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Pereira SSS, Pinto IP, Santos VCDP, Silva RC, Costa EOA, da Cruz AS, da Cruz AD, da Silva CC, Minasi LB. Analysis of parental origin of de novo pathogenic CNVs in patients with intellectual disability. Genet Mol Biol 2024; 47:e20230313. [PMID: 39136576 PMCID: PMC11320663 DOI: 10.1590/1678-4685-gmb-2023-0313] [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: 11/01/2023] [Accepted: 06/25/2024] [Indexed: 08/16/2024] Open
Abstract
Chromosomal Microarray Analysis (CMA) has increased the comprehension of the mechanisms of copy number variation (CNV) formation, classification of these rearrangements, type of recurrence, and its origin, and has also been a powerful approach to identifying CNVs in individuals with intellectual disability. The aim of this study was to establish the parental origin of de novo pathogenic CNV in a cohort of patients with intellectual disability from the public health system of Goiás-Brazil. CMA was done in 76 trios and we identified 15 de novo pathogenic CNVs in 12 patients with intellectual disability. In a total of 15 de novo pathogenic CNV, 60% were derived from the maternal germline and 40% from the paternal germline. CNV flanked by low copy repeats (LCR) were identified in 46.7% and most of them were of maternal origin. No significant association was observed between paternal age and the mutation rate of de novo CNVs. The presence of high-identity LCRs increases the occurrence of CNV formation mediated by non-allelic homologous recombination and the majority of paternal CNVs are non-recurrent. The mechanism of formation of these CNV may have been by microhomology-mediated break-induced replication or non-homologous end joining.
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Affiliation(s)
- Samara Socorro Silva Pereira
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
- Universidade Federal de Goiás, Programa de Pós-Graduação em Genética e Biologia Molecular, Goiânia, GO, Brazil
| | - Irene Plaza Pinto
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
| | - Victor Cortázio do Prado Santos
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
- Universidade Federal de Goiás, Programa de Pós-Graduação em Genética e Biologia Molecular, Goiânia, GO, Brazil
| | - Rafael Carneiro Silva
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
| | - Emília Oliveira Alves Costa
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
| | - Alex Silva da Cruz
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
| | - Aparecido Divino da Cruz
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
- Secretaria Estadual de Saúde de Goiás, Centro Estadual de Reabilitação e Readaptação Dr. Henrique Santillo, Goiânia, GO, Brazil
- Universidade Federal de Goiás, Programa de Pós-Graduação em Genética e Biologia Molecular, Goiânia, GO, Brazil
| | - Cláudio Carlos da Silva
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
- Secretaria Estadual de Saúde de Goiás, Centro Estadual de Reabilitação e Readaptação Dr. Henrique Santillo, Goiânia, GO, Brazil
| | - Lysa Bernardes Minasi
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
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2
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Chang S, Liu JJ, Zhao Y, Pang T, Zheng X, Song Z, Zhang A, Gao X, Luo L, Guo Y, Liu J, Yang L, Lu L. Whole-genome sequencing identifies novel genes for autism in Chinese trios. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2564-8. [PMID: 39126614 DOI: 10.1007/s11427-023-2564-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/16/2024] [Indexed: 08/12/2024]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with high genetic heritability but heterogeneity. Fully understanding its genetics requires whole-genome sequencing (WGS), but the ASD studies utilizing WGS data in Chinese population are limited. In this study, we present a WGS study for 334 individuals, including 112 ASD patients and their non-ASD parents. We identified 146 de novo variants in coding regions in 85 cases and 60 inherited variants in coding regions. By integrating these variants with an association model, we identified 33 potential risk genes (P<0.001) enriched in neuron and regulation related biological process. Besides the well-known ASD genes (SCN2A, NF1, SHANK3, CHD8 etc.), several high confidence genes were highlighted by a series of functional analyses, including CTNND1, DGKZ, LRP1, DDN, ZNF483, NR4A2, SMAD6, INTS1, and MRPL12, with more supported evidence from GO enrichment, expression and network analysis. We also integrated RNA-seq data to analyze the effect of the variants on the gene expression and found 12 genes in the individuals with the related variants had relatively biased expression. We further presented the clinical phenotypes of the proband carrying the risk genes in both our samples and Caucasian samples to show the effect of the risk genes on phenotype. Regarding variants in non-coding regions, a total of 74 de novo variants and 30 inherited variants were predicted as pathogenic with high confidence, which were mapped to specific genes or regulatory features. The number of de novo variants found in patient was significantly associated with the parents' ages at the birth of the child, and gender with trend. We also identified small de novo structural variants in ASD trios. The results in this study provided important evidence for understanding the genetic mechanism of ASD.
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Affiliation(s)
- Suhua Chang
- Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking University Sixth Hospital, Beijing, 100191, China
- Chinese Academy of Medical Sciences Research Unit (No.2018RU006), Peking University, Beijing, 100191, China
| | - Jia Jia Liu
- Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking University Sixth Hospital, Beijing, 100191, China
- School of Nursing, Peking University, Beijing, 100191, China
| | - Yilu Zhao
- Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking University Sixth Hospital, Beijing, 100191, China
| | - Tao Pang
- Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking University Sixth Hospital, Beijing, 100191, China
| | - Xiangyu Zheng
- Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking University Sixth Hospital, Beijing, 100191, China
| | | | - Anyi Zhang
- Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking University Sixth Hospital, Beijing, 100191, China
| | - Xuping Gao
- Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking University Sixth Hospital, Beijing, 100191, China
| | - Lingxue Luo
- Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking University Sixth Hospital, Beijing, 100191, China
| | - Yanqing Guo
- Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking University Sixth Hospital, Beijing, 100191, China.
| | - Jing Liu
- Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking University Sixth Hospital, Beijing, 100191, China.
| | - Li Yang
- Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking University Sixth Hospital, Beijing, 100191, China.
| | - Lin Lu
- Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking University Sixth Hospital, Beijing, 100191, China.
- Chinese Academy of Medical Sciences Research Unit (No.2018RU006), Peking University, Beijing, 100191, China.
