eat-me" signal immunoglobulin G (IgG) to identify targets for phagocytosis. We tested whether prior encounters with IgG influence macrophage appetite. IgG is recognized by the Fc receptor. To temporally control Fc receptor activation, we engineered an Fc receptor that is activated by the light-induced oligomerization of Cry2, triggering phagocytosis. Using this tool, we demonstrate that subthreshold Fc receptor activation primes mouse bone-marrow-derived macrophages to be more sensitive to IgG in future encounters. Macrophages that have previously experienced subthreshold Fc receptor activation eat more IgG-bound human cancer cells. Increased phagocytosis occurs by two discrete mechanisms-a short- and long-term priming. Long-term priming requires new protein synthesis and Erk activity. Short-term priming does not require new protein synthesis and correlates with an increase in Fc receptor mobility. Our work demonstrates that IgG primes macrophages for increased phagocytosis, suggesting that therapeutic antibodies may become more effective after initial priming doses.
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Affiliation(s)
- Annalise Bond
- Molecular Cellular and Developmental Biology Department, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Sareen Fiaz
- Molecular Cellular and Developmental Biology Department, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Kirstin Rollins
- Molecular Cellular and Developmental Biology Department, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Jazz Elaiza Q Nario
- Molecular Cellular and Developmental Biology Department, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Erika T Snyder
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Dixon J Atkins
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Samuel J Rosen
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Alyssa Granados
- Molecular Cellular and Developmental Biology Department, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Siddharth S Dey
- Chemical Engineering Department, University of California, Santa Barbara, Santa Barbara, CA, USA; Bioengineering Department, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Maxwell Z Wilson
- Molecular Cellular and Developmental Biology Department, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Meghan A Morrissey
- Molecular Cellular and Developmental Biology Department, University of California, Santa Barbara, Santa Barbara, CA, USA.
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6
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Taylor DJ, Eizenga JM, Li Q, Das A, Jenike KM, Kenny EE, Miga KH, Monlong J, McCoy RC, Paten B, Schatz MC. Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References. Annu Rev Genomics Hum Genet 2024; 25:77-104. [PMID: 38663087 DOI: 10.1146/annurev-genom-021623-081639] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
The Human Genome Project was an enormous accomplishment, providing a foundation for countless explorations into the genetics and genomics of the human species. Yet for many years, the human genome reference sequence remained incomplete and lacked representation of human genetic diversity. Recently, two major advances have emerged to address these shortcomings: complete gap-free human genome sequences, such as the one developed by the Telomere-to-Telomere Consortium, and high-quality pangenomes, such as the one developed by the Human Pangenome Reference Consortium. Facilitated by advances in long-read DNA sequencing and genome assembly algorithms, complete human genome sequences resolve regions that have been historically difficult to sequence, including centromeres, telomeres, and segmental duplications. In parallel, pangenomes capture the extensive genetic diversity across populations worldwide. Together, these advances usher in a new era of genomics research, enhancing the accuracy of genomic analysis, paving the path for precision medicine, and contributing to deeper insights into human biology.
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Affiliation(s)
- Dylan J Taylor
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA; , ,
| | - Jordan M Eizenga
- Genomics Institute, University of California, Santa Cruz, California, USA; , ,
| | - Qiuhui Li
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA; ,
| | - Arun Das
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA; ,
| | - Katharine M Jenike
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA;
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA;
| | - Karen H Miga
- Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
- Genomics Institute, University of California, Santa Cruz, California, USA; , ,
| | - Jean Monlong
- Institut de Recherche en Santé Digestive, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France;
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA; , ,
| | - Benedict Paten
- Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
- Genomics Institute, University of California, Santa Cruz, California, USA; , ,
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA; ,
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA; , ,
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7
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Talbot BM, Clennon JA, Rakotoarison MFN, Rautman L, Durry S, Ragazzo LJ, Wright PC, Gillespie TR, Read TD. Metagenome-wide characterization of shared antimicrobial resistance genes in sympatric people and lemurs in rural Madagascar. PeerJ 2024; 12:e17805. [PMID: 39099658 PMCID: PMC11296303 DOI: 10.7717/peerj.17805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 07/03/2024] [Indexed: 08/06/2024] Open
Abstract
Background Tracking the spread of antibiotic resistant bacteria is critical to reduce global morbidity and mortality associated with human and animal infections. There is a need to understand the role that wild animals in maintenance and transfer of antibiotic resistance genes (ARGs). Methods This study used metagenomics to identify and compare the abundance of bacterial species and ARGs detected in the gut microbiomes from sympatric humans and wild mouse lemurs in a forest-dominated, roadless region of Madagascar near Ranomafana National Park. We examined the contribution of human geographic location toward differences in ARG abundance and compared the genomic similarity of ARGs between host source microbiomes. Results Alpha and beta diversity of species and ARGs between host sources were distinct but maintained a similar number of detectable ARG alleles. Humans were differentially more abundant for four distinct tetracycline resistance-associated genes compared to lemurs. There was no significant difference in human ARG diversity from different locations. Human and lemur microbiomes shared 14 distinct ARGs with highly conserved in nucleotide identity. Synteny of ARG-associated assemblies revealed a distinct multidrug-resistant gene cassette carrying dfrA1 and aadA1 present in human and lemur microbiomes without evidence of geographic overlap, suggesting that these resistance genes could be widespread in this ecosystem. Further investigation into intermediary processes that maintain drug-resistant bacteria in wildlife settings is needed.
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Affiliation(s)
- Brooke M. Talbot
- Program in Population Biology, Ecology, and Evolution, Emory University, Atlanta, GA, United States of America
- Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA, United States of America
| | - Julie A. Clennon
- Department of Environmental Sciences, Emory University, Atlanta, GA, United States of America
| | | | - Lydia Rautman
- Department of Environmental Sciences, Emory University, Atlanta, GA, United States of America
| | - Sarah Durry
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States of America
| | - Leo J. Ragazzo
- Department of Environmental Sciences, Emory University, Atlanta, GA, United States of America
| | - Patricia C. Wright
- Centre ValBio, Ranomafana, Madagascar
- Institute for the Conservation of Tropical Ecosystems, State University of New York at Stony Brook, Stony Brook, NY, United States of America
| | - Thomas R. Gillespie
- Program in Population Biology, Ecology, and Evolution, Emory University, Atlanta, GA, United States of America
- Department of Environmental Sciences, Emory University, Atlanta, GA, United States of America
- Centre ValBio, Ranomafana, Madagascar
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States of America
| | - Timothy D. Read
- Program in Population Biology, Ecology, and Evolution, Emory University, Atlanta, GA, United States of America
- Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA, United States of America
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8
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Lin MJ, Langmead B, Safonova Y. IGLoo: Profiling the Immunoglobulin Heavy chain locus in Lymphoblastoid Cell Lines with PacBio High-Fidelity Sequencing reads. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.20.604421. [PMID: 39091872 PMCID: PMC11291057 DOI: 10.1101/2024.07.20.604421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
New high-quality human genome assemblies derived from lymphoblastoid cell lines (LCLs) provide reference genomes and pangenomes for genomics studies. However, the characteristics of LCLs pose technical challenges to profiling immunoglobulin (IG) genes. IG loci in LCLs contain a mixture of germline and somatically recombined haplotypes, making them difficult to genotype or assemble accurately. To address these challenges, we introduce IGLoo, a software tool that implements novel methods for analyzing sequence data and genome assemblies derived from LCLs. IGLoo characterizes somatic V(D)J recombination events in the sequence data and identifies the breakpoints and missing IG genes in the LCL-based assemblies. Furthermore, IGLoo implements a novel reassembly framework to improve germline assembly quality by integrating information about somatic events and population structural variantions in the IG loci. We applied IGLoo to study the assemblies from the Human Pangenome Reference Consortium, providing new insights into the mechanisms, gene usage, and patterns of V(D)J recombination, causes of assembly fragmentation in the IG heavy chain (IGH) locus, and improved representation of the IGH assemblies.
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Affiliation(s)
- Mao-Jan Lin
- Department of Computer Science, Johns Hopkins University
| | - Ben Langmead
- Department of Computer Science, Johns Hopkins University
| | - Yana Safonova
- Department of Computer Science, Johns Hopkins University
- Computer Science and Engineering Department, Pennsylvania State University
- Huck Institutes of Life Sciences, Pennsylvania State University
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9
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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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10
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Sandoval-Velasco M, Dudchenko O, Rodríguez JA, Pérez Estrada C, Dehasque M, Fontsere C, Mak SST, Khan R, Contessoto VG, Oliveira Junior AB, Kalluchi A, Zubillaga Herrera BJ, Jeong J, Roy RP, Christopher I, Weisz D, Omer AD, Batra SS, Shamim MS, Durand NC, O'Connell B, Roca AL, Plikus MV, Kusliy MA, Romanenko SA, Lemskaya NA, Serdyukova NA, Modina SA, Perelman PL, Kizilova EA, Baiborodin SI, Rubtsov NB, Machol G, Rath K, Mahajan R, Kaur P, Gnirke A, Garcia-Treviño I, Coke R, Flanagan JP, Pletch K, Ruiz-Herrera A, Plotnikov V, Pavlov IS, Pavlova NI, Protopopov AV, Di Pierro M, Graphodatsky AS, Lander ES, Rowley MJ, Wolynes PG, Onuchic JN, Dalén L, Marti-Renom MA, Gilbert MTP, Aiden EL. Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample. Cell 2024; 187:3541-3562.e51. [PMID: 38996487 DOI: 10.1016/j.cell.2024.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 03/07/2024] [Accepted: 06/03/2024] [Indexed: 07/14/2024]
Abstract
Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth's death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.
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Affiliation(s)
| | - Olga Dudchenko
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA.
| | - Juan Antonio Rodríguez
- Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark; Centre Nacional d'Anàlisi Genòmica, CNAG, 08028 Barcelona, Spain
| | - Cynthia Pérez Estrada
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Marianne Dehasque
- Centre for Palaeogenetics, SE-106 91 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Claudia Fontsere
- Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark
| | - Sarah S T Mak
- Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark
| | - Ruqayya Khan
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | - Achyuth Kalluchi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Bernardo J Zubillaga Herrera
- Department of Physics, Northeastern University, Boston, MA 02115, USA; Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02215, USA
| | - Jiyun Jeong
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Renata P Roy
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Departments of Biology and Physics, Texas Southern University, Houston, TX 77004, USA
| | - Ishawnia Christopher
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arina D Omer
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sanjit S Batra
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muhammad S Shamim
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neva C Durand
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brendan O'Connell
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Alfred L Roca
- Department of Animal Sciences and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Maksim V Plikus
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Mariya A Kusliy
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia
| | | | - Natalya A Lemskaya
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia
| | | | - Svetlana A Modina
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia
| | - Elena A Kizilova
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | | | - Nikolai B Rubtsov
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | - Gur Machol
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Krisha Rath
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ragini Mahajan
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77005, USA
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, University of Western Australia, Perth, WA 6009, Australia
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Rob Coke
- San Antonio Zoo, San Antonio, TX 78212, USA
| | | | | | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia and Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | | | | | - Naryya I Pavlova
- Institute of Biological Problems of Cryolitezone SB RAS, Yakutsk 677000, Russia
| | - Albert V Protopopov
- Academy of Sciences of Sakha Republic, Yakutsk 677000, Russia; North-Eastern Federal University, Yakutsk 677027, Russia
| | - Michele Di Pierro
- Department of Physics, Northeastern University, Boston, MA 02115, USA; Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02215, USA
| | | | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77005, USA; Departments of Physics, Astronomy, & Chemistry, Rice University, Houston, TX 77005, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77005, USA; Departments of Physics, Astronomy, & Chemistry, Rice University, Houston, TX 77005, USA
| | - Love Dalén
- Centre for Palaeogenetics, SE-106 91 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Marc A Marti-Renom
- Centre Nacional d'Anàlisi Genòmica, CNAG, 08028 Barcelona, Spain; Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain; ICREA, 08010 Barcelona, Spain; Universitat Pompeu Fabra, 08002 Barcelona, Spain.
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark; University Museum NTNU, 7012 Trondheim, Norway.
| | - Erez Lieberman Aiden
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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11
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Jimenez N, Norton T, Diadala G, Bell E, Valenti M, Farland LV, Mahnert N, Herbst-Kralovetz MM. Vaginal and rectal microbiome contribute to genital inflammation in chronic pelvic pain. BMC Med 2024; 22:283. [PMID: 38972981 PMCID: PMC11229265 DOI: 10.1186/s12916-024-03500-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024] Open
Abstract
BACKGROUND Chronic pelvic pain (CPP) is a multifactorial syndrome that can substantially affect a patient's quality of life. Endometriosis is one cause of CPP, and alterations of the immune and microbiome profiles have been observed in patients with endometriosis. The objective of this pilot study was to investigate differences in the vaginal and gastrointestinal microbiomes and cervicovaginal immune microenvironment in patients with CPP and endometriosis diagnosis compared to those with CPP without endometriosis and no CPP. METHODS Vaginal swabs, rectal swabs, and cervicovaginal lavages (CVL) were collected among individuals undergoing gynecologic laparoscopy. Participants were grouped based on patients seeking care for chronic pain and/or pathology results: CPP and endometriosis (CPP-Endo) (n = 35), CPP without endometriosis (n = 23), or patients without CPP or endometriosis (controls) (n = 15). Sensitivity analyses were performed on CPP with endometriosis location, stage, and co-occurring gynecologic conditions (abnormal uterine bleeding, fibroids). 16S rRNA sequencing was performed to profile the microbiome, and a panel of soluble immune mediators was quantified using a multiplex assay. Statistical analysis was conducted with SAS, R, MicrobiomeAnalyst, MetaboAnalyst, and QIIME 2. RESULTS Significant differences were observed between participants with CPP alone, CPP-Endo, and surgical controls for body mass index, ethnicity, diagnosis of ovarian cysts, and diagnosis of fibroids. In rectal microbiome analysis, both CPP alone and CPP-Endo exhibited lower alpha diversity than controls, and both CPP groups revealed enrichment of irritable bowel syndrome-associated bacteria. CPP-Endo exhibited an increased abundance of vaginal Streptococcus anginosus and rectal Ruminococcus. Patients with CPP and endometrioma (s) demonstrated increased vaginal Streptococcus, Lactobacillus, and Prevotella compared to other endometriosis sites. Further, abnormal uterine bleeding was associated with an increased abundance of bacterial vaginosis-associated bacteria. Immunoproteomic profiles were distinctly clustered by CPP alone and CPP-Endo compared to controls. CPP-Endo was enriched in TNF⍺, MDC, and IL-1⍺. CONCLUSIONS Vaginal and rectal microbiomes were observed to differ between patients with CPP alone and CPP with endometriosis, which may be useful in personalized treatment for individuals with CPP and endometriosis from those with other causes of CPP. Further investigation is warranted in patients with additional co-occurring conditions, such as AUB/fibroids, which add additional complexity to these conditions and reveal the enrichment of distinct pathogenic bacteria in both mucosal sites. This study provides foundational microbiome-immunoproteomic knowledge related to chronic pelvic pain, endometriosis, and co-occurring gynecologic conditions that can help improve the treatment of patients seeking care for pain.