- National Institute on Drug Dependence, Peking University, Beijing, 100191, China.
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3
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Porubsky D, Dashnow H, Sasani TA, Logsdon GA, Hallast P, Noyes MD, Kronenberg ZN, Mokveld T, Koundinya N, Nolan C, Steely CJ, Guarracino A, Dolzhenko E, Harvey WT, Rowell WJ, Grigorev K, Nicholas TJ, Oshima KK, Lin J, Ebert P, Watkins WS, Leung TY, Hanlon VCT, McGee S, Pedersen BS, Goldberg ME, Happ HC, Jeong H, Munson KM, Hoekzema K, Chan DD, Wang Y, Knuth J, Garcia GH, Fanslow C, Lambert C, Lee C, Smith JD, Levy S, Mason CE, Garrison E, Lansdorp PM, Neklason DW, Jorde LB, Quinlan AR, Eberle MA, Eichler EE. A familial, telomere-to-telomere reference for human de novo mutation and recombination from a four-generation pedigree. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.05.606142. [PMID: 39149261 PMCID: PMC11326147 DOI: 10.1101/2024.08.05.606142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Using five complementary short- and long-read sequencing technologies, we phased and assembled >95% of each diploid human genome in a four-generation, 28-member family (CEPH 1463) allowing us to systematically assess de novo mutations (DNMs) and recombination. From this family, we estimate an average of 192 DNMs per generation, including 75.5 de novo single-nucleotide variants (SNVs), 7.4 non-tandem repeat indels, 79.6 de novo indels or structural variants (SVs) originating from tandem repeats, 7.7 centromeric de novo SVs and SNVs, and 12.4 de novo Y chromosome events per generation. STRs and VNTRs are the most mutable with 32 loci exhibiting recurrent mutation through the generations. We accurately assemble 288 centromeres and six Y chromosomes across the generations, documenting de novo SVs, and demonstrate that the DNM rate varies by an order of magnitude depending on repeat content, length, and sequence identity. We show a strong paternal bias (75-81%) for all forms of germline DNM, yet we estimate that 17% of de novo SNVs are postzygotic in origin with no paternal bias. We place all this variation in the context of a high-resolution recombination map (∼3.5 kbp breakpoint resolution). We observe a strong maternal recombination bias (1.36 maternal:paternal ratio) with a consistent reduction in the number of crossovers with increasing paternal (r=0.85) and maternal (r=0.65) age. However, we observe no correlation between meiotic crossover locations and de novo SVs, arguing against non-allelic homologous recombination as a predominant mechanism. The use of multiple orthogonal technologies, near-telomere-to-telomere phased genome assemblies, and a multi-generation family to assess transmission has created the most comprehensive, publicly available "truth set" of all classes of genomic variants. The resource can be used to test and benchmark new algorithms and technologies to understand the most fundamental processes underlying human genetic variation.
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4
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López-Cortegano E, Chebib J, Jonas A, Vock A, Künzel S, Tautz D, Keightley PD. Variation in the Spectrum of New Mutations among Inbred Strains of Mice. Mol Biol Evol 2024; 41:msae163. [PMID: 39101589 PMCID: PMC11327921 DOI: 10.1093/molbev/msae163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 07/06/2024] [Accepted: 07/31/2024] [Indexed: 08/06/2024] Open
Abstract
The mouse serves as a mammalian model for understanding the nature of variation from new mutations, a question that has both evolutionary and medical significance. Previous studies suggest that the rate of single-nucleotide mutations (SNMs) in mice is ∼50% of that in humans. However, information largely comes from studies involving the C57BL/6 strain, and there is little information from other mouse strains. Here, we study the mutations that accumulated in 59 mouse lines derived from four inbred strains that are commonly used in genetics and clinical research (BALB/cAnNRj, C57BL/6JRj, C3H/HeNRj, and FVB/NRj), maintained for eight to nine generations by brother-sister mating. By analyzing Illumina whole-genome sequencing data, we estimate that the average rate of new SNMs in mice is ∼μ = 6.7 × 10-9. However, there is substantial variation in the spectrum of SNMs among strains, so the burden from new mutations also varies among strains. For example, the FVB strain has a spectrum that is markedly skewed toward C→A transversions and is likely to experience a higher deleterious load than other strains, due to an increased frequency of nonsense mutations in glutamic acid codons. Finally, we observe substantial variation in the rate of new SNMs among DNA sequence contexts, CpG sites, and their adjacent nucleotides playing an important role.
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Affiliation(s)
| | - Jobran Chebib
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Anika Jonas
- Department for Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Anastasia Vock
- Department for Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Sven Künzel
- Department for Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Diethard Tautz
- Department for Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Peter D Keightley
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, EH9 3FL, UK
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5
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Bishnoi IR, Bordt EA. The missing half: Paternal immune activation's role in transgenerational sex differences. Brain Behav Immun 2024; 120:288-289. [PMID: 38862065 DOI: 10.1016/j.bbi.2024.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 06/08/2024] [Indexed: 06/13/2024] Open
Affiliation(s)
- Indra R Bishnoi
- Department of Pediatrics, Lurie Center for Autism, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Evan A Bordt
- Department of Pediatrics, Lurie Center for Autism, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA.