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Affiliation(s)
- Nicole Jimenez
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
| | - Taylor Norton
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
- Department of Obstetrics and Gynecology, Banner University Medical Center Phoenix, Phoenix, AZ, USA
| | - Gurbeen Diadala
- Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Building ABC-1, Lab 331E, 425 N. 5 St, Phoenix, AZ, 85004, USA
| | - Emerald Bell
- Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Building ABC-1, Lab 331E, 425 N. 5 St, Phoenix, AZ, 85004, USA
- University of Arizona College of Nursing, Tucson, AZ, USA
| | - Michelle Valenti
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
| | - Leslie V Farland
- UA Cancer Center, University of Arizona, Tucson, AZ, USA
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
- Department of Obstetrics and Gynecology, College of Medicine Tucson, University of Arizona, Tucson, AZ, USA
| | - Nichole Mahnert
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
- Department of Obstetrics and Gynecology, Banner University Medical Center Phoenix, Phoenix, AZ, USA
| | - Melissa M Herbst-Kralovetz
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA.
- Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Building ABC-1, Lab 331E, 425 N. 5 St, Phoenix, AZ, 85004, USA.
- UA Cancer Center, University of Arizona, Tucson, AZ, USA.
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12
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Schweiger R, Lee S, Zhou C, Yang TP, Smith K, Li S, Sanghvi R, Neville M, Mitchell E, Nessa A, Wadge S, Small KS, Campbell PJ, Sudmant PH, Rahbari R, Durbin R. Insights into non-crossover recombination from long-read sperm sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.05.602249. [PMID: 39005338 PMCID: PMC11245106 DOI: 10.1101/2024.07.05.602249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Meiotic recombination is a fundamental process that generates genetic diversity by creating new combinations of existing alleles. Although human crossovers have been studied at the pedigree, population and single-cell level, the more frequent non-crossover events that lead to gene conversion are harder to study, particularly at the individual level. Here we show that single high-fidelity long sequencing reads from sperm can capture both crossovers and non-crossovers, allowing effectively arbitrary sample sizes for analysis from one male. Using fifteen sperm samples from thirteen donors we demonstrate variation between and within donors for the rates of different types of recombination. Intriguingly, we observe a tendency for non-crossover gene conversions to occur upstream of nearby PRDM9 binding sites, whereas crossover locations have a slight downstream bias. We further provide evidence for two distinct non-crossover processes. One gives rise to the vast majority of non-crossovers with mean conversion tract length under 50bp, which we suggest is an outcome of standard PRDM9-induced meiotic recombination. In contrast ~2% of non-crossovers have much longer mean tract length, and potentially originate from the same process as complex events with more than two haplotype switches, which is not associated with PRDM9 binding sites and is also seen in somatic cells.
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Affiliation(s)
- Regev Schweiger
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, United Kingdom
| | - Sangjin Lee
- Wellcome Sanger Institute, Cancer Ageing and Somatic Mutation, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Chenxi Zhou
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, United Kingdom
| | - Tsun-Po Yang
- Wellcome Sanger Institute, Cancer Ageing and Somatic Mutation, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Katie Smith
- Wellcome Sanger Institute, Cancer Ageing and Somatic Mutation, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Stacy Li
- Department of Integrative Biology, University of California Berkeley, Berkeley, USA
| | - Rashesh Sanghvi
- Wellcome Sanger Institute, Cancer Ageing and Somatic Mutation, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Matthew Neville
- Wellcome Sanger Institute, Cancer Ageing and Somatic Mutation, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Emily Mitchell
- Wellcome Sanger Institute, Cancer Ageing and Somatic Mutation, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Ayrun Nessa
- Kings College London, Department of Twin Research & Genetic Epidemiology, London, United Kingdom
| | - Sam Wadge
- Kings College London, Department of Twin Research & Genetic Epidemiology, London, United Kingdom
| | - Kerrin S Small
- Kings College London, Department of Twin Research & Genetic Epidemiology, London, United Kingdom
| | - Peter J Campbell
- Wellcome Sanger Institute, Cancer Ageing and Somatic Mutation, Hinxton, Cambridge CB10 1SA, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
| | - Peter H Sudmant
- Department of Integrative Biology, University of California Berkeley, Berkeley, USA
- Center for Computational Biology, University of California Berkeley, Berkeley, USA
| | - Raheleh Rahbari
- Wellcome Sanger Institute, Cancer Ageing and Somatic Mutation, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, United Kingdom
- Wellcome Sanger Institute, Cancer Ageing and Somatic Mutation, Hinxton, Cambridge CB10 1SA, United Kingdom
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13
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Ahting S, Nährlich L, Held I, Henn C, Krill A, Landwehr K, Meister J, Nährig S, Nolde A, Remke K, Ruppel R, Sauer-Heilborn A, Schebek M, Schopper G, Schulte-Hubbert B, Schwarz C, Smaczny C, Wege S, Hentschel J. Every CFTR variant counts - Target-capture based next-generation-sequencing for molecular diagnosis in the German CF Registry. J Cyst Fibros 2024; 23:774-781. [PMID: 37867076 DOI: 10.1016/j.jcf.2023.10.009] [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: 07/13/2023] [Revised: 10/01/2023] [Accepted: 10/09/2023] [Indexed: 10/24/2023]
Abstract
BACKGROUND In times of genotype guided therapy options, a total of 3.2 % of people with CF (pwCF) in the German CF Registry[1] only have one or no CFTR-variant detected after genetic analysis. Additionally, genetic data in the Registry can be documented as free text and can therefore be prone to error. In order to allow the greatest possible amount of pwCF access to modern therapies, we conducted a re-evaluation of free text entries and established a custom-whole-CFTR-locus NGS-approach for all pwCF who remained without genetic confirmation afterwards. METHODS To this end, we assembled 731 free text variants of 655 pwCF in the German CF Registry. All variants were evaluated using ClinVar, HGMD and CFTR1/2, corrected in the Registries' database and uploaded to ClinVar. PwCF whose diagnosis remained uncertain as well as additional pwCF or pwCFTR-RD that were assembled through a nationwide call for testing of unclear cases were offered genetic analysis. Samples were analysed using a target-capture based NGS-custom-design-panel covering the entire CFTR-locus. RESULTS Evaluation of free text variants led to the discovery of 43 variants not formerly reported in the context of CF. The Registries' dropdown list was extended by 497 variants and over 500 pwCF were provided with their most up-to-date genotype. Samples of 47 pwCF/pwCFTR-RD were sequenced via NGS with an overall success rate of 61.7 %, resulting in implementation of entire CFTR-genotyping into routine diagnostics. CONCLUSION Entire CFTR-genotyping can greatly increase the genetic diagnostic rate of pwCF/pwCFTR-RD and should be considered after inconspicuous CFTR screening panels in CFTR-diagnostics.
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Affiliation(s)
- Simone Ahting
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig, Germany.
| | - Lutz Nährlich
- Department of Pediatrics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Inka Held
- Pediatric Practice Friesenweg, Cystic Fibrosis Center Altona, Hamburg, Germany
| | - Constance Henn
- Division of pediatric Pulmonology and Allergology, Hospital for children and adolescents, University Medical Center Leipzig, Leipzig, Germany
| | - Angelika Krill
- Division of Pneumology, University Medical Center Homburg, Homburg/Saar, Germany
| | - Kerstin Landwehr
- Division of Allergology and Pediatric Pneumology, University Children's Hospital Bethel, University Medical Center Ostwestfalen-Lippe, Bielefeld, Germany
| | - Jochen Meister
- Division of Pneumology, Allergology and Psychotherapy, Children's Hospital, Helios Hospital Aue, Aue, Germany
| | - Susanne Nährig
- Cystic Fibrosis Center for Adults, Med. Klinik V, University Hospital LMU, Munich, Germany
| | - Anna Nolde
- Division of Pneumology, II. Department of Medicine and University Transplant Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katharina Remke
- Department for General Paediatrics, Neonatology and Paediatric Cardiology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Renate Ruppel
- University Children's Hospital, University Medical Center Erlangen, Erlangen, Germany
| | | | - Martin Schebek
- Division of Pediatric Pneumology, Center for Pediatric and Women's Medicine Kassel, Kassel, Germany
| | - Gudrun Schopper
- University Children's Hospital Schwabing, Technical University of Munich, Munich, Germany
| | - Bernhard Schulte-Hubbert
- Department of medical clinic I, Medical Center Carl Gustav Carus, Technical University of Dresden, Dresden, Germany
| | - Carsten Schwarz
- Department Medicine, HMU-Health and Medical University Potsdam and Director CF Center Westbrandenburg, Division Cystic Fibrosis, Clinic Westbrandenburg, Potsdam, Germany
| | - Christina Smaczny
- Christiane Herzog CF-centre Frankfurt/Main, University Medical Center Frankfurt, Goethe-University Frankfurt, Frankfurt/Main, Germany
| | - Sabine Wege
- Cystic Fibrosis Center, Thoraxklinik Heidelberg, University Medical Center Heidelberg, Heidelberg, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig, Germany
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Mishra R, Thunuguntla P, Perkin A, Duraiyan D, Bagwill K, Gonzales S, Brizuela V, Daly S, Chang YJ, Abebe M, Rajana Y, Wichmann K, Bolick C, King J, Fiala M, Fortier J, Jayasinghe R, Schroeder M, Ding L, Vij R, Silva-Fisher J. LINC01432 binds to CELF2 in newly diagnosed multiple myeloma promoting short progression-free survival to standard therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.600975. [PMID: 38979159 PMCID: PMC11230414 DOI: 10.1101/2024.06.27.600975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Multiple Myeloma (MM) is a highly prevalent and incurable form of cancer that arises from malignant plasma cells, with over 35,000 new cases diagnosed annually in the United States. While there are a growing number of approved therapies, MM remains incurable and nearly all patients will relapse and exhaust all available treatment options. Mechanisms for disease progression are unclear and in particular, little is known regarding the role of long non-coding RNAs (lncRNA) in mediating disease progression and response to treatment. In this study, we used transcriptome sequencing to compare newly diagnosed MM patients who had short progression-free survival (PFS) to standard first-line treatment (PFS < 24 months) to patients who had prolonged PFS (PFS > 24 months). We identified 157 differentially upregulated lncRNAs with short PFS and focused our efforts on characterizing the most upregulated lncRNA, LINC01432. We investigated LINC01432 overexpression and CRISPR/Cas9 knockdown in MM cell lines to show that LINC01432 overexpression significantly increases cell viability and reduces apoptosis, while knockdown significantly reduces viability and increases apoptosis, supporting the clinical relevance of this lncRNA. Next, we used individual-nucleotide resolution cross-linking immunoprecipitation with RT-qPCR to show that LINC01432 directly interacts with the RNA binding protein, CELF2. Lastly, we showed that LINC01432-targeted locked nucleic acid antisense oligonucleotides reduce viability and increases apoptosis. In summary, this fundamental study identified lncRNAs associated with short PFS to standard NDMM treatment and further characterized LINC01432, which inhibits apoptosis.
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15
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Henglin M, Ghareghani M, Harvey W, Porubsky D, Koren S, Eichler EE, Ebert P, Marschall T. Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580432. [PMID: 38529499 PMCID: PMC10962706 DOI: 10.1101/2024.02.15.580432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Haplotype information is crucial for biomedical and population genetics research. However, current strategies to produce de-novo haplotype-resolved assemblies often require either difficult-to-acquire parental data or an intermediate haplotype-collapsed assembly. Here, we present Graphasing, a workflow which synthesizes the global phase signal of Strand-seq with assembly graph topology to produce chromosome-scale de-novo haplotypes for diploid genomes. Graphasing readily integrates with any assembly workflow that both outputs an assembly graph and has a haplotype assembly mode. Graphasing performs comparably to trio-phasing in contiguity, phasing accuracy, and assembly quality, outperforms Hi-C in phasing accuracy, and generates human assemblies with over 18 chromosome-spanning haplotypes.
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Affiliation(s)
- Mir Henglin
- Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Germany
| | - Maryam Ghareghani
- Department of Mathematics and Computer Science, Freie Universität Berlin, Germany
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - William Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - 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
| | - Peter Ebert
- Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Germany
- Core Unit Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany
| | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Germany
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16
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Greiner AM, Mehdi H, Cevan C, Gutmann R, London B. The role of GPD1L, a sodium channel interacting gene, in the pathogenesis of Brugada Syndrome. Front Med (Lausanne) 2024; 10:1159586. [PMID: 38962240 PMCID: PMC11221213 DOI: 10.3389/fmed.2023.1159586] [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: 02/06/2023] [Accepted: 03/06/2023] [Indexed: 07/05/2024] Open
Abstract
Background Brugada Syndrome (BrS) is an inherited arrhythmia syndrome in which mutations in the cardiac sodium channel SCN5A (NaV1.5) account for approximately 20% of cases. Mutations in sodium channel-modifying genes may account for additional BrS cases, though BrS may be polygenic given common SNPs associated with BrS have been identified. Recent analysis, however, has suggested that SCN5A should be regarded as the sole monogenic cause of BrS. Objective We sought to re-assess the genetic underpinnings of BrS in a large mutligenerational family with a putative mutation in GPD1L that affects surface membrane expression of NaV1.5 in vitro. Methods Fine linkage mapping was performed in the family using the Illumina Global Screening Array. Whole exome sequencing of the proband was performed to identify rare variants and mutations, and Sanger sequencing was used to assay previously-reported risk single nucleotide polymorphsims (SNPs) for BrS. Results Linkage analysis decreased the size of the previously-reported microsatellite linkage region to approximately 3 Mb. GPD1L-A280V was the only coding non-synonymous variation present at less than 1% allele frequency in the proband within the linkage region. No rare non-synonymous variants were present outside the linkage area in affected individuals in genes associated with BrS. Risk SNPs known to predispose to BrS were overrepresented in affected members of the family. Conclusion Together, our data suggest GPD1L-A280V remains the most likely cause of BrS in this large multigenerational family. While care should be taken in interpreting variant pathogenicity given the genetic uncertainty of BrS, our data support inclusion of other putative BrS genes in clinical genetic panels.