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6
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Liscovitch-Brauer N, Mesika R, Rabinowitz T, Volkov H, Grad M, Matar RT, Basel-Salmon L, Tadmor O, Beker A, Shomron N. Machine learning-enhanced noninvasive prenatal testing of monogenic disorders. Prenat Diagn 2024; 44:1024-1032. [PMID: 38687007 DOI: 10.1002/pd.6570] [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: 10/10/2023] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 05/02/2024]
Abstract
OBJECTIVE Single-nucleotide variants (SNVs) are of great significance in prenatal diagnosis as they are the leading cause of inherited single-gene disorders (SGDs). Identifying SNVs in a non-invasive prenatal screening (NIPS) scenario is particularly challenging for maternally inherited SNVs. We present an improved method to predict inherited SNVs from maternal or paternal origin in a genome-wide manner. METHODS We performed SNV-NIPS based on the combination of fragments of cell free DNA (cfDNA) features, Bayesian inference and a machine-learning (ML) prediction refinement step using random forest (RF) classifiers trained on millions of non-pathogenic variants. We next evaluate the real-world performance of our refined method in a clinical setting by testing our models on 16 families with singleton pregnancies and varying fetal fraction (FF) levels, and validate the results over millions of inherited variants in each fetus. RESULTS The average area under the ROC curve (AUC) values are 0.996 over all families for paternally inherited variants, 0.81 for the challenging maternally inherited variants, 0.86 for homozygous biallelic variants and 0.95 for compound heterozygous variants. Discriminative AUCs were achieved even in families with a low FF. We further investigate the performance of our method in correctly predicting SNVs in coding regions of clinically relevant genes and demonstrate significantly improved AUCs in these regions. Finally, we focus on the pathogenic variants in our cohort and show that our method correctly predicts if the fetus is unaffected or affected in all (10/10, 100%) of the families containing a pathogenic SNV. CONCLUSIONS Overall, we demonstrate our ability to perform genome-wide NIPS for maternal and homozygous biallelic variants and showcase the utility of our method in a clinical setting.
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Affiliation(s)
| | | | - Tom Rabinowitz
- Identifai-Genetics Ltd., Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hadas Volkov
- Identifai-Genetics Ltd., Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Meitar Grad
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Reut Tomashov Matar
- Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
| | - Lina Basel-Salmon
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
- Felsenstein Medical Research Center, Tel-Aviv University, Tel-Aviv, Israel
| | | | - Amir Beker
- Identifai-Genetics Ltd., Tel Aviv, Israel
| | - Noam Shomron
- Identifai-Genetics Ltd., Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
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7
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Yu Z, Coorens THH, Uddin MM, Ardlie KG, Lennon N, Natarajan P. Genetic variation across and within individuals. Nat Rev Genet 2024; 25:548-562. [PMID: 38548833 DOI: 10.1038/s41576-024-00709-x] [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] [Accepted: 02/09/2024] [Indexed: 04/12/2024]
Abstract
Germline variation and somatic mutation are intricately connected and together shape human traits and disease risks. Germline variants are present from conception, but they vary between individuals and accumulate over generations. By contrast, somatic mutations accumulate throughout life in a mosaic manner within an individual due to intrinsic and extrinsic sources of mutations and selection pressures acting on cells. Recent advancements, such as improved detection methods and increased resources for association studies, have drastically expanded our ability to investigate germline and somatic genetic variation and compare underlying mutational processes. A better understanding of the similarities and differences in the types, rates and patterns of germline and somatic variants, as well as their interplay, will help elucidate the mechanisms underlying their distinct yet interlinked roles in human health and biology.
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Affiliation(s)
- Zhi Yu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Md Mesbah Uddin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Niall Lennon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pradeep Natarajan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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8
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Ha AS, Scott M, Zhang CA, Li S, Langroudi AP, Glover F, Basran S, Del Giudice F, Shaw GM, Eisenberg ML. Sociodemographic Trends and Perinatal Outcomes in Fathers 50 Years and Older. JAMA Netw Open 2024; 7:e2425269. [PMID: 39088214 PMCID: PMC11294967 DOI: 10.1001/jamanetworkopen.2024.25269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 06/04/2024] [Indexed: 08/02/2024] Open
Abstract
Importance The age of fathers at childbirth is rising, with an increasing number of births attributed to older fathers. While the impact of advanced paternal age has been documented, sociodemographic data about fathers aged 50 years and older remain scarce. Objectives To explore sociodemographic and temporal trends among the oldest US fathers (age ≥50 years) and their associations with perinatal outcomes. Design, Setting, and Participants This retrospective cross-sectional study included data from all US births from 2011 to 2022 using the National Vital Statistics System. Data were analyzed from August 2023 and May 2024. Exposures Reported paternal age at childbirth. Main Outcomes and Measures Outcomes of interest were sociodemographic factors, temporal trends in older fatherhood, and perinatal outcomes, including preterm birth, low birth weight, gestational diabetes, gestational hypertension, assisted reproductive technology (ART), rates of maternal primiparity, and the infant sex ratio. Results From 2011 to 2022, the US recorded 46 195 453 births, with an overall mean (SD) paternal age of 31.5 (6.8) years and 484 507 (1.1%) involving fathers aged 50 years or older, 47 785 (0.1%) aged 60 years or older, and 3777 (0.008%) aged 70 years or older. Births to fathers aged 50 years or older increased from 1.1% in 2011 to 1.3% in 2022 (P for trend < .001). Fathers aged 50 years or older were more diverse, with variations in educational achievement and race and ethnicity. Marital status and maternal racial and ethnic and educational backgrounds also varied by paternal age and race. Despite controlling for maternal age and other sociodemographic and perinatal factors, every 10-year increase in paternal age was consistently associated with greater use of ART (eg, age 50-59 years: adjusted odds ratio [aOR], 2.23; 95% CI, 2.19-2.27), higher likelihood of first maternal birth (eg, age 50-59 years: aOR, 1.16; 95% CI, 1.15-1.17), and increased risks of preterm birth (eg, age 50-59 years: aOR, 1.16; 95% CI, 1.15-1.18) and low birth weight (eg, age 50-59 years: aOR, 1.14; 95% CI, 1.13-1.15) compared with fathers aged 30 to 39 years. No significant changes in the infant sex ratio were observed, except among fathers aged 70 years or older (aOR, 0.92; 95% CI, 0.86-0.99) and 75 years or older (aOR, 0.84; 95% CI, 0.73-0.97), who showed a decreased likelihood of having male offspring. Conclusions and Relevance In this cross-sectional study of all US births from 2011 to 2022, the percentage attributed to older fathers, while small, increased. Notable variations in paternal and maternal race and education were identified. Older fatherhood was associated with increased ART use, first-time maternal births, adverse perinatal outcomes, and altered sex ratio. Further research of this population is crucial for improving patient counseling and family planning.
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Affiliation(s)
- Albert S. Ha
- Department of Urology, School of Medicine, Stanford University, Stanford, California
| | - Michael Scott
- Department of Urology, School of Medicine, Stanford University, Stanford, California
| | - Chiyuan Amy Zhang
- Department of Urology, School of Medicine, Stanford University, Stanford, California
| | - Shufeng Li
- Department of Urology, School of Medicine, Stanford University, Stanford, California
| | - Ashkan P Langroudi
- Department of Urology, School of Medicine, Stanford University, Stanford, California
| | - Frank Glover
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Satvir Basran
- Department of Urology, School of Medicine, Stanford University, Stanford, California
| | - Francesco Del Giudice
- Department of Maternal Infant and Urological Sciences, “Sapienza” University of Rome, Rome, Italy
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University, Stanford, California
| | - Michael L. Eisenberg
- Department of Urology, School of Medicine, Stanford University, Stanford, California
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9
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Wood KA, Tong RS, Motta M, Cordeddu V, Scimone ER, Bush SJ, Maxwell DW, Giannoulatou E, Caputo V, Traversa A, Mancini C, Ferrero GB, Benedicenti F, Grammatico P, Melis D, Steindl K, Brunetti-Pierri N, Trevisson E, Wilkie AO, Lin AE, Cormier-Daire V, Twigg SR, Tartaglia M, Goriely A. SMAD4 mutations causing Myhre syndrome are under positive selection in the male germline. Am J Hum Genet 2024:S0002-9297(24)00250-7. [PMID: 39116879 DOI: 10.1016/j.ajhg.2024.07.006] [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: 06/07/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 08/10/2024] Open
Abstract
While it is widely thought that de novo mutations (DNMs) occur randomly, we previously showed that some DNMs are enriched because they are positively selected in the testes of aging men. These "selfish" mutations cause disorders with a shared presentation of features, including exclusive paternal origin, significant increase of the father's age, and high apparent germline mutation rate. To date, all known selfish mutations cluster within the components of the RTK-RAS-MAPK signaling pathway, a critical modulator of testicular homeostasis. Here, we demonstrate the selfish nature of the SMAD4 DNMs causing Myhre syndrome (MYHRS). By analyzing 16 informative trios, we show that MYHRS-causing DNMs originated on the paternally derived allele in all cases. We document a statistically significant epidemiological paternal age effect of 6.3 years excess for fathers of MYHRS probands. We developed an ultra-sensitive assay to quantify spontaneous MYHRS-causing SMAD4 variants in sperm and show that pathogenic variants at codon 500 are found at elevated level in sperm of most men and exhibit a strong positive correlation with donor's age, indicative of a high apparent germline mutation rate. Finally, we performed in vitro assays to validate the peculiar functional behavior of the clonally selected DNMs and explored the basis of the pathophysiology of the different SMAD4 sperm-enriched variants. Taken together, these data provide compelling evidence that SMAD4, a gene operating outside the canonical RAS-MAPK signaling pathway, is associated with selfish spermatogonial selection and raises the possibility that other genes/pathways are under positive selection in the aging human testis.
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Affiliation(s)
- Katherine A Wood
- MRC Weatherall Institute of Molecular Medicine, Oxford OX39DS, UK; Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX39DS, UK; NIHR Oxford Biomedical Research Centre, Oxford OX39DU, UK
| | - R Spencer Tong
- MRC Weatherall Institute of Molecular Medicine, Oxford OX39DS, UK; Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX39DS, UK; NIHR Oxford Biomedical Research Centre, Oxford OX39DU, UK
| | - Marialetizia Motta
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Viviana Cordeddu
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Eleanor R Scimone
- Medical Genetics, Mass General Brigham, Harvard Medical School, Harvard University, Boston, MA 02114, USA
| | - Stephen J Bush
- MRC Weatherall Institute of Molecular Medicine, Oxford OX39DS, UK; Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX39DS, UK; NIHR Oxford Biomedical Research Centre, Oxford OX39DU, UK
| | - Dale W Maxwell
- MRC Weatherall Institute of Molecular Medicine, Oxford OX39DS, UK; Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX39DS, UK; NIHR Oxford Biomedical Research Centre, Oxford OX39DU, UK
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, NSW 2010, Australia; School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Viviana Caputo
- Department of Experimental Medicine, Sapienza University, 00161 Rome, Italy
| | - Alice Traversa
- Department of Experimental Medicine, Sapienza University, 00161 Rome, Italy
| | - Cecilia Mancini
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Giovanni B Ferrero
- Department of Clinical and Biological Science, University of Torino, 10126 Turin, Italy
| | | | - Paola Grammatico
- Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, 00152 Rome, Italy
| | - Daniela Melis
- Department of Medicine, Surgery and Dentistry, University of Salerno, 84081 Salerno, Italy
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University, 80131 Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine Program, University of Naples Federico II, Naples, Italy
| | - Eva Trevisson
- Department of Women's and Children's Health, University of Padova, 35128 Padua, Italy
| | - Andrew Om Wilkie
- MRC Weatherall Institute of Molecular Medicine, Oxford OX39DS, UK; Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX39DS, UK; NIHR Oxford Biomedical Research Centre, Oxford OX39DU, UK
| | - Angela E Lin
- Medical Genetics, Mass General Brigham, Harvard Medical School, Harvard University, Boston, MA 02114, USA
| | - Valerie Cormier-Daire
- Université Paris Cité, Service de Médecine Génomique des Maladies Rares, INSERM UMR 1163, Institut Imagine, Hôpital Necker-Enfants Malades, 75015 Paris, France
| | - Stephen Rf Twigg
- MRC Weatherall Institute of Molecular Medicine, Oxford OX39DS, UK; Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX39DS, UK; NIHR Oxford Biomedical Research Centre, Oxford OX39DU, UK
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy.
| | - Anne Goriely
- MRC Weatherall Institute of Molecular Medicine, Oxford OX39DS, UK; Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX39DS, UK; NIHR Oxford Biomedical Research Centre, Oxford OX39DU, UK.