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Affiliation(s)
- Alexander M. Greiner
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, United States
- Department of Internal Medicine, Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City, IA, United States
- University of Iowa Interdisciplinary Graduate Program in Genetics, Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, United States
| | - Haider Mehdi
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, United States
- Department of Internal Medicine, Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Chloe Cevan
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Rebecca Gutmann
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Barry London
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, United States
- Department of Internal Medicine, Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City, IA, United States
- University of Iowa Interdisciplinary Graduate Program in Genetics, Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, United States
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17
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Kraemer D, Terumalai D, Famiglietti ML, Filges I, Joset P, Koller S, Maurer F, Meier S, Nouspikel T, Sanz J, Zweier C, Abramowicz M, Berger W, Cichon S, Schaller A, Superti-Furga A, Barbié V, Rauch A. SwissGenVar: A Platform for Clinical-Grade Interpretation of Genetic Variants to Foster Personalized Healthcare in Switzerland. J Pers Med 2024; 14:648. [PMID: 38929869 PMCID: PMC11204794 DOI: 10.3390/jpm14060648] [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: 04/04/2024] [Revised: 05/28/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Large-scale next-generation sequencing (NGS) germline testing is technically feasible today, but variant interpretation represents a major bottleneck in analysis workflows. This includes extensive variant prioritization, annotation, and time-consuming evidence curation. The scale of the interpretation problem is massive, and variants of uncertain significance (VUSs) are a challenge to personalized medicine. This challenge is further compounded by the complexity and heterogeneity of the standards used to describe genetic variants and the associated phenotypes when searching for relevant information to support clinical decision making. To address this, all five Swiss academic institutions for Medical Genetics joined forces with the Swiss Institute of Bioinformatics (SIB) to create SwissGenVar as a user-friendly nationwide repository and sharing platform for genetic variant data generated during routine diagnostic procedures and research sequencing projects. Its aim is to provide a protected environment for expert evidence sharing about individual variants to harmonize and upscale their significance interpretation at the clinical grade according to international standards. To corroborate the clinical assessment, the variant-related data will be combined with consented high-quality clinical information. Broader visibility will be achieved by interfacing with international databases, thus supporting global initiatives in personalized healthcare.
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Affiliation(s)
- Dennis Kraemer
- Institute of Medical Genetics (IMG), University of Zurich (UZH), Wagistrasse 12, CH-8952 Zurich, Switzerland;
| | - Dillenn Terumalai
- Swiss Institute of Bioinformatics (SIB), Clinical Bioinformatics, CH-1202 Geneva, Switzerland; (D.T.); (V.B.)
| | | | - Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, CH-4031 Basel, Switzerland; (I.F.); (P.J.); (S.M.); (S.C.)
| | - Pascal Joset
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, CH-4031 Basel, Switzerland; (I.F.); (P.J.); (S.M.); (S.C.)
| | - Samuel Koller
- Institute of Medical Molecular Genetics (IMMG), University of Zurich (UZH), Wagistrasse 12, CH-8952 Zurich, Switzerland; (S.K.); (W.B.)
| | - Fabienne Maurer
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), CH-1011 Lausanne, Switzerland; (F.M.); (A.S.-F.)
| | - Stéphanie Meier
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, CH-4031 Basel, Switzerland; (I.F.); (P.J.); (S.M.); (S.C.)
| | - Thierry Nouspikel
- Genetic Medicine Division, Diagnostics Department/Center for Genomic Medicine, Geneva University Hospitals (HUG), 1206 Geneva, Switzerland; (T.N.); (M.A.)
| | - Javier Sanz
- Department of Human Genetics, Inselspital, Bern University Hospital, CH-3010 Bern, Switzerland; (J.S.); (C.Z.); (A.S.)
| | - Christiane Zweier
- Department of Human Genetics, Inselspital, Bern University Hospital, CH-3010 Bern, Switzerland; (J.S.); (C.Z.); (A.S.)
| | - Marc Abramowicz
- Genetic Medicine Division, Diagnostics Department/Center for Genomic Medicine, Geneva University Hospitals (HUG), 1206 Geneva, Switzerland; (T.N.); (M.A.)
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics (IMMG), University of Zurich (UZH), Wagistrasse 12, CH-8952 Zurich, Switzerland; (S.K.); (W.B.)
- Neuroscience Center Zurich (ZNZ), University and ETH Zurich, CH-8057 Zurich, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, CH-8057 Zurich, Switzerland
| | - Sven Cichon
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, CH-4031 Basel, Switzerland; (I.F.); (P.J.); (S.M.); (S.C.)
| | - André Schaller
- Department of Human Genetics, Inselspital, Bern University Hospital, CH-3010 Bern, Switzerland; (J.S.); (C.Z.); (A.S.)
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), CH-1011 Lausanne, Switzerland; (F.M.); (A.S.-F.)
| | - Valérie Barbié
- Swiss Institute of Bioinformatics (SIB), Clinical Bioinformatics, CH-1202 Geneva, Switzerland; (D.T.); (V.B.)
| | - Anita Rauch
- Institute of Medical Genetics (IMG), University of Zurich (UZH), Wagistrasse 12, CH-8952 Zurich, Switzerland;
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18
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Spisak N, de Manuel M, Milligan W, Sella G, Przeworski M. The clock-like accumulation of germline and somatic mutations can arise from the interplay of DNA damage and repair. PLoS Biol 2024; 22:e3002678. [PMID: 38885262 PMCID: PMC11213356 DOI: 10.1371/journal.pbio.3002678] [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: 11/17/2023] [Revised: 06/28/2024] [Accepted: 05/14/2024] [Indexed: 06/20/2024] Open
Abstract
The rates at which mutations accumulate across human cell types vary. To identify causes of this variation, mutations are often decomposed into a combination of the single-base substitution (SBS) "signatures" observed in germline, soma, and tumors, with the idea that each signature corresponds to one or a small number of underlying mutagenic processes. Two such signatures turn out to be ubiquitous across cell types: SBS signature 1, which consists primarily of transitions at methylated CpG sites thought to be caused by spontaneous deamination, and the more diffuse SBS signature 5, which is of unknown etiology. In cancers, the number of mutations attributed to these 2 signatures accumulates linearly with age of diagnosis, and thus the signatures have been termed "clock-like." To better understand this clock-like behavior, we develop a mathematical model that includes DNA replication errors, unrepaired damage, and damage repaired incorrectly. We show that mutational signatures can exhibit clock-like behavior because cell divisions occur at a constant rate and/or because damage rates remain constant over time, and that these distinct sources can be teased apart by comparing cell lineages that divide at different rates. With this goal in mind, we analyze the rate of accumulation of mutations in multiple cell types, including soma as well as male and female germline. We find no detectable increase in SBS signature 1 mutations in neurons and only a very weak increase in mutations assigned to the female germline, but a significant increase with time in rapidly dividing cells, suggesting that SBS signature 1 is driven by rounds of DNA replication occurring at a relatively fixed rate. In contrast, SBS signature 5 increases with time in all cell types, including postmitotic ones, indicating that it accumulates independently of cell divisions; this observation points to errors in DNA repair as the key underlying mechanism. Thus, the two "clock-like" signatures observed across cell types likely have distinct origins, one set by rates of cell division, the other by damage rates.
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Affiliation(s)
- Natanael Spisak
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Marc de Manuel
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - William Milligan
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Guy Sella
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
- Program for Mathematical Genomics, Columbia University, New York, New York, United States of America
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
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19
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DeGroat W, Inoue F, Ashuach T, Yosef N, Ahituv N, Kreimer A. Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595375. [PMID: 38826254 PMCID: PMC11142193 DOI: 10.1101/2024.05.22.595375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Background Increasing evidence suggests that a substantial proportion of disease-associated mutations occur in enhancers, regions of non-coding DNA essential to gene regulation. Understanding the structures and mechanisms of regulatory programs this variation affects can shed light on the apparatuses of human diseases. Results We collected epigenetic and gene expression datasets from seven early time points during neural differentiation. Focusing on this model system, we constructed networks of enhancer-promoter interactions, each at an individual stage of neural induction. These networks served as the base for a rich series of analyses, through which we demonstrated their temporal dynamics and enrichment for various disease-associated variants. We applied the Girvan-Newman clustering algorithm to these networks to reveal biologically relevant substructures of regulation. Additionally, we demonstrated methods to validate predicted enhancer-promoter interactions using transcription factor overexpression and massively parallel reporter assays. Conclusions Our findings suggest a generalizable framework for exploring gene regulatory programs and their dynamics across developmental processes. This includes a comprehensive approach to studying the effects of disease-associated variation on transcriptional networks. The techniques applied to our networks have been published alongside our findings as a computational tool, E-P-INAnalyzer. Our procedure can be utilized across different cellular contexts and disorders.
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Affiliation(s)
- William DeGroat
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, 679 Hoes Lane West, Piscataway, NJ 08854, UAS
| | - Fumitaka Inoue
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Tal Ashuach
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, 387 Soda Hall, Berkeley, CA 94720, USA
| | - Nir Yosef
- Department of Systems Immunology, Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel
- Chan-Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
- Department of Systems Immunology, Ragon Institute of MGH, MIT, and Harvard Institute of Science, 400 Technology Square, Cambridge, MA 02139, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 513 Parnassus Ave, CA 94143, USA
- Institute for Human Genetics, University of California, San Francisco, 513 Parnassus Ave, CA 94143, USA
| | - Anat Kreimer
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, 679 Hoes Lane West, Piscataway, NJ 08854, UAS
- Department of Biochemistry and Molecular Biology, Rutgers, The State University of New Jersey, 604 Allison Road, Piscataway, NJ 08854, USA
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20
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Chao KH, Heinz JM, Hoh C, Mao A, Shumate A, Pertea M, Salzberg SL. Combining DNA and protein alignments to improve genome annotation with LiftOn. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.593026. [PMID: 38798552 PMCID: PMC11118573 DOI: 10.1101/2024.05.16.593026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
As the number and variety of assembled genomes continues to grow, the number of annotated genomes is falling behind, particularly for eukaryotes. DNA-based mapping tools help to address this challenge, but they are only able to transfer annotation between closely-related species. Here we introduce LiftOn, a homology-based software tool that integrates DNA and protein alignments to enhance the accuracy of genome-scale annotation and to allow mapping between relatively distant species. LiftOn's protein-centric algorithm considers both types of alignments, chooses optimal open reading frames, resolves overlapping gene loci, and finds additional gene copies where they exist. LiftOn can reliably transfer annotation between genomes representing members of the same species, as we demonstrate on human, mouse, honey bee, rice, and Arabidopsis thaliana. It can further map annotation effectively across species pairs as far apart as mouse and rat or Drosophila melanogaster and D. erecta.
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Affiliation(s)
- Kuan-Hao Chao
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jakob M. Heinz
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Celine Hoh
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alan Mao
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alaina Shumate
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Mihaela Pertea
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Steven L Salzberg
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21211, USA
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21
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Vilà-Valls L, Abdeli A, Lucas-Sánchez M, Bekada A, Calafell F, Benhassine T, Comas D. Understanding the genomic heterogeneity of North African Imazighen: from broad to microgeographical perspectives. Sci Rep 2024; 14:9979. [PMID: 38693301 PMCID: PMC11063056 DOI: 10.1038/s41598-024-60568-8] [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: 02/01/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024] Open
Abstract
The strategic location of North Africa has led to cultural and demographic shifts, shaping its genetic structure. Historical migrations brought different genetic components that are evident in present-day North African genomes, along with autochthonous components. The Imazighen (plural of Amazigh) are believed to be the descendants of autochthonous North Africans and speak various Amazigh languages, which belong to the Afro-Asiatic language family. However, the arrival of different human groups, especially during the Arab conquest, caused cultural and linguistic changes in local populations, increasing their heterogeneity. We aim to characterize the genetic structure of the region, using the largest Amazigh dataset to date and other reference samples. Our findings indicate microgeographical genetic heterogeneity among Amazigh populations, modeled by various admixture waves and different effective population sizes. A first admixture wave is detected group-wide around the twelfth century, whereas a second wave appears in some Amazigh groups around the nineteenth century. These events involved populations with higher genetic ancestry from south of the Sahara compared to the current North Africans. A plausible explanation would be the historical trans-Saharan slave trade, which lasted from the Roman times to the nineteenth century. Furthermore, our investigation shows that assortative mating in North Africa has been rare.
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Affiliation(s)
- Laura Vilà-Valls
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Amine Abdeli
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté Des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Marcel Lucas-Sánchez
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Asmahan Bekada
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 (Ahmad Ben Bella), Oran, Algeria
| | - Francesc Calafell
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Traki Benhassine
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté Des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - David Comas
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain.