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10
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Vahedi Raad M, Firouzabadi AM, Tofighi Niaki M, Henkel R, Fesahat F. The impact of mitochondrial impairments on sperm function and male fertility: a systematic review. Reprod Biol Endocrinol 2024; 22:83. [PMID: 39020374 PMCID: PMC11253428 DOI: 10.1186/s12958-024-01252-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 06/27/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND Besides adenine triphosphate (ATP) production for sustaining motility, the mitochondria of sperm also host other critical cellular functions during germ cell development and fertilization including calcium homeostasis, generation of reactive oxygen species (ROS), apoptosis, and in some cases steroid hormone biosynthesis. Normal mitochondrial membrane potential with optimal mitochondrial performance is essential for sperm motility, capacitation, acrosome reaction, and DNA integrity. RESULTS Defects in the sperm mitochondrial function can severely harm the fertility potential of males. The role of sperm mitochondria in fertilization and its final fate after fertilization is still controversial. Here, we review the current knowledge on human sperm mitochondria characteristics and their physiological and pathological conditions, paying special attention to improvements in assistant reproductive technology and available treatments to ameliorate male infertility. CONCLUSION Although mitochondrial variants associated with male infertility have potential clinical use, research is limited. Further understanding is needed to determine how these characteristics lead to adverse pregnancy outcomes and affect male fertility potential.
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Affiliation(s)
- Minoo Vahedi Raad
- Department of Biology & Anatomical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Masoud Firouzabadi
- Reproductive Immunology Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Department of Physiology, School of Medical Sciences, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Maryam Tofighi Niaki
- Health Reproductive Research Center, Sari Branch, Islamic Azad University, Sari, Iran
| | - Ralf Henkel
- LogixX Pharma, Theale, Berkshire, UK.
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
- Department of Medical Bioscience, University of the Western Cape, Bellville, South Africa.
| | - Farzaneh Fesahat
- Reproductive Immunology Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
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11
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Marsh JI, Johri P. Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection. Mol Biol Evol 2024; 41:msae118. [PMID: 38874402 PMCID: PMC11245712 DOI: 10.1093/molbev/msae118] [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: 04/15/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024] Open
Abstract
Inferring the demographic history of populations provides fundamental insights into species dynamics and is essential for developing a null model to accurately study selective processes. However, background selection and selective sweeps can produce genomic signatures at linked sites that mimic or mask signals associated with historical population size change. While the theoretical biases introduced by the linked effects of selection have been well established, it is unclear whether ancestral recombination graph (ARG)-based approaches to demographic inference in typical empirical analyses are susceptible to misinference due to these effects. To address this, we developed highly realistic forward simulations of human and Drosophila melanogaster populations, including empirically estimated variability of gene density, mutation rates, recombination rates, purifying, and positive selection, across different historical demographic scenarios, to broadly assess the impact of selection on demographic inference using a genealogy-based approach. Our results indicate that the linked effects of selection minimally impact demographic inference for human populations, although it could cause misinference in populations with similar genome architecture and population parameters experiencing more frequent recurrent sweeps. We found that accurate demographic inference of D. melanogaster populations by ARG-based methods is compromised by the presence of pervasive background selection alone, leading to spurious inferences of recent population expansion, which may be further worsened by recurrent sweeps, depending on the proportion and strength of beneficial mutations. Caution and additional testing with species-specific simulations are needed when inferring population history with non-human populations using ARG-based approaches to avoid misinference due to the linked effects of selection.
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Affiliation(s)
- Jacob I Marsh
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Parul Johri
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
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12
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Wertenbroek R, Hofmeister RJ, Xenarios I, Thoma Y, Delaneau O. Improving population scale statistical phasing with whole-genome sequencing data. PLoS Genet 2024; 20:e1011092. [PMID: 38959269 PMCID: PMC11251608 DOI: 10.1371/journal.pgen.1011092] [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: 12/07/2023] [Revised: 07/16/2024] [Accepted: 06/11/2024] [Indexed: 07/05/2024] Open
Abstract
Haplotype estimation, or phasing, has gained significant traction in large-scale projects due to its valuable contributions to population genetics, variant analysis, and the creation of reference panels for imputation and phasing of new samples. To scale with the growing number of samples, haplotype estimation methods designed for population scale rely on highly optimized statistical models to phase genotype data, and usually ignore read-level information. Statistical methods excel in resolving common variants, however, they still struggle at rare variants due to the lack of statistical information. In this study we introduce SAPPHIRE, a new method that leverages whole-genome sequencing data to enhance the precision of haplotype calls produced by statistical phasing. SAPPHIRE achieves this by refining haplotype estimates through the realignment of sequencing reads, particularly targeting low-confidence phase calls. Our findings demonstrate that SAPPHIRE significantly enhances the accuracy of haplotypes obtained from state of the art methods and also provides the subset of phase calls that are validated by sequencing reads. Finally, we show that our method scales to large data sets by its successful application to the extensive 3.6 Petabytes of sequencing data of the last UK Biobank 200,031 sample release.
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Affiliation(s)
- Rick Wertenbroek
- University of Lausanne, Lausanne, Vaud, Switzerland
- School of Engineering and Management Vaud (HEIG-VD), HES-SO University of Applied Sciences and Arts Western Switzerland, Yverdon-les-Bains, Vaud, Switzerland
| | | | | | - Yann Thoma
- School of Engineering and Management Vaud (HEIG-VD), HES-SO University of Applied Sciences and Arts Western Switzerland, Yverdon-les-Bains, Vaud, Switzerland
| | - Olivier Delaneau
- Regeneron Genetics Center, Tarrytown, New York, United States of America
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13
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Zhang L, Chang M, Liu C, Xu Y, Feng Q, Yin S, Wu W. A case of de novo -α 3.7 thalassaemia and the utility of CATSA for detecting de novo mutations in thalassaemia. Br J Haematol 2024; 205:360-363. [PMID: 38757312 DOI: 10.1111/bjh.19507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024]
Affiliation(s)
- Lei Zhang
- Medical Genetics Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, China
| | - Ming Chang
- Department of Hematology, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Chao Liu
- Medical Genetics Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, China
| | - Yong Xu
- Medical Genetics Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, China
| | - Qing Feng
- Medical Genetics Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, China
| | - Shanshan Yin
- Medical Genetics Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, China
| | - Weiqing Wu
- Medical Genetics Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, China
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14
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Kay AC, Wells J, Goriely A, Hallowell N. Professionals' views on providing personalized recurrence risks for de novo mutations: Implications for genetic counseling. J Genet Couns 2024. [PMID: 38924179 DOI: 10.1002/jgc4.1910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 06/28/2024]
Abstract
When an apparent de novo (new) genetic change has been identified as the cause of a serious genetic condition in a child, many couples would like to know the risk of this happening again in a future pregnancy. Current practice provides families with a population average risk of 1%-2%. However, this figure is not accurate for any specific couple, and yet, they are asked to make decisions about having another child and/or whether to have prenatal testing. The PREcision Genetic Counseling And REproduction (PREGCARE) study is a new personalized assessment strategy that refines a couple's recurrence risk prior to a new pregnancy, by analyzing several samples from the parent-child trio (blood, saliva, swabs, and father's sperm) using deep sequencing and haplotyping. Overall, this approach can reassure ~2/3 of couples who have a negligible (<0.1%) recurrence risk and focus support on those at higher risk (i.e. when mosaicism is identified in one of the parents). Here we present a qualitative interview study with UK clinical genetics professionals (n = 20), which investigate the potential implications of introducing such a strategy in genetics clinics. While thematic analysis of the interviews indicated perceived clinical utility, it also indicates a need to prepare couples for the psychosocial implications of parent-of-origin information and to support their understanding of the assessment being offered. When dealing with personalized reproductive risk, a traditional non-directive approach may not meet the needs of practitioner and client(s) and shared decision-making provides an additional framework that may relieve some patient burden. Further qualitative investigation with couples is planned.
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Affiliation(s)
- Alison C Kay
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
- The Centre for Personalised Medicine, University of Oxford, Oxford, UK
| | - Jonathan Wells
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
- Clinical Genetics, St. Michael's Hospital, Bristol, UK
| | - Anne Goriely
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
| | - Nina Hallowell
- Ethox Centre and Wellcome Centre for Ethics and Humanities, University of Oxford, Oxford, UK
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15
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Parsons BL, Beal MA, Dearfield KL, Douglas GR, Gi M, Gollapudi BB, Heflich RH, Horibata K, Kenyon M, Long AS, Lovell DP, Lynch AM, Myers MB, Pfuhler S, Vespa A, Zeller A, Johnson GE, White PA. Severity of effect considerations regarding the use of mutation as a toxicological endpoint for risk assessment: A report from the 8th International Workshop on Genotoxicity Testing (IWGT). ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024. [PMID: 38828778 DOI: 10.1002/em.22599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/13/2024] [Accepted: 04/15/2024] [Indexed: 06/05/2024]
Abstract
Exposure levels without appreciable human health risk may be determined by dividing a point of departure on a dose-response curve (e.g., benchmark dose) by a composite adjustment factor (AF). An "effect severity" AF (ESAF) is employed in some regulatory contexts. An ESAF of 10 may be incorporated in the derivation of a health-based guidance value (HBGV) when a "severe" toxicological endpoint, such as teratogenicity, irreversible reproductive effects, neurotoxicity, or cancer was observed in the reference study. Although mutation data have been used historically for hazard identification, this endpoint is suitable for quantitative dose-response modeling and risk assessment. As part of the 8th International Workshops on Genotoxicity Testing, a sub-group of the Quantitative Analysis Work Group (WG) explored how the concept of effect severity could be applied to mutation. To approach this question, the WG reviewed the prevailing regulatory guidance on how an ESAF is incorporated into risk assessments, evaluated current knowledge of associations between germline or somatic mutation and severe disease risk, and mined available data on the fraction of human germline mutations expected to cause severe disease. Based on this review and given that mutations are irreversible and some cause severe human disease, in regulatory settings where an ESAF is used, a majority of the WG recommends applying an ESAF value between 2 and 10 when deriving a HBGV from mutation data. This recommendation may need to be revisited in the future if direct measurement of disease-causing mutations by error-corrected next generation sequencing clarifies selection of ESAF values.
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Affiliation(s)
- Barbara L Parsons
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Marc A Beal
- Bureau of Chemical Safety, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Kerry L Dearfield
- U.S. Environmental Protection Agency and U.S. Department of Agriculture, Washington, DC, USA
| | - George R Douglas
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Min Gi
- Department of Environmental Risk Assessment, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | | | - Robert H Heflich
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Michelle Kenyon
- Portfolio and Regulatory Strategy, Drug Safety Research and Development, Pfizer, Groton, Connecticut, USA
| | - Alexandra S Long
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - David P Lovell
- Population Health Research Institute, St George's Medical School, University of London, London, UK
| | | | - Meagan B Myers
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Alisa Vespa
- Pharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Andreas Zeller
- Pharmaceutical Sciences, pRED Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
| | - George E Johnson
- Swansea University Medical School, Swansea University, Swansea, Wales, UK
| | - Paul A White
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
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16
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Willführ KP, Klüsener S. The current 'dramatically' high paternal ages at childbirth are not unprecedented. Hum Reprod 2024; 39:1161-1166. [PMID: 38569672 DOI: 10.1093/humrep/deae067] [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: 02/07/2024] [Revised: 03/15/2024] [Indexed: 04/05/2024] Open
Abstract
There is strong individual-level evidence that late fatherhood is related to a wide range of health disorders and conditions in offspring. Over the last decades, mean paternal ages at childbirth have risen drastically. This has alarmed researchers from a wide range of fields. However, existing studies have an important shortcoming in that they lack a long-term perspective. This article is a step change in providing such a long-term perspective. We unveil that in many countries the current mean paternal ages at childbirth and proportions of fathers of advanced age at childbirth are not unprecedented. Taking the detected U-shaped trend pattern into account, we discuss individual- and population-level implications of the recent increases in paternal ages at childbirth and highlight important knowledge gaps. At the individual level, some of the biological mechanisms that are responsible for the paternal age-related health risk might, at least to some degree, be counterbalanced by various social factors. Further, how these individual-level effects are linked to population health and human cognitive development might be influenced by various factors, including technical advances and regulations in prenatal diagnostics.