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22
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Bilgrav Saether K, Eisfeldt J, Bengtsson J, Lun MY, Grochowski CM, Mahmoud M, Chao HT, Rosenfeld JA, Liu P, Schuy J, Ameur A, Hwang JP, Sedlazeck FJ, Bi W, Marom R, Nordgren A, Carvalho CMB, Lindstrand A. Mind the gap: the relevance of the genome reference to resolve rare and pathogenic inversions. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.22.24305780. [PMID: 38712270 PMCID: PMC11071548 DOI: 10.1101/2024.04.22.24305780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Both long-read genome sequencing (lrGS) and the recently published Telomere to Telomere (T2T) reference genome provide increased coverage and resolution across repetitive regions promising heightened structural variant detection and improved mapping. Inversions (INV), intrachromosomal segments which are rotated 180° and inserted back into the same chromosome, are a class of structural variants particularly challenging to detect due to their copy-number neutral state and association with repetitive regions. Inversions represent about 1/20 of all balanced structural chromosome aberrations and can lead to disease by gene disruption or altering regulatory regions of dosage sensitive genes in cis . Here we remapped the genome data from six individuals carrying unsolved cytogenetically detected inversions. An INV6 and INV10 were resolved using GRCh38 and T2T-CHM13. Finally, an INV9 required optical genome mapping, de novo assembly of lrGS data and T2T-CHM13. This inversion disrupted intron 25 of EHMT1, confirming a diagnosis of Kleefstra syndrome 1 (MIM#610253). These three inversions, only mappable in specific references, prompted us to investigate the presence and population frequencies of differential reference regions (DRRs) between T2T-CHM13, GRCh37, GRCh38, the chimpanzee and bonobo, and hundreds of megabases of DRRs were identified. Our results emphasize the significance of the chosen reference genome and the added benefits of lrGS and optical genome mapping in solving rearrangements in challenging regions of the genome. This is particularly important for inversions and may impact clinical diagnostics.
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23
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Kim TS, Ikeuchi T, Theofilou VI, Williams DW, Greenwell-Wild T, June A, Adade EE, Li L, Abusleme L, Dutzan N, Yuan Y, Brenchley L, Bouladoux N, Sakamachi Y, Palmer RJ, Iglesias-Bartolome R, Trinchieri G, Garantziotis S, Belkaid Y, Valm AM, Diaz PI, Holland SM, Moutsopoulos NM. Epithelial-derived interleukin-23 promotes oral mucosal immunopathology. Immunity 2024; 57:859-875.e11. [PMID: 38513665 PMCID: PMC11058479 DOI: 10.1016/j.immuni.2024.02.020] [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: 08/28/2023] [Revised: 01/05/2024] [Accepted: 02/29/2024] [Indexed: 03/23/2024]
Abstract
At mucosal surfaces, epithelial cells provide a structural barrier and an immune defense system. However, dysregulated epithelial responses can contribute to disease states. Here, we demonstrated that epithelial cell-intrinsic production of interleukin-23 (IL-23) triggers an inflammatory loop in the prevalent oral disease periodontitis. Epithelial IL-23 expression localized to areas proximal to the disease-associated microbiome and was evident in experimental models and patients with common and genetic forms of disease. Mechanistically, flagellated microbial species of the periodontitis microbiome triggered epithelial IL-23 induction in a TLR5 receptor-dependent manner. Therefore, unlike other Th17-driven diseases, non-hematopoietic-cell-derived IL-23 served as an initiator of pathogenic inflammation in periodontitis. Beyond periodontitis, analysis of publicly available datasets revealed the expression of epithelial IL-23 in settings of infection, malignancy, and autoimmunity, suggesting a broader role for epithelial-intrinsic IL-23 in human disease. Collectively, this work highlights an important role for the barrier epithelium in the induction of IL-23-mediated inflammation.
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Affiliation(s)
- Tae Sung Kim
- Oral Immunity and Infection Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tomoko Ikeuchi
- Oral Immunity and Infection Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vasileios Ionas Theofilou
- Oral Immunity and Infection Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA; Department of Oncology and Diagnostic Sciences, School of Dentistry, University of Maryland, Baltimore, MD 21201, USA
| | - Drake Winslow Williams
- Oral Immunity and Infection Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Teresa Greenwell-Wild
- Oral Immunity and Infection Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Armond June
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, University at Buffalo, Buffalo, NY 14214, USA
| | - Emmanuel E Adade
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12210, USA
| | - Lu Li
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, University at Buffalo, Buffalo, NY 14214, USA
| | - Loreto Abusleme
- Department of Pathology and Oral Medicine, Faculty of Dentistry, University of Chile, Santiago, Chile
| | - Nicolas Dutzan
- Department of Conservative Dentistry, Faculty of Dentistry, University of Chile, Santiago, Chile
| | - Yao Yuan
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laurie Brenchley
- Oral Immunity and Infection Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicolas Bouladoux
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yosuke Sakamachi
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Robert J Palmer
- Oral Immunity and Infection Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ramiro Iglesias-Bartolome
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Giorgio Trinchieri
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stavros Garantziotis
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alex M Valm
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12210, USA
| | - Patricia I Diaz
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, University at Buffalo, Buffalo, NY 14214, USA
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Niki M Moutsopoulos
- Oral Immunity and Infection Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA.
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24
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Atkins D, Rosas JM, Månsson LK, Shahverdi N, Dey SS, Pitenis AA. Survival-Associated Cellular Response Maintained in Pancreatic Ductal Adenocarcinoma (PDAC) Switched Between Soft and Stiff 3D Microgel Culture. ACS Biomater Sci Eng 2024; 10:2177-2187. [PMID: 38466617 PMCID: PMC11005012 DOI: 10.1021/acsbiomaterials.3c01079] [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: 08/03/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) accounts for about 90% of all pancreatic cancer cases. Five-year survival rates have remained below 12% since the 1970s, in part due to the difficulty in detection prior to metastasis (migration and invasion into neighboring organs and glands). Mechanical memory is a concept that has emerged over the past decade that may provide a path toward understanding how invading PDAC cells "remember" the mechanical properties of their diseased ("stiff", elastic modulus, E ≈ 10 kPa) microenvironment even while invading a healthy ("soft", E ≈ 1 kPa) microenvironment. Here, we investigated the role of mechanical priming by culturing a dilute suspension of PDAC (FG) cells within a 3D, rheologically tunable microgel platform from hydrogels with tunable mechanical properties. We conducted a suite of acute (short-term) priming studies where we cultured PDAC cells in either a soft (E ≈ 1 kPa) or stiff (E ≈ 10 kPa) environment for 6 h, then removed and placed them into a new soft or stiff 3D environment for another 18 h. Following these steps, we conducted RNA-seq analyses to quantify gene expression. Initial priming in the 3D culture showed persistent gene expression for the duration of the study, regardless of the subsequent environments (stiff or soft). Stiff 3D culture was associated with the downregulation of tumor suppressors (LATS1, BCAR3, CDKN2C), as well as the upregulation of cancer-associated genes (RAC3). Immunofluorescence staining (BCAR3, RAC3) further supported the persistence of this cellular response, with BCAR3 upregulated in soft culture and RAC3 upregulated in stiff-primed culture. Stiff-primed genes were stratified against patient data found in The Cancer Genome Atlas (TCGA). Upregulated genes in stiff-primed 3D culture were associated with decreased survival in patient data, suggesting a link between patient survival and mechanical priming.
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Affiliation(s)
- Dixon
J. Atkins
- Department
of Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Jonah M. Rosas
- Department
of Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Lisa K. Månsson
- Materials
Department, University of California Santa
Barbara, Santa
Barbara, California 93106, United States
| | - Nima Shahverdi
- Molecular,
Cellular, and Developmental Biology Department, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Siddharth S. Dey
- Department
of Chemical Engineering, University
of California Santa Barbara, Santa
Barbara, California 93106, United States
- Department
of Bioengineering, University of California
Santa Barbara, Santa Barbara, California 93106, United States
| | - Angela A. Pitenis
- Materials
Department, University of California Santa
Barbara, Santa
Barbara, California 93106, United States
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25
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Miller JR, Adjeroh DA. Machine learning on alignment features for parent-of-origin classification of simulated hybrid RNA-seq. BMC Bioinformatics 2024; 25:109. [PMID: 38475727 DOI: 10.1186/s12859-024-05728-3] [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: 07/28/2023] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Parent-of-origin allele-specific gene expression (ASE) can be detected in interspecies hybrids by virtue of RNA sequence variants between the parental haplotypes. ASE is detectable by differential expression analysis (DEA) applied to the counts of RNA-seq read pairs aligned to parental references, but aligners do not always choose the correct parental reference. RESULTS We used public data for species that are known to hybridize. We measured our ability to assign RNA-seq read pairs to their proper transcriptome or genome references. We tested software packages that assign each read pair to a reference position and found that they often favored the incorrect species reference. To address this problem, we introduce a post process that extracts alignment features and trains a random forest classifier to choose the better alignment. On each simulated hybrid dataset tested, our machine-learning post-processor achieved higher accuracy than the aligner by itself at choosing the correct parent-of-origin per RNA-seq read pair. CONCLUSIONS For the parent-of-origin classification of RNA-seq, machine learning can improve the accuracy of alignment-based methods. This approach could be useful for enhancing ASE detection in interspecies hybrids, though RNA-seq from real hybrids may present challenges not captured by our simulations. We believe this is the first application of machine learning to this problem domain.
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Affiliation(s)
- Jason R Miller
- Department of Computer Science, Mathematics, Engineering, Shepherd University, Shepherdstown, WV, USA.
- EVOGENE, Department of Biosciences, University of Oslo, Oslo, Norway.
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, USA.
| | - Donald A Adjeroh
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, USA
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26
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Zhou Z, Du J, Wang J, Liu L, Gordon MG, Ye CJ, Powell JE, Li MJ, Rao S. SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues. Database (Oxford) 2024; 2024:baae010. [PMID: 38459946 PMCID: PMC10924434 DOI: 10.1093/database/baae010] [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: 09/04/2023] [Revised: 01/09/2024] [Accepted: 02/11/2024] [Indexed: 03/11/2024]
Abstract
Mapping of expression quantitative trait loci (eQTLs) and other molecular QTLs can help characterize the modes of action of disease-associated genetic variants. However, current eQTL databases present data from bulk RNA-seq approaches, which cannot shed light on the cell type- and environment-specific regulation of disease-associated genetic variants. Here, we introduce our Single-cell eQTL Interactive Database which collects single-cell eQTL (sc-eQTL) datasets and provides online visualization of sc-eQTLs across different cell types in a user-friendly manner. Although sc-eQTL mapping is still in its early stage, our database curates the most comprehensive summary statistics of sc-eQTLs published to date. sc-eQTL studies have revolutionized our understanding of gene regulation in specific cellular contexts, and we anticipate that our database will further accelerate the research of functional genomics. Database URL: http://www.sqraolab.com/scqtl.
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Affiliation(s)
- Zhiwei Zhou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin 300020, China
- Tianjin Institutes of Health Science, 28 Tuanbo Avenue, Tianjin 301600, China
| | - Jingyi Du
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin 300020, China
- Tianjin Institutes of Health Science, 28 Tuanbo Avenue, Tianjin 301600, China
| | - Jianhua Wang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, 22 Qixiangtai Road, Tianjin 300070, China
| | - Liangyi Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin 300020, China
| | - M Gracie Gordon
- Biological and Medical Informatics Graduate Program, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA
- Division of Rheumatology, Department of Medicine, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA
- Department of Epidemiology and Biostatistics, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA
- Parker Institute for Cancer Immunotherapy, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA
- Chan Zuckerberg Biohub, 499 Illinois Street, San Francisco, CA 94158, USA
- Bakar Computational Health Sciences Institute, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia
- UNSW Cellular Genomics Futures Institute, University of New South Wales, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Mulin Jun Li
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, 22 Qixiangtai Road, Tianjin 300070, China
| | - Shuquan Rao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin 300020, China
- Tianjin Institutes of Health Science, 28 Tuanbo Avenue, Tianjin 301600, China
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27
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Li J, Song S, Zhang J. Where Are the Formerly Y-linked Genes in the Ryukyu Spiny Rat that has Lost its Y Chromosome? Genome Biol Evol 2024; 16:evae046. [PMID: 38478711 PMCID: PMC10959550 DOI: 10.1093/gbe/evae046] [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] [Accepted: 03/07/2024] [Indexed: 03/23/2024] Open
Abstract
It has been predicted that the highly degenerate mammalian Y chromosome will be lost eventually. Indeed, Y was lost in the Ryukyu spiny rat Tokudaia osimensis, but the fate of the formerly Y-linked genes is not completely known. We looked for all 12 ancestrally Y-linked genes in a draft T. osimensis genome sequence. Zfy1, Zfy2, Kdm5d, Eif2s3y, Usp9y, Uty, and Ddx3y are putatively functional and are now located on the X chromosome, whereas Rbmy, Uba1y, Ssty1, Ssty2, and Sry are missing or pseudogenized. Tissue expressions of the mouse orthologs of the retained genes are significantly broader/higher than those of the lost genes, suggesting that the destinies of the formerly Y-linked genes are related to their original expressions. Interestingly, patterns of gene retention/loss are significantly more similar than by chance across four rodent lineages where Y has been independently lost, indicating a level of certainty in the fate of Y-linked genes even when the chromosome is gone.
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Affiliation(s)
- Jiachen Li
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Siliang Song
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Mukhametzyanova L, Schmitt LT, Torres-Rivera J, Rojo-Romanos T, Lansing F, Paszkowski-Rogacz M, Hollak H, Brux M, Augsburg M, Schneider PM, Buchholz F. Activation of recombinases at specific DNA loci by zinc-finger domain insertions. Nat Biotechnol 2024:10.1038/s41587-023-02121-y. [PMID: 38297187 DOI: 10.1038/s41587-023-02121-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 12/22/2023] [Indexed: 02/02/2024]
Abstract
Recombinases have several potential advantages as genome editing tools compared to nucleases and other editing enzymes, but the process of engineering them to efficiently recombine predetermined DNA targets demands considerable investment of time and labor. Here we sought to harness zinc-finger DNA-binding domains (ZFDs) to program recombinase binding by developing fusions, in which ZFDs are inserted into recombinase coding sequences. By screening libraries of hybrid proteins, we optimized the insertion site, linker length, spacing and ZFD orientation and generated Cre-type recombinases that remain dormant unless the insertionally fused ZFD binds its target site placed in the vicinity of the recombinase binding site. The developed fusion improved targeted editing efficiencies of recombinases by four-fold and abolished measurable off-target activity in mammalian cells. The ZFD-dependent activity is transferable to a recombinase with relaxed specificity, providing the means for developing fully programmable recombinases. Our engineered recombinases provide improved genome editing tools with increased precision and efficiency.
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Affiliation(s)
- Liliya Mukhametzyanova
- Medical Systems Biology, Medical Faculty, Technical University Dresden, Dresden, Germany
| | - Lukas Theo Schmitt
- Medical Systems Biology, Medical Faculty, Technical University Dresden, Dresden, Germany
- Seamless Therapeutics GmbH, Dresden, Germany
| | - Julia Torres-Rivera
- Medical Systems Biology, Medical Faculty, Technical University Dresden, Dresden, Germany
| | - Teresa Rojo-Romanos
- Medical Systems Biology, Medical Faculty, Technical University Dresden, Dresden, Germany
- Seamless Therapeutics GmbH, Dresden, Germany
| | - Felix Lansing
- Medical Systems Biology, Medical Faculty, Technical University Dresden, Dresden, Germany
- Seamless Therapeutics GmbH, Dresden, Germany
| | | | - Heike Hollak
- Medical Systems Biology, Medical Faculty, Technical University Dresden, Dresden, Germany
- Seamless Therapeutics GmbH, Dresden, Germany
| | - Melanie Brux
- Medical Systems Biology, Medical Faculty, Technical University Dresden, Dresden, Germany
| | - Martina Augsburg
- Medical Systems Biology, Medical Faculty, Technical University Dresden, Dresden, Germany
| | - Paul Martin Schneider
- Medical Systems Biology, Medical Faculty, Technical University Dresden, Dresden, Germany
- Seamless Therapeutics GmbH, Dresden, Germany
| | - Frank Buchholz
- Medical Systems Biology, Medical Faculty, Technical University Dresden, Dresden, Germany.
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29
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Goodheart JA, Rio RA, Taraporevala NF, Fiorenza RA, Barnes SR, Morrill K, Jacob MAC, Whitesel C, Masterson P, Batzel GO, Johnston HT, Ramirez MD, Katz PS, Lyons DC. A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes. BMC Biol 2024; 22:9. [PMID: 38233809 PMCID: PMC10795318 DOI: 10.1186/s12915-024-01814-3] [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: 08/07/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum have long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. RESULTS The final assembled and filtered Berghia genome is comparable to other high-quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes) and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. CONCLUSIONS Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.
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Affiliation(s)
- Jessica A Goodheart
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA.
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
| | - Robin A Rio
- Bioengineering Department, Stanford University, Stanford, CA, USA
| | - Neville F Taraporevala
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Wildland Resources, Utah State University, Logan, UT, USA
| | - Rose A Fiorenza
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Seth R Barnes
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kevin Morrill
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mark Allan C Jacob
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Carl Whitesel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Park Masterson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Grant O Batzel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hereroa T Johnston
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - M Desmond Ramirez
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Paul S Katz
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Deirdre C Lyons
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
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30
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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. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.11.24301165. [PMID: 38260490 PMCID: PMC10802764 DOI: 10.1101/2024.01.11.24301165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
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 (UDN) and Genomics Research to Elucidate the Genetics of Rare Disease (GREGoR) Consortium. We identified 2,800 genes with build-dependent quantification across six routinely-collected biospecimens, including 1,391 protein-coding genes and 341 known rare disease genes. We further observed multiple genes that only have detectable expression in a subset of genome builds. Finally, we characterized how genome build impacts the detection of outlier transcriptomic events. 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
- Department of Pathology, School of Medicine, Stanford University
| | - Pagé C. Goddard
- Department of Genetics, School of Medicine, Stanford University
- Department of Pathology, School of Medicine, Stanford University
| | - Tanner D. Jensen
- Department of Genetics, School of Medicine, Stanford University
- Department of Pathology, School of Medicine, Stanford University
| | | | - Kevin S. Smith
- Department of Pathology, School of Medicine, Stanford University
| | | | | | - Devon E. Bonner
- Department of Pediatrics, School of Medicine, Stanford University
- Stanford Center for Undiagnosed Diseases, Stanford University
| | | | - Matthew T. Wheeler
- Department of Cardiovascular Medicine, School of Medicine, Stanford University
| | - Stephen B. Montgomery
- Department of Genetics, School of Medicine, Stanford University
- Department of Pathology, School of Medicine, Stanford University
- Department of Biomedical Data Science, Stanford University
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31
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Genovese G, Rockweiler NB, Gorman BR, Bigdeli TB, Pato MT, Pato CN, Ichihara K, McCarroll SA. BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies. Bioinformatics 2024; 40:btae038. [PMID: 38261650 PMCID: PMC10832354 DOI: 10.1093/bioinformatics/btae038] [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: 10/16/2023] [Revised: 12/07/2023] [Accepted: 01/18/2024] [Indexed: 01/25/2024] Open
Abstract
MOTIVATION Many genetics studies report results tied to genomic coordinates of a legacy genome assembly. However, as assemblies are updated and improved, researchers are faced with either realigning raw sequence data using the updated coordinate system or converting legacy datasets to the updated coordinate system to be able to combine results with newer datasets. Currently available tools to perform the conversion of genetic variants have numerous shortcomings, including poor support for indels and multi-allelic variants, that lead to a higher rate of variants being dropped or incorrectly converted. As a result, many researchers continue to work with and publish using legacy genomic coordinates. RESULTS Here we present BCFtools/liftover, a tool to convert genomic coordinates across genome assemblies for variants encoded in the variant call format with improved support for indels represented by different reference alleles across genome assemblies and full support for multi-allelic variants. It further supports variant annotation fields updates whenever the reference allele changes across genome assemblies. The tool has the lowest rate of variants being dropped with an order of magnitude less indels dropped or incorrectly converted and is an order of magnitude faster than other tools typically used for the same task. It is particularly suited for converting variant callsets from large cohorts to novel telomere-to-telomere assemblies as well as summary statistics from genome-wide association studies tied to legacy genome assemblies. AVAILABILITY AND IMPLEMENTATION The tool is written in C and freely available under the MIT open source license as a BCFtools plugin available at http://github.com/freeseek/score.
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Affiliation(s)
- Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Stanley Center, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
| | - Nicole B Rockweiler
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Stanley Center, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
| | - Bryan R Gorman
- Center for Data and Computational Sciences, VA Boston HealthCare System, Boston, MA 02130, United States
- Booz Allen Hamilton Inc, McLean, VA 22102, United States
| | - Tim B Bigdeli
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, United States
- Institute for Genomics in Health, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, United States
- Cooperative Studies Program, VA New York Harbor Healthcare System, Brooklyn, NY 11209, United States
| | - Michelle T Pato
- Department of Psychiatry, Robert Wood Johnson Medical School, New Brunswick, NJ 08901, United States
| | - Carlos N Pato
- Department of Psychiatry, Robert Wood Johnson Medical School, New Brunswick, NJ 08901, United States
| | - Kiku Ichihara
- Stanley Center, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Stanley Center, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
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Tominaga Y, Kawamura T, Ito E, Takeda M, Harada A, Torigata K, Sakaniwa R, Sawa Y, Miyagawa S. Pleiotropic effects of extracellular vesicles from induced pluripotent stem cell-derived cardiomyocytes on ischemic cardiomyopathy: A preclinical study. J Heart Lung Transplant 2024; 43:85-99. [PMID: 37611882 DOI: 10.1016/j.healun.2023.08.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/29/2023] [Accepted: 08/16/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Stem cell-secreted extracellular vesicles (EVs) play essential roles in intercellular communication and restore cardiac function in animal models of ischemic heart disease. However, few studies have used EVs derived from clinical-grade stem cells and their derivatives with stable quality. Moreover, there is little information on the mechanism and time course of the multifactorial effect of EV therapy from the acute to the chronic phase, the affected cells, and whether the effects are direct or indirect. METHODS Induced pluripotent stem cell-derived cardiomyocytes (iPSCM) were produced using a clinical-grade differentiation induction system. EVs were isolated from the conditioned medium by ultracentrifugation and characterized in silico, in vitro, and in vivo. A rat model of myocardial infarction was established by left anterior descending artery ligation and treated with iPSCM-derived EVs. RESULTS iPSCM-derived EVs contained microRNAs and proteins associated with angiogenesis, antifibrosis, promotion of M2 macrophage polarization, cell proliferation, and antiapoptosis. iPSCM-derived EV treatment improved left ventricular function and reduced mortality in the rat model by improving vascularization and suppressing fibrosis and chronic inflammation in the heart. EVs were uptaken by cardiomyocytes, endothelial cells, fibroblasts, and macrophages in the cardiac tissues. The pleiotropic effects occurred due to the direct effects of microRNAs and proteins encapsulated in EVs and indirect paracrine effects on M2 macrophages. CONCLUSIONS Clinical-grade iPSCM-derived EVs improve cardiac function by regulating various genes and pathways in various cell types and may have clinical potential for treating ischemic heart disease.
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Affiliation(s)
- Yuji Tominaga
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Takuji Kawamura
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Emiko Ito
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Maki Takeda
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Akima Harada
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kosuke Torigata
- Department of Frontier Regenerative Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Ryoto Sakaniwa
- Public Health, Department of Social Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoshiki Sawa
- Department of Future Medicine, Division of Health Science, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Shigeru Miyagawa
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Osaka, Japan.
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Fewlass H, Zavala EI, Fagault Y, Tuna T, Bard E, Hublin JJ, Hajdinjak M, Wilczyński J. Chronological and genetic analysis of an Upper Palaeolithic female infant burial from Borsuka Cave, Poland. iScience 2023; 26:108283. [PMID: 38047066 PMCID: PMC10690573 DOI: 10.1016/j.isci.2023.108283] [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: 04/01/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 12/05/2023] Open
Abstract
Six infant human teeth and 112 animal tooth pendants from Borsuka Cave were identified as the oldest burial in Poland. However, uncertainties around the dating and the association of the teeth to the pendants have precluded their association with an Upper Palaeolithic archaeological industry. Using <67 mg per tooth, we combined dating and genetic analyses of two human teeth and six herbivore tooth pendants to address these questions. Our interdisciplinary approach yielded informative results despite limited sampling material, and high levels of degradation and contamination. Our results confirm the Palaeolithic origin of the human remains and herbivore pendants, and permit us to identify the infant as female and discuss the association of the assemblage with different Palaeolithic industries. This study exemplifies the progress that has been made toward minimally destructive methods and the benefits of integrating methods to maximize data retrieval from precious but highly degraded and contaminated prehistoric material.
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Affiliation(s)
- Helen Fewlass
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Ancient Genomics Lab, Francis Crick Institute, London NW1 1AT, UK
| | - Elena I. Zavala
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Department of Cell and Molecular Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
| | - Yoann Fagault
- CEREGE, Aix Marseille Université, CNRS, IRD, INRA, Collège de France, Technopôle de l’Arbois BP 80, 13545 Aix-en-Provence Cedex 4, France
| | - Thibaut Tuna
- CEREGE, Aix Marseille Université, CNRS, IRD, INRA, Collège de France, Technopôle de l’Arbois BP 80, 13545 Aix-en-Provence Cedex 4, France
| | - Edouard Bard
- CEREGE, Aix Marseille Université, CNRS, IRD, INRA, Collège de France, Technopôle de l’Arbois BP 80, 13545 Aix-en-Provence Cedex 4, France
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB (UMR 7241 – U1050), Collège de France, 75231 Paris, France
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Jarosław Wilczyński
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Krakow, Poland
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34
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Ma B, Gavzy SJ, France M, Song Y, Lwin HW, Kensiski A, Saxena V, Piao W, Lakhan R, Iyyathurai J, Li L, Paluskievicz C, Wu L, WillsonShirkey M, Mongodin EF, Mas VR, Bromberg JS. Rapid intestinal and systemic metabolic reprogramming in an immunosuppressed environment. BMC Microbiol 2023; 23:394. [PMID: 38066426 PMCID: PMC10709923 DOI: 10.1186/s12866-023-03141-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
Intrinsic metabolism shapes the immune environment associated with immune suppression and tolerance in settings such as organ transplantation and cancer. However, little is known about the metabolic activities in an immunosuppressive environment. In this study, we employed metagenomic, metabolomic, and immunological approaches to profile the early effects of the immunosuppressant drug tacrolimus, antibiotics, or both in gut lumen and circulation using a murine model. Tacrolimus induced rapid and profound alterations in metabolic activities within two days of treatment, prior to alterations in gut microbiota composition and structure. The metabolic profile and gut microbiome after seven days of treatment was distinct from that after two days of treatment, indicating continuous drug effects on both gut microbial ecosystem and host metabolism. The most affected taxonomic groups are Clostriales and Verrucomicrobiae (i.e., Akkermansia muciniphila), and the most affected metabolic pathways included a group of interconnected amino acids, bile acid conjugation, glucose homeostasis, and energy production. Highly correlated metabolic changes were observed between lumen and serum metabolism, supporting their significant interactions. Despite a small sample size, this study explored the largely uncharacterized microbial and metabolic events in an immunosuppressed environment and demonstrated that early changes in metabolic activities can have significant implications that may serve as antecedent biomarkers of immune activation or quiescence. To understand the intricate relationships among gut microbiome, metabolic activities, and immune cells in an immune suppressed environment is a prerequisite for developing strategies to monitor and optimize alloimmune responses that determine transplant outcomes.
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Affiliation(s)
- Bing Ma
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | - Samuel J Gavzy
- Department of Surgery, University of Maryland Medical Center, Baltimore, MD, 21201, USA
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Michael France
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Yang Song
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Hnin Wai Lwin
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Allison Kensiski
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Vikas Saxena
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Wenji Piao
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Ram Lakhan
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Jegan Iyyathurai
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Lushen Li
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Christina Paluskievicz
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Long Wu
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Marina WillsonShirkey
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Emmanuel F Mongodin
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Division of Lung Diseases, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Valeria R Mas
- Department of Surgery, University of Maryland Medical Center, Baltimore, MD, 21201, USA
| | - Jonathan S Bromberg
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Surgery, University of Maryland Medical Center, Baltimore, MD, 21201, USA.