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Affiliation(s)
- Kai P Willführ
- Institute for Social Sciences, School of Educational and Social Sciences, Carl von Ossietzky University, Oldenburg, Germany
- Center for Economic Demography, Department of Economic History, Lund University, Sweden
| | - Sebastian Klüsener
- Ageing, Mortality and Population Dynamics, Federal Institute for Population Research (BiB), Wiesbaden, Germany
- Institute of Sociology and Social Psychology (ISS), University of Cologne, Cologne, Germany
- Centre for Demographic Research, Vytautas Magnus University, Kaunas, Lithuania
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17
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Castellini C, Cordeschi G, Tienforti D, Barbonetti A. Relationship between male aging and semen quality: a retrospective study on over 2500 men. Arch Gynecol Obstet 2024; 309:2843-2852. [PMID: 38551703 PMCID: PMC11147833 DOI: 10.1007/s00404-024-07448-8] [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: 11/16/2023] [Accepted: 02/25/2024] [Indexed: 06/04/2024]
Abstract
PURPOSE We aimed to evaluate whether and to what extent an association exists between male aging and worsening of semen parameters and to determine whether a threshold age can be identified above which the decline in semen quality becomes statistically significant. METHODS 2612 men (age: 16-56 years) attending an andrology outpatient clinic for semen analysis and clinical evaluation were studied. Semen analyses were performed according to the ongoing WHO-recommended procedures. Total motile count (TMC) and total progressive motile count (TPMC) were calculated by multiplying total sperm number by total motility and progressive motility, respectively. RESULTS Significant negative correlations were found between age and total motility (r = - 0.131, p < 0.0001), progressive motility (r = - 0.112, p < 0.0001), TPMC (r = - 0.042, p = 0.037), and normal sperm morphology (r = - 0.053, p = 0.007). All these associations persisted in multivariate regression models adjusted for abstinence time, smoking, history of male accessory gland infections, varicocele and the year in which semen analysis was performed. When comparisons were performed among quartiles of increasing age, the fourth quartile, corresponding to the age group > 40 years, was associated with a significant decrease in total and progressive motility. An earlier decline in the TPMC and percentage of normal forms was also observed. CONCLUSION Advancing male age exhibits an independent association with a decrease in the percentage of motile and morphologically normal spermatozoa, with greater evidence from the age of > 40 years. Further studies are warranted to elucidate the mechanisms and clinical reflections of these associations.
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Affiliation(s)
- Chiara Castellini
- Andrology Unit, Department of Clinical Medicine, Life, Health and Environmental Sciences, University of L'Aquila, Coppito, 67100, L'Aquila, Italy
| | - Giuliana Cordeschi
- Andrology Unit, Department of Clinical Medicine, Life, Health and Environmental Sciences, University of L'Aquila, Coppito, 67100, L'Aquila, Italy
| | - Daniele Tienforti
- Andrology Unit, Department of Clinical Medicine, Life, Health and Environmental Sciences, University of L'Aquila, Coppito, 67100, L'Aquila, Italy
| | - Arcangelo Barbonetti
- Andrology Unit, Department of Clinical Medicine, Life, Health and Environmental Sciences, University of L'Aquila, Coppito, 67100, L'Aquila, Italy.
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18
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Jakkamsetti V, Ma Q, Angulo G, Scudder W, Beutler B, Pascual JM. Genetic influences on motor learning and performance and superperforming mutants revealed by random mutational survey of the mouse genome. J Physiol 2024; 602:2649-2664. [PMID: 38299894 PMCID: PMC11142877 DOI: 10.1113/jp285505] [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: 08/21/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
Evolution depends upon genetic variations that influence physiology. As defined in a genetic screen, phenotypic performance may be enhanced or degraded by such mutations. We set out to detect mutations that influence motor function, including motor learning. Thus, we tested the motor effects of 36,444 non-synonymous coding/splicing mutations induced in the germline of C57BL/6J mice with N-ethyl-N-nitrosourea by measuring changes in the performance of repetitive rotarod trials while blinded to genotype. Automated meiotic mapping was used to implicate individual mutations in causation. In total, 32,726 mice bearing all the variant alleles were screened. This was complemented with the simultaneous testing of 1408 normal mice for reference. In total, 16.3% of autosomal genes were thus rendered detectably hypomorphic or nullified by mutations in homozygosity and motor tested in at least three mice. This approach allowed us to identify superperformance mutations in Rif1, Tk1, Fan1 and Mn1. These genes are primarily related, among other less well-characterized functions, to nucleic acid biology. We also associated distinct motor learning patterns with groups of functionally related genes. These functional sets included, preferentially, histone H3 methyltransferase activity for mice that learnt at an accelerated rate relative to the remaining mutant mice. The results allow for an estimation of the fraction of mutations that can modify a behaviour influential for evolution such as locomotion. They may also enable, once the loci are further validated and the mechanisms elucidated, the harnessing of the activity of the newly identified genes to enhance motor ability or to counterbalance disability or disease. KEY POINTS: We studied the effect of chemically induced random mutations on mouse motor performance. An array of mutations influenced the rate of motor learning. DNA regulation genes predominated among these mutant loci. Several mutations in unsuspected genes led to superperformance. Assuming little-biased mutagenicity, the results allow for an estimation of the probability for any spontaneous mutation to influence a behaviour such as motor learning and ultimate performance.