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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Selçuk B, Aksu T, Dereli O, Adebali O. Downregulated NPAS4 in multiple brain regions is associated with major depressive disorder. Sci Rep 2023; 13:21596. [PMID: 38062059 PMCID: PMC10703936 DOI: 10.1038/s41598-023-48646-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Major Depressive Disorder (MDD) is a commonly observed psychiatric disorder that affects more than 2% of the world population with a rising trend. However, disease-associated pathways and biomarkers are yet to be fully comprehended. In this study, we analyzed previously generated RNA-seq data across seven different brain regions from three distinct studies to identify differentially and co-expressed genes for patients with MDD. Differential gene expression (DGE) analysis revealed that NPAS4 is the only gene downregulated in three different brain regions. Furthermore, co-expressing gene modules responsible for glutamatergic signaling are negatively enriched in these regions. We used the results of both DGE and co-expression analyses to construct a novel MDD-associated pathway. In our model, we propose that disruption in glutamatergic signaling-related pathways might be associated with the downregulation of NPAS4 and many other immediate-early genes (IEGs) that control synaptic plasticity. In addition to DGE analysis, we identified the relative importance of KEGG pathways in discriminating MDD phenotype using a machine learning-based approach. We anticipate that our study will open doors to developing better therapeutic approaches targeting glutamatergic receptors in the treatment of MDD.
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Affiliation(s)
- Berkay Selçuk
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey
| | - Tuana Aksu
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey
| | - Onur Dereli
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey
| | - Ogün Adebali
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey.
- TÜBİTAK Research Institute for Fundamental Sciences, 41470, Gebze, Turkey.
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Todero J, Douillet C, Shumway AJ, Koller BH, Kanke M, Phuong DJ, Stýblo M, Sethupathy P. Molecular and Metabolic Analysis of Arsenic-Exposed Humanized AS3MT Mice. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:127021. [PMID: 38150313 PMCID: PMC10752418 DOI: 10.1289/ehp12785] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 10/30/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023]
Abstract
BACKGROUND Chronic exposure to inorganic arsenic (iAs) has been associated with type 2 diabetes (T2D). However, potential sex divergence and the underlying mechanisms remain understudied. iAs is not metabolized uniformly across species, which is a limitation of typical exposure studies in rodent models. The development of a new "humanized" mouse model overcomes this limitation. In this study, we leveraged this model to study sex differences in the context of iAs exposure. OBJECTIVES The aim of this study was to determine if males and females exhibit different liver and adipose molecular profiles and metabolic phenotypes in the context of iAs exposure. METHODS Our study was performed on wild-type (WT) 129S6/SvEvTac and humanized arsenic + 3 methyl transferase (human AS3MT) 129S6/SvEvTac mice treated with 400 ppb of iAs via drinking water ad libitum. After 1 month, mice were sacrificed and the liver and gonadal adipose depots were harvested for iAs quantification and sequencing-based microRNA and gene expression analysis. Serum blood was collected for fasting blood glucose, fasting plasma insulin, and homeostatic model assessment for insulin resistance (HOMA-IR). RESULTS We detected sex divergence in liver and adipose markers of diabetes (e.g., miR-34a, insulin signaling pathways, fasting blood glucose, fasting plasma insulin, and HOMA-IR) only in humanized (not WT) mice. In humanized female mice, numerous genes that promote insulin sensitivity and glucose tolerance in both the liver and adipose are elevated compared to humanized male mice. We also identified Klf11 as a putative master regulator of the sex divergence in gene expression in humanized mice. DISCUSSION Our study underscored the importance of future studies leveraging the humanized mouse model to study iAs-associated metabolic disease. The findings suggested that humanized males are at increased risk for metabolic dysfunction relative to humanized females in the context of iAs exposure. Future investigations should focus on the detailed mechanisms that underlie the sex divergence. https://doi.org/10.1289/EHP12785.
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Affiliation(s)
- Jenna Todero
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Christelle Douillet
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Alexandria J. Shumway
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Beverly H. Koller
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Daryl J. Phuong
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Miroslav Stýblo
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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Margasyuk S, Zavileyskiy L, Cao C, Pervouchine D. Long-range RNA structures in the human transcriptome beyond evolutionarily conserved regions. PeerJ 2023; 11:e16414. [PMID: 38047033 PMCID: PMC10691357 DOI: 10.7717/peerj.16414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/17/2023] [Indexed: 12/05/2023] Open
Abstract
RNA structure has been increasingly recognized as a critical player in the biogenesis and turnover of many transcripts classes. In eukaryotes, the prediction of RNA structure by thermodynamic modeling meets fundamental limitations due to the large sizes and complex, discontinuous organization of eukaryotic genes. Signatures of functional RNA structures can be found by detecting compensatory substitutions in homologous sequences, but a comparative approach is applicable only within conserved sequence blocks. Here, we developed a computational pipeline called PHRIC, which is not limited to conserved regions and relies on RNA contacts derived from RNA in situ conformation sequencing (RIC-seq) experiments. It extracts pairs of short RNA fragments surrounded by nested clusters of RNA contacts and predicts long, nearly perfect complementary base pairings formed between these fragments. In application to a panel of RIC-seq experiments in seven human cell lines, PHRIC predicted ~12,000 stable long-range RNA structures with equilibrium free energy below -15 kcal/mol, the vast majority of which fall outside of regions annotated as conserved among vertebrates. These structures, nevertheless, show some level of sequence conservation and remarkable compensatory substitution patterns in other clades. Furthermore, we found that introns have a higher propensity to form stable long-range RNA structures between each other, and moreover that RNA structures tend to concentrate within the same intron rather than connect adjacent introns. These results for the first time extend the application of proximity ligation assays to RNA structure prediction beyond conserved regions.
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Affiliation(s)
- Sergey Margasyuk
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Lev Zavileyskiy
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Changchang Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Dmitri Pervouchine
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
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Harris DN, Platt A, Hansen MEB, Fan S, McQuillan MA, Nyambo T, Mpoloka SW, Mokone GG, Belay G, Fokunang C, Njamnshi AK, Tishkoff SA. Diverse African genomes reveal selection on ancient modern human introgressions in Neanderthals. Curr Biol 2023; 33:4905-4916.e5. [PMID: 37837965 PMCID: PMC10841429 DOI: 10.1016/j.cub.2023.09.066] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/18/2023] [Accepted: 09/26/2023] [Indexed: 10/16/2023]
Abstract
Comparisons of Neanderthal genomes to anatomically modern human (AMH) genomes show a history of Neanderthal-to-AMH introgression stemming from interbreeding after the migration of AMHs from Africa to Eurasia. All non-sub-Saharan African AMHs have genomic regions genetically similar to Neanderthals that descend from this introgression. Regions of the genome with Neanderthal similarities have also been identified in sub-Saharan African populations, but their origins have been unclear. To better understand how these regions are distributed across sub-Saharan Africa, the source of their origin, and what their distribution within the genome tells us about early AMH and Neanderthal evolution, we analyzed a dataset of high-coverage, whole-genome sequences from 180 individuals from 12 diverse sub-Saharan African populations. In sub-Saharan African populations with non-sub-Saharan African ancestry, as much as 1% of their genomes can be attributed to Neanderthal sequence introduced by recent migration, and subsequent admixture, of AMH populations originating from the Levant and North Africa. However, most Neanderthal homologous regions in sub-Saharan African populations originate from migration of AMH populations from Africa to Eurasia ∼250 kya, and subsequent admixture with Neanderthals, resulting in ∼6% AMH ancestry in Neanderthals. These results indicate that there have been multiple migration events of AMHs out of Africa and that Neanderthal and AMH gene flow has been bi-directional. Observing that genomic regions where AMHs show a depletion of Neanderthal introgression are also regions where Neanderthal genomes show a depletion of AMH introgression points to deleterious interactions between introgressed variants and background genomes in both groups-a hallmark of incipient speciation.
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Affiliation(s)
- Daniel N Harris
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexander Platt
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shaohua Fan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai 200438, China
| | - Michael A McQuillan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thomas Nyambo
- Department of Biochemistry and Molecular Biology, Hubert Kairuki Memorial University, Dar es Salaam, Tanzania
| | - Sununguko Wata Mpoloka
- Department of Biological Sciences, Faculty of Science, University of Botswana, Private Bag UB 0022, Gaborone, Botswana
| | - Gaonyadiwe George Mokone
- Department of Biomedical Sciences, Faculty of Medicine, University of Botswana, Private Bag UB 0022, Gaborone, Botswana
| | - Gurja Belay
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, P.O. Box 337, Yaoundé, Cameroon
| | - Alfred K Njamnshi
- Brain Research Africa Initiative (BRAIN), P.O. Box 25625, Yaoundé, Cameroon; Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Shapira G, Volkov H, Fabian I, Mohr DW, Bettinotti M, Shomron N, Avery RK, Arav-Boger R. Genomic Markers Associated with Cytomegalovirus DNAemia in Kidney Transplant Recipients. Viruses 2023; 15:2227. [PMID: 38005904 PMCID: PMC10674338 DOI: 10.3390/v15112227] [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: 10/05/2023] [Revised: 10/29/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
Human cytomegalovirus (CMV) is a major pathogen after solid organ transplantation, leading to high morbidity and mortality. Transplantation from a CMV-seropositive donor to a CMV-seronegative recipient (D+/R-) is associated with high risk of CMV disease. However, that risk is not uniform, suggesting a role for host factors in immune control of CMV. To identify host genetic factors that control CMV DNAemia post transplantation, we performed a whole-exome association study in two cohorts of D+/R- kidney transplant recipients. Quantitative CMV DNA was measured for at least one year following transplantation. Several CMV-protective single-nucleotide polymorphisms (SNPs) were identified in the first cohort (72 patients) but were not reproducible in the second cohort (126 patients). A meta-analysis of both cohorts revealed several SNPs that were significantly associated with protection from CMV DNAemia. The copy number variation of several genes was significantly different between recipients with and without CMV DNAemia. Amongst patients with CMV DNAemia in the second cohort, several variants of interest (p < 5 × 10-5), the most common of which was NLRC5, were associated with peak viral load. We provide new predictive genetic markers for protection of CMV DNAemia. These markers should be validated in larger cohorts.
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Affiliation(s)
- Guy Shapira
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (G.S.)
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Hadas Volkov
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (G.S.)
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Itai Fabian
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (G.S.)
| | - David W. Mohr
- Johns Hopkins Genetic Resources Core Facility, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Maria Bettinotti
- Immunogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA;
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (G.S.)
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Robin K. Avery
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA;
| | - Ravit Arav-Boger
- Department of Pediatrics, Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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40
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Alagöz G, Eising E, Mekki Y, Bignardi G, Fontanillas P, Nivard MG, Luciano M, Cox NJ, Fisher SE, Gordon RL. The shared genetic architecture and evolution of human language and musical rhythm. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.01.564908. [PMID: 37961248 PMCID: PMC10634981 DOI: 10.1101/2023.11.01.564908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Rhythm and language-related traits are phenotypically correlated, but their genetic overlap is largely unknown. Here, we leveraged two large-scale genome-wide association studies performed to shed light on the shared genetics of rhythm (N=606,825) and dyslexia (N=1,138,870). Our results reveal an intricate shared genetic and neurobiological architecture, and lay groundwork for resolving longstanding debates about the potential co-evolution of human language and musical traits.
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Affiliation(s)
- Gökberk Alagöz
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands
| | - Else Eising
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands
| | - Yasmina Mekki
- Department of Otolaryngology - Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Giacomo Bignardi
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands
- Max Planck School of Cognition, Leipzig, Germany
| | | | - Michel G Nivard
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Michelle Luciano
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Nancy J Cox
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500 HB Nijmegen, The Netherlands
| | - Reyna L Gordon
- Department of Otolaryngology - Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
- The Curb Center, Vanderbilt University, Nashville, TN, USA
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Runkel A, Braig D, Bogner B, Schmid A, Lausch U, Boneberg A, Brugger Z, Eisenhardt A, Kiefer J, Pauli T, Boerries M, Fuellgraf H, Kurowski K, Bronsert P, Scholber J, Grosu AL, Rovedo P, Bamberg F, Eisenhardt SU, Jung M. Non-invasive monitoring of neoadjuvant radiation therapy response in soft tissue sarcomas by multiparametric MRI and quantification of circulating tumor DNA-A study protocol. PLoS One 2023; 18:e0285580. [PMID: 37910565 PMCID: PMC10619790 DOI: 10.1371/journal.pone.0285580] [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: 11/18/2022] [Accepted: 04/03/2023] [Indexed: 11/03/2023] Open
Abstract
BACKGROUND Wide resection remains the cornerstone of localized soft-tissue sarcomas (STS) treatment. Neoadjuvant radiation therapy (NRT) may decrease the risk of local recurrences; however, its effectiveness for different histological STS subtypes has not been systematically investigated. The proposed prospective study evaluates the NRT response in STS using liquid biopsies and the correlation of multiparametric magnetic resonance imaging (mpMRI) with histopathology and immunohistochemistry. METHODS Patients with localized high-grade STS, who qualify for NRT, are included in this study. LIQUID BIOPSIES Quantification of circulating tumor DNA (ctDNA) in patient blood samples is performed by targeted next-generation sequencing. Soft-tissue sarcoma subtype-specific panel sequencing in combination with patient-specific exome sequencing allows the detection of individual structural variants and point mutations. Circulating free DNA is isolated from peritherapeutically collected patient plasma samples and ctDNA quantified therein. Identification of breakpoints is carried out using FACTERA. Bioinformatic analysis is performed using samtools, picard, fgbio, and the MIRACUM Pipeline. MPMRI Combination of conventional MRI sequences with diffusion-weighted imaging, intravoxel-incoherent motion, and dynamic contrast enhancement. Multiparametric MRI is performed before, during, and after NRT. We aim to correlate mpMRI data with the resected specimen's macroscopical, histological, and immunohistochemical findings. RESULTS Preliminary data support the notion that quantification of ctDNA in combination with tumor mass characterization through co-registration of mpMRI and histopathology can predict NRT response of STS. CLINICAL RELEVANCE The methods presented in this prospective study are necessary to assess therapy response in heterogeneous tumors and lay the foundation of future patient- and tumor-specific therapy concepts. These methods can be applied to various tumor entities. Thus, the participation and support of a wider group of oncologic surgeons are needed to validate these findings on a larger patient cohort.
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Affiliation(s)
- Alexander Runkel
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Berta-Ottenstein-Programme, University of Freiburg, Freiburg, Germany
| | - David Braig
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Balazs Bogner
- Faculty of Medicine, Department of Radiology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Adrian Schmid
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Ute Lausch
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Anika Boneberg
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Zacharias Brugger
- Faculty of Medicine, Department of Medicine I, Medical Center—University of Freiburg, Freiburg, Germany
| | - Anja Eisenhardt
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Jurij Kiefer
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Thomas Pauli
- Faculty of Medicine, Institute of Medical Bioinformatics, Medical Center—University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Faculty of Medicine, Institute of Medical Bioinformatics, Medical Center—University of Freiburg, Freiburg, Germany
| | - Hannah Fuellgraf
- Faculty of Medicine, Institute of Surgical Pathology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Konrad Kurowski
- Faculty of Medicine, Institute of Surgical Pathology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Peter Bronsert
- Faculty of Medicine, Institute of Surgical Pathology, Medical Center—University of Freiburg, Freiburg, Germany
- Tumorbank Comprehensive Cancer Center Freiburg, Medical Center—University of Freiburg, Freiburg, Germany
- Core Facility for Histopathology and Digital Pathology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Jutta Scholber
- Faculty of Medicine, Department of Radiation Oncology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Anca-Ligia Grosu
- Faculty of Medicine, Department of Radiation Oncology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Philipp Rovedo
- Faculty of Medicine, Department of Radiology, Medical Physics, Medical Center-University of Freiburg, Freiburg, Germany
| | - Fabian Bamberg
- Faculty of Medicine, Department of Radiology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Steffen Ulrich Eisenhardt
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Matthias Jung
- Faculty of Medicine, Berta-Ottenstein-Programme, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Department of Radiology, Medical Center—University of Freiburg, Freiburg, Germany
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Chen Y, Wan R, Zou Z, Lao L, Shao G, Zheng Y, Tang L, Yuan Y, Ge Y, He C, Lin S. O-GlcNAcylation determines the translational regulation and phase separation of YTHDF proteins. Nat Cell Biol 2023; 25:1676-1690. [PMID: 37945829 DOI: 10.1038/s41556-023-01258-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 09/13/2023] [Indexed: 11/12/2023]
Abstract
N6-methyladenosine (m6A) is the most abundant internal mRNA nucleotide modification in mammals, regulating critical aspects of cell physiology and differentiation. The YTHDF proteins are the primary readers of m6A modifications and exert physiological functions of m6A in the cytosol. Elucidating the regulatory mechanisms of YTHDF proteins is critical to understanding m6A biology. Here we report a mechanism that protein post-translational modifications control the biological functions of the YTHDF proteins. We find that YTHDF1 and YTHDF3, but not YTHDF2, carry high levels of nutrient-sensing O-GlcNAc modifications. O-GlcNAcylation attenuates the translation-promoting function of YTHDF1 and YTHDF3 by blocking their interactions with proteins associated with mRNA translation. We further demonstrate that O-GlcNAc modifications on YTHDF1 and YTHDF3 regulate the assembly, stability and disassembly of stress granules to enable better recovery from stress. Therefore, our results discover an important regulatory pathway of YTHDF functions, adding an additional layer of complexity to the post-transcriptional regulation function of mRNA m6A.
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Affiliation(s)
- Yulin Chen
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Ruixi Wan
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Zhongyu Zou
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Lihui Lao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Guojian Shao
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yingying Zheng
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Ling Tang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Ying Yuan
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yun Ge
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
| | - Shixian Lin
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.
- Shaoxing Institute, Zhejiang University, Shaoxing, China.
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Cancer Center, Zhejiang University, Hangzhou, China.
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43
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Carlisle SG, Albasha H, Michelena H, Sabate-Rotes A, Bianco L, De Backer J, Mosquera LM, Yetman AT, Bissell MM, Andreassi MG, Foffa I, Hui DS, Caffarelli A, Kim YY, Guo DC, Citro R, De Marco M, Tretter JT, McBride KL, Milewicz DM, Body SC, Prakash SK. Rare Genomic Copy Number Variants Implicate New Candidate Genes for Bicuspid Aortic Valve. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.23.23297397. [PMID: 37961530 PMCID: PMC10635161 DOI: 10.1101/2023.10.23.23297397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Bicuspid aortic valve (BAV), the most common congenital heart defect, is a major cause of aortic valve disease requiring valve interventions and thoracic aortic aneurysms predisposing to acute aortic dissections. The spectrum of BAV ranges from early onset valve and aortic complications (EBAV) to sporadic late onset disease. Rare genomic copy number variants (CNVs) have previously been implicated in the development of BAV and thoracic aortic aneurysms. We determined the frequency and gene content of rare CNVs in EBAV probands (n = 272) using genome-wide SNP microarray analysis and three complementary CNV detection algorithms (cnvPartition, PennCNV, and QuantiSNP). Unselected control genotypes from the Database of Genotypes and Phenotypes were analyzed using identical methods. We filtered the data to select large genic CNVs that were detected by multiple algorithms. Findings were replicated in cohorts with late onset sporadic disease (n = 5040). We identified 34 large and rare (< 1:1000 in controls) CNVs in EBAV probands. The burden of CNVs intersecting with genes known to cause BAV when mutated was increased in case-control analysis. CNVs intersecting with GATA4 and DSCAM were enriched in cases, recurrent in other datasets, and segregated with disease in families. In total, we identified potentially pathogenic CNVs in 8% of EBAV cases, implicating alterations of candidate genes at these loci in the pathogenesis of BAV.
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Affiliation(s)
- Steven G Carlisle
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | - Hasan Albasha
- UCD School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Hector Michelena
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Anna Sabate-Rotes
- Department of Pediatric Cardiology, Hospital Vall d'Hebron, Facultad de Medicina, Universidad Autònoma Barcelona, Barcelona, Spain
| | - Lisa Bianco
- Department of Pediatric Cardiology, Hospital Vall d'Hebron, Facultad de Medicina, Universidad Autònoma Barcelona, Barcelona, Spain
| | - Julie De Backer
- Centre for Medical Genetics, Ghent University Hospital, Ghent, Belgium; VASCERN HTAD European Reference Centre, Belgium; Department of Pediatrics, Division of Pediatric Cardiology, Ghent University Hospital, Ghent, Belgium; Department of Cardiology, Ghent University Hospital, Ghent, Belgium
| | | | - Anji T Yetman
- Children's Hospital and Medical Center, University of Nebraska, Omaha, Nebraska
| | - Malenka M Bissell
- Deparmentt of Biomedical Imaging Science, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | | | - Ilenia Foffa
- Consiglio Nazionale delle Richerche (CNR), Instituto di Fisiologia Clinica, Pisa, Italy
| | - Dawn S Hui
- Department of Cardiothoracic Surgery, University of Texas Health Science Center San Antonio, Texas
| | - Anthony Caffarelli
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Yuli Y Kim
- Division of Cardiovascular Medicine, The Hospital of the University of Pennsylvania, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania; Philadelphia Adult Congenital Heart Center, The Children's Hospital of Philadelphia, Perelman Center for Advanced Medicine, Penn Medicine, Philadelphia, Pennsylvania
| | - Dong-Chuan Guo
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | - Rodolfo Citro
- Cardio-Thoracic and Vascular Department, University Hospital "San Giovanni di Dio e Ruggi d'Aragona," Salerno, Italy
| | - Margot De Marco
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Italy
| | - Justin T Tretter
- Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Kim L McBride
- Division of Human Genetics, Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Dianna M Milewicz
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | - Simon C Body
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts
| | - Siddharth K Prakash
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas
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Tan A, Murugapiran S, Mikalauskas A, Koble J, Kennedy D, Hyde F, Ruotti V, Law E, Jensen J, Schroth GP, Macklaim JM, Kuersten S, LeFrançois B, Gohl DM. Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes. BMC Microbiol 2023; 23:299. [PMID: 37864136 PMCID: PMC10588151 DOI: 10.1186/s12866-023-03037-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/03/2023] [Indexed: 10/22/2023] Open
Abstract
The microbiota that colonize the human gut and other tissues are dynamic, varying both in composition and functional state between individuals and over time. Gene expression measurements can provide insights into microbiome composition and function. However, efficient and unbiased removal of microbial ribosomal RNA (rRNA) presents a barrier to acquiring metatranscriptomic data. Here we describe a probe set that achieves efficient enzymatic rRNA removal of complex human-associated microbial communities. We demonstrate that the custom probe set can be further refined through an iterative design process to efficiently deplete rRNA from a range of human microbiome samples. Using synthetic nucleic acid spike-ins, we show that the rRNA depletion process does not introduce substantial quantitative error in gene expression profiles. Successful rRNA depletion allows for efficient characterization of taxonomic and functional profiles, including during the development of the human gut microbiome. The pan-human microbiome enzymatic rRNA depletion probes described here provide a powerful tool for studying the transcriptional dynamics and function of the human microbiome.
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Affiliation(s)
- Asako Tan
- Illumina, Inc, Madison, WI, 53719, USA
| | | | | | - Jeff Koble
- Illumina, Inc, San Diego, CA, 92122, USA
| | | | - Fred Hyde
- Illumina, Inc, Madison, WI, 53719, USA
| | | | - Emily Law
- Diversigen, Inc, New Brighton, MN, 55112, USA
| | | | | | | | | | | | - Daryl M Gohl
- Diversigen, Inc, New Brighton, MN, 55112, USA.
- University of Minnesota Genomics Center, Minneapolis, MN, 55455, USA.
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, 55455, USA.
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45
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Fourreau CJL, Kise H, Santander MD, Pirro S, Maronna MM, Poliseno A, Santos ME, Reimer JD. Genome sizes and repeatome evolution in zoantharians (Cnidaria: Hexacorallia: Zoantharia). PeerJ 2023; 11:e16188. [PMID: 37868064 PMCID: PMC10586311 DOI: 10.7717/peerj.16188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/06/2023] [Indexed: 10/24/2023] Open
Abstract
Across eukaryotes, large variations of genome sizes have been observed even between closely related species. Transposable elements as part of the repeated DNA have been proposed and confirmed as one of the most important contributors to genome size variation. However, the evolutionary implications of genome size variation and transposable element dynamics are not well understood. Together with phenotypic traits, they are commonly referred to as the "C-value enigma". The order Zoantharia are benthic cnidarians found from intertidal zones to the deep sea, and some species are particularly abundant in coral reefs. Despite their high ecological relevance, zoantharians have yet to be largely studied from the genomic point of view. This study aims at investigating the role of the repeatome (total content of repeated elements) in genome size variations across the order Zoantharia. To this end, whole-genomes of 32 zoantharian species representing five families were sequenced. Genome sizes were estimated and the abundances of different repeat classes were assessed. In addition, the repeat overlap between species was assessed by a sequence clustering method. The genome sizes in the dataset varied up to 2.4 fold magnitude. Significant correlations between genome size, repeated DNA content and transposable elements, respectively (Pearson's correlation test R2 = 0.47, p = 0.0016; R2 = 0.22, p = 0.05) were found, suggesting their involvement in the dynamics of genome expansion and reduction. In all species, long interspersed nuclear elements and DNA transposons were the most abundant identified elements. These transposable elements also appeared to have had a recent expansion event. This was in contrast to the comparative clustering analysis which revealed species-specific patterns of satellite elements' amplification. In summary, the genome sizes of zoantharians likely result from the complex dynamics of repeated elements. Finally, the majority of repeated elements (up to 70%) could not be annotated to a known repeat class, highlighting the need to further investigate non-model cnidarian genomes. More research is needed to understand how repeated DNA dynamics relate to zoantharian evolution and their biology.
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Affiliation(s)
- Chloé Julie Loïs Fourreau
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Hiroki Kise
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- AIST Tsukuba Central, Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Mylena Daiana Santander
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Stacy Pirro
- Iridian Genomes, Bethesda, United States of America
| | - Maximiliano M. Maronna
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- Faculdade de Ciências, Universidade Estadual Paulista (UNESP), Bauru, Brazil
| | - Angelo Poliseno
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Maria E.A. Santos
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
| | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, United States of America
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46
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Rattanapan Y, Charong N, Narkpetch S, Chareonsirisuthigul T. Genotyping of the rare Para-Bombay blood group in southern Thailand. Hematol Transfus Cell Ther 2023; 45:449-455. [PMID: 36241527 PMCID: PMC10627842 DOI: 10.1016/j.htct.2022.08.004] [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: 04/18/2022] [Revised: 06/15/2022] [Accepted: 08/12/2022] [Indexed: 06/16/2023] Open
Abstract
INTRODUCTION The para-Bombay phenotype, or H-deficient secretor, results from different mutations of the FUT1, with or without the FUT2 mutation. Consequently, there is an absent or weak expression of the H antigen on red blood cells (RBCs). Routine ABO blood grouping for two siblings with blood group O showed discrepant results with their parental blood group AB. Fragments encompassing the entire coding region of the FUT1 and FUT2 genes were investigated. METHODS Blood and saliva specimens were collected to verify the correct ABO grouping by cell grouping, serum grouping and the hemagglutination inhibition (HI) test, respectively. The FUT1 and FUT2 genomes were identified using the whole-exome sequencing (WES) in two children's DNA blood specimens and may have caused, or been relative to, their blood group. Genetic variations of the FUT1 and FUT2 genes have been investigated in the other family members using the Sanger sequencing. RESULTS The serologic reaction results of the proband revealed that A, B and H antigens were absent on RBCs, and that the serum contained anti-H. However, ABH and AH antigens were present in the saliva PB1 and PB2, respectively. The probands PB1 and PB2 were assigned as AB and A blood groups, respectively. Blood genotyping confirmed that heterozygous mutations of the FUT1 gene, c.551_552delAG, were identified. Three family members, PB3, PB, and PB8, also showed normal ABO blood groups, but their genotypes were also the FUT1 mutation c.551_552delAG. CONCLUSIONS The FUT1 mutation c.551_552delAG may result in the reduced or absent H antigen production on RBCs, which characterizes the para-Bombay phenotypes. Blood genotyping is essential if these individuals need a blood transfusion or are planning to donate blood.
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Affiliation(s)
- Yanisa Rattanapan
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand; Hematology and Transfusion Science Research Center, Walailak University, Nakhon Si Thammarat, Thailand
| | - Nurdina Charong
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand; Hematology and Transfusion Science Research Center, Walailak University, Nakhon Si Thammarat, Thailand
| | - Sodsai Narkpetch
- Blood Bank, Maharaj Nakhon Si Thammarat Hospital, Nakhon Si Thammarat, Thailand
| | - Takol Chareonsirisuthigul
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
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47
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Thomson AJ, Rehn JA, Heatley SL, Eadie LN, Page EC, Schutz C, McClure BJ, Sutton R, Dalla-Pozza L, Moore AS, Greenwood M, Kotecha RS, Fong CY, Yong ASM, Yeung DT, Breen J, White DL. Reproducible Bioinformatics Analysis Workflows for Detecting IGH Gene Fusions in B-Cell Acute Lymphoblastic Leukaemia Patients. Cancers (Basel) 2023; 15:4731. [PMID: 37835427 PMCID: PMC10571859 DOI: 10.3390/cancers15194731] [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: 09/15/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
B-cell acute lymphoblastic leukaemia (B-ALL) is characterised by diverse genomic alterations, the most frequent being gene fusions detected via transcriptomic analysis (mRNA-seq). Due to its hypervariable nature, gene fusions involving the Immunoglobulin Heavy Chain (IGH) locus can be difficult to detect with standard gene fusion calling algorithms and significant computational resources and analysis times are required. We aimed to optimize a gene fusion calling workflow to achieve best-case sensitivity for IGH gene fusion detection. Using Nextflow, we developed a simplified workflow containing the algorithms FusionCatcher, Arriba, and STAR-Fusion. We analysed samples from 35 patients harbouring IGH fusions (IGH::CRLF2 n = 17, IGH::DUX4 n = 15, IGH::EPOR n = 3) and assessed the detection rates for each caller, before optimizing the parameters to enhance sensitivity for IGH fusions. Initial results showed that FusionCatcher and Arriba outperformed STAR-Fusion (85-89% vs. 29% of IGH fusions reported). We found that extensive filtering in STAR-Fusion hindered IGH reporting. By adjusting specific filtering steps (e.g., read support, fusion fragments per million total reads), we achieved a 94% reporting rate for IGH fusions with STAR-Fusion. This analysis highlights the importance of filtering optimization for IGH gene fusion events, offering alternative workflows for difficult-to-detect high-risk B-ALL subtypes.
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Affiliation(s)
- Ashlee J. Thomson
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.A.R.); (S.L.H.); (L.N.E.); (E.C.P.); (B.J.M.); (A.S.M.Y.); (D.T.Y.); (D.L.W.)
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia;
| | - Jacqueline A. Rehn
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.A.R.); (S.L.H.); (L.N.E.); (E.C.P.); (B.J.M.); (A.S.M.Y.); (D.T.Y.); (D.L.W.)
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia;
| | - Susan L. Heatley
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.A.R.); (S.L.H.); (L.N.E.); (E.C.P.); (B.J.M.); (A.S.M.Y.); (D.T.Y.); (D.L.W.)
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia;
- Australian and New Zealand Children’s Oncology Group (ANZCHOG), Clayton, VIC 3168, Australia
| | - Laura N. Eadie
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.A.R.); (S.L.H.); (L.N.E.); (E.C.P.); (B.J.M.); (A.S.M.Y.); (D.T.Y.); (D.L.W.)
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia;
| | - Elyse C. Page
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.A.R.); (S.L.H.); (L.N.E.); (E.C.P.); (B.J.M.); (A.S.M.Y.); (D.T.Y.); (D.L.W.)
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia;
| | - Caitlin Schutz
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia;
| | - Barbara J. McClure
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.A.R.); (S.L.H.); (L.N.E.); (E.C.P.); (B.J.M.); (A.S.M.Y.); (D.T.Y.); (D.L.W.)
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia;
| | - Rosemary Sutton
- Molecular Diagnostics, Children’s Cancer Institute, Kensington, NSW 2750, Australia;
| | - Luciano Dalla-Pozza
- The Cancer Centre for Children, The Children’s Hospital at Westmead, Westmead, NSW 2145, Australia;
| | - Andrew S. Moore
- Oncology Service, Children’s Health Queensland Hospital and Health Service, Brisbane, QLD 4101, Australia;
- Child Health Research Centre, The University of Queensland, Brisbane, QLD 4000, Australia
| | - Matthew Greenwood
- Department of Haematology and Transfusion Services, Royal North Shore Hospital, Sydney, NSW 2065, Australia;
- Faculty of Health and Medicine, University of Sydney, Sydney, NSW 2006, Australia
| | - Rishi S. Kotecha
- Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children’s Hospital, Perth, WA 6009, Australia;
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia
- Curtin Medical School, Curtin University, Perth, WA 6845, Australia
| | - Chun Y. Fong
- Department of Clinical Haematology, Austin Health, Heidelberg, VIC 3083, Australia;
| | - Agnes S. M. Yong
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.A.R.); (S.L.H.); (L.N.E.); (E.C.P.); (B.J.M.); (A.S.M.Y.); (D.T.Y.); (D.L.W.)
- South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia
- Division of Pathology & Laboratory, University of Western Australia Medical School, Perth, WA 6009, Australia
- Department of Haematology, Royal Perth Hospital, Perth, WA 6000, Australia
| | - David T. Yeung
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.A.R.); (S.L.H.); (L.N.E.); (E.C.P.); (B.J.M.); (A.S.M.Y.); (D.T.Y.); (D.L.W.)
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia;
- Haematology Department, Royal Adelaide Hospital and SA Pathology, Adelaide, SA 5000, Australia
| | - James Breen
- Black Ochre Data Labs, Indigenous Genomics, Telethon Kids Institute, Adelaide, SA 5000, Australia
- James Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Deborah L. White
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.A.R.); (S.L.H.); (L.N.E.); (E.C.P.); (B.J.M.); (A.S.M.Y.); (D.T.Y.); (D.L.W.)
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia;
- Australian and New Zealand Children’s Oncology Group (ANZCHOG), Clayton, VIC 3168, Australia
- Australian Genomics Health Alliance (AGHA), The Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
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Ma B, Gavzy SJ, France M, Song Y, Lwin HW, Kensiski A, Saxena V, Piao W, Lakhan R, Iyyathurai J, Li L, Paluskievicz C, Wu L, WillsonShirkey M, Mongodin EF, Mas VR, Bromberg J. Rapid intestinal and systemic metabolic reprogramming in an immunosuppressed environment. RESEARCH SQUARE 2023:rs.3.rs-3364037. [PMID: 37790403 PMCID: PMC10543476 DOI: 10.21203/rs.3.rs-3364037/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Intrinsic metabolism shapes the immune environment associated with immune suppression and tolerance in settings such as organ transplantation and cancer. However, little is known about the metabolic activities in an immunosuppressive environment. In this study, we employed metagenomic, metabolomic, and immunological approaches to profile the early effects of the immunosuppressant drug tacrolimus, antibiotics, or both in gut lumen and circulation using a murine model. Tacrolimus induced rapid and profound alterations in metabolic activities within two days of treatment, prior to alterations in gut microbiota composition and structure. The metabolic profile and gut microbiome after seven days of treatment was distinct from that after two days of treatment, indicating continuous drug effects on both gut microbial ecosystem and host metabolism. The most affected taxonomic groups are Clostriales and Verrucomicrobiae (i.e., Akkermansia muciniphila), and the most affected metabolic pathways included a group of interconnected amino acids, bile acid conjugation, glucose homeostasis, and energy production. Highly correlated metabolic changes were observed between lumen and serum metabolism, supporting their significant interactions. Despite a small sample size, this study explored the largely uncharacterized microbial and metabolic events in an immunosuppressed environment and demonstrated that early changes in metabolic activities can have significant implications that may serve as antecedent biomarkers of immune activation or quiescence. To understand the intricate relationships among gut microbiome, metabolic activities, and immune cells in an immune suppressed environment is a prerequisite for developing strategies to monitor and optimize alloimmune responses that determine transplant outcomes.
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Affiliation(s)
- Bing Ma
- University of Maryland, Baltimore
| | | | | | | | | | | | | | | | | | | | | | | | - Long Wu
- University of Maryland, Baltimore
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Hng SY, Thinakaran AS, Ooi CJ, Eg KP, Thong MK, Tae SK, Goh SH, Chew KS, Tan LT, Koh MT, Chong LA, Khalid F, Ng RT, Nathan AM, de Bruyne JA. Morbidity and treatment costs of cystic fibrosis in a middle-income country. Singapore Med J 2023:386391. [PMID: 37870036 DOI: 10.4103/singaporemedj.smj-2022-093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Introduction : Asian children with cystic fibrosis (CF) managed in Malaysia have significant morbidity with limited access to life-sustaining treatments. We determined the morbidity and treatment cost of CF in a resource-limited country. Methods This cross-sectional study included all children diagnosed with CF in our centre. Data on clinical presentation, genetic mutation, serial spirometry results and complications were collected. Out-of-pocket (OOP) and healthcare costs over 1 year were retrieved for patients who were alive. Cohen's d and odds ratio (OR) were used to determine the effect size. Results Twenty-four patients were diagnosed with CF. Five patients died at a median (range) age of 18 (0.3-22) years. F508deletion (c. 1521_1523delCTT) was found in 20% of the alleles, while 89% of the variants were detected in nine patients. Body mass index (BMI) Z score was >-1.96 in 70.6% of patients. Two thirds (68%) were colonised with Pseudomonas aeruginosa, and this was associated with lower weight (P = 0.009) and BMI (P = 0.02) Z scores. Only 18% had FEV1 Z scores >-1.96. Early symptom onset (d = 0.74), delayed diagnosis (d = 2.07), a low FEF25-75 Z score (d = 0.82) and a high sweat conductance (d = 1.19) were associated with death. Inpatient cost was mainly from diagnostic tests, while medications contributed to half of the outpatient cost. Healthcare utilisation cost was catastrophic, amounting to 20% of the total income. Conclusion Asian children with CF suffer significant complications such as low weight, low lung function and shortened lifespan. P. aeruginosa colonisation was frequent and associated with poor growth. Healthcare cost to parents was catastrophic.
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Affiliation(s)
- Shih Ying Hng
- Department of Paediatrics, Paediatric Respiratory Unit, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Chiou Jia Ooi
- Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kah Peng Eg
- Department of Paediatrics, Paediatric Respiratory Unit, University of Malaya, Kuala Lumpur, Malaysia
| | - Meow Keong Thong
- Department of Paediatrics, Genetics and Metabolism Unit, University of Malaya, Kuala Lumpur, Malaysia
| | - Sok Kun Tae
- Department of Paediatrics, Genetics and Metabolism Unit, University of Malaya, Kuala Lumpur, Malaysia
| | - Saw Huan Goh
- Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kee Seang Chew
- Department of Paediatrics, Paediatric Gastroenterology Unit, University of Malaya, Kuala Lumpur, Malaysia
| | - Lay Teng Tan
- Department of Paediatrics, Paediatric Infectious Disease Unit, University of Malaya, Kuala Lumpur, Malaysia
| | - Mia Tuang Koh
- Department of Paediatrics, Paediatric Infectious Disease Unit, University of Malaya, Kuala Lumpur, Malaysia
| | - Li Ai Chong
- Department of Paediatrics, Paediatric Palliative Unit, University of Malaya, Kuala Lumpur, Malaysia
| | - Farah Khalid
- Department of Paediatrics, Paediatric Palliative Unit, University of Malaya, Kuala Lumpur, Malaysia
| | - Ruey Teng Ng
- Department of Paediatrics, Paediatric Gastroenterology Unit, University of Malaya, Kuala Lumpur, Malaysia
| | - Anna Marie Nathan
- Department of Paediatrics, Paediatric Respiratory Unit, University of Malaya, Kuala Lumpur, Malaysia
| | - Jessie Anne de Bruyne
- Department of Paediatrics, Paediatric Respiratory Unit, University of Malaya, Kuala Lumpur, Malaysia
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Spisak N, de Manuel M, Milligan W, Sella G, Przeworski M. Disentangling sources of clock-like mutations in germline and soma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.07.556720. [PMID: 37745549 PMCID: PMC10515775 DOI: 10.1101/2023.09.07.556720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The rates of mutations vary across cell types. To identify causes of this variation, mutations are often decomposed into a combination of the single base substitution (SBS) "signatures" observed in germline, soma and tumors, with the idea that each signature corresponds to one or a small number of underlying mutagenic processes. Two such signatures turn out to be ubiquitous across cell types: SBS signature 1, which consists primarily of transitions at methylated CpG sites caused by spontaneous deamination, and the more diffuse SBS signature 5, which is of unknown etiology. In cancers, the number of mutations attributed to these two signatures accumulates linearly with age of diagnosis, and thus the signatures have been termed "clock-like." To better understand this clock-like behavior, we develop a mathematical model that includes DNA replication errors, unrepaired damage, and damage repaired incorrectly. We show that mutational signatures can exhibit clock-like behavior because cell divisions occur at a constant rate and/or because damage rates remain constant over time, and that these distinct sources can be teased apart by comparing cell lineages that divide at different rates. With this goal in mind, we analyze the rate of accumulation of mutations in multiple cell types, including soma as well as male and female germline. We find no detectable increase in SBS signature 1 mutations in neurons and only a very weak increase in mutations assigned to the female germline, but a significant increase with time in rapidly-dividing cells, suggesting that SBS signature 1 is driven by rounds of DNA replication occurring at a relatively fixed rate. In contrast, SBS signature 5 increases with time in all cell types, including post-mitotic ones, indicating that it accumulates independently of cell divisions; this observation points to errors in DNA repair as the key underlying mechanism. Thus, the two "clock-like" signatures observed across cell types likely have distinct origins, one set by rates of cell division, the other by damage rates.
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Affiliation(s)
- Natanael Spisak
- Department of Biological Sciences, Columbia University, New York, United States
| | - Marc de Manuel
- Department of Biological Sciences, Columbia University, New York, United States
| | - William Milligan
- Department of Biological Sciences, Columbia University, New York, United States
| | - Guy Sella
- Department of Biological Sciences, Columbia University, New York, United States
- Program for Mathematical Genomics, Columbia University, New York, United States
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, United States
- Department of Systems Biology, Columbia University, New York, United States
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