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Affiliation(s)
- Vikram Jakkamsetti
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Qian Ma
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Gustavo Angulo
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - William Scudder
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Bruce Beutler
- Center for Genetics of Host Defense, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Juan M. Pascual
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Eugene McDermott Center for Human Growth & Development / Center for Human Genetics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
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19
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Baur J, Koppik M, Savković U, Đorđević M, Stojkovic B, Berger D. Coevolution of longevity and female germline maintenance. Proc Biol Sci 2024; 291:20240532. [PMID: 38864321 DOI: 10.1098/rspb.2024.0532] [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: 11/24/2023] [Accepted: 04/11/2024] [Indexed: 06/13/2024] Open
Abstract
An often-overlooked aspect of life-history optimization is the allocation of resources to protect the germline and secure safe transmission of genetic information. While failure to do so renders significant fitness consequences in future generations, germline maintenance comes with substantial costs. Thus, germline allocation should trade off with other life-history decisions and be optimized in accordance with an organism's reproductive schedule. Here, we tested this hypothesis by studying germline maintenance in lines of seed beetle, selected for early (E) or late (L) reproduction for 350 and 240 generations, respectively. Female animals provide maintenance and screening of male gametes in their reproductive tract and oocytes. Here, we reveal the ability of young and aged E- and L-females to provide this form of germline maintenance by mating them to males with ejaculates with artificially elevated levels of protein and DNA damage. We find that germline maintenance in E-females peaks at young age and then declines, while the opposite is true for L-females, in accordance with the age of reproduction in the respective regime. These findings identify the central role of allocation to secure germline integrity in life-history evolution and highlight how females can play a crucial role in mitigating the effects of male germline decisions on mutation rate and offspring quality.
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Affiliation(s)
- Julian Baur
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Mareike Koppik
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Animal Ecology, Department of Zoology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Uroš Savković
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", National Institute of the Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade 11000, Serbia
| | - Mirko Đorđević
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", National Institute of the Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade 11000, Serbia
| | - Biljana Stojkovic
- Institute of Zoology, Chair of Genetics and Evolution, Faculty of Biology, Studentski trg 16, 11000 Belgrade, Serbia
| | - David Berger
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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20
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Linga BG, Mohammed SGAA, Farrell T, Rifai HA, Al-Dewik N, Qoronfleh MW. Genomic Newborn Screening for Pediatric Cancer Predisposition Syndromes: A Holistic Approach. Cancers (Basel) 2024; 16:2017. [PMID: 38893137 PMCID: PMC11171256 DOI: 10.3390/cancers16112017] [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: 04/19/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
As next-generation sequencing (NGS) has become more widely used, germline and rare genetic variations responsible for inherited illnesses, including cancer predisposition syndromes (CPSs) that account for up to 10% of childhood malignancies, have been found. The CPSs are a group of germline genetic disorders that have been identified as risk factors for pediatric cancer development. Excluding a few "classic" CPSs, there is no agreement regarding when and how to conduct germline genetic diagnostic studies in children with cancer due to the constant evolution of knowledge in NGS technologies. Various clinical screening tools have been suggested to aid in the identification of individuals who are at greater risk, using diverse strategies and with varied outcomes. We present here an overview of the primary clinical and molecular characteristics of various CPSs and summarize the existing clinical genomics data on the prevalence of CPSs in pediatric cancer patients. Additionally, we discuss several ethical issues, challenges, limitations, cost-effectiveness, and integration of genomic newborn screening for CPSs into a healthcare system. Furthermore, we assess the effectiveness of commonly utilized decision-support tools in identifying patients who may benefit from genetic counseling and/or direct genetic testing. This investigation highlights a tailored and systematic approach utilizing medical newborn screening tools such as the genome sequencing of high-risk newborns for CPSs, which could be a practical and cost-effective strategy in pediatric cancer care.
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Affiliation(s)
- BalaSubramani Gattu Linga
- Department of Research, Women’s Wellness and Research Center, Hamad Medical Corporation (HMC), P.O. Box 3050, Doha 0974, Qatar
- Translational and Precision Medicine Research, Women’s Wellness and Research Center (WWRC), Hamad Medical Corporation (HMC), Doha 0974, Qatar
| | | | - Thomas Farrell
- Department of Research, Women’s Wellness and Research Center, Hamad Medical Corporation (HMC), P.O. Box 3050, Doha 0974, Qatar
| | - Hilal Al Rifai
- Neonatal Intensive Care Unit (NICU), Newborn Screening Unit, Department of Pediatrics and Neonatology, Women’s Wellness and Research Center (WWRC), Hamad Medical Corporation (HMC), Doha 0974, Qatar
| | - Nader Al-Dewik
- Department of Research, Women’s Wellness and Research Center, Hamad Medical Corporation (HMC), P.O. Box 3050, Doha 0974, Qatar
- Translational and Precision Medicine Research, Women’s Wellness and Research Center (WWRC), Hamad Medical Corporation (HMC), Doha 0974, Qatar
- Neonatal Intensive Care Unit (NICU), Newborn Screening Unit, Department of Pediatrics and Neonatology, Women’s Wellness and Research Center (WWRC), Hamad Medical Corporation (HMC), Doha 0974, Qatar
- Genomics and Precision Medicine (GPM), College of Health & Life Science (CHLS), Hamad Bin Khalifa University (HBKU), Doha 0974, Qatar
- Faculty of Health and Social Care Sciences, Kingston University and St George’s University of London, Kingston upon Thames, Surrey, London KT1 2EE, UK
| | - M. Walid Qoronfleh
- Healthcare Research & Policy Division, Q3 Research Institute (QRI), Ann Arbor, MI 48197, USA
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21
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Kim Y, Jeong M, Koh IG, Kim C, Lee H, Kim JH, Yurko R, Kim IB, Park J, Werling DM, Sanders SJ, An JY. CWAS-Plus: estimating category-wide association of rare noncoding variation from whole-genome sequencing data with cell-type-specific functional data. Brief Bioinform 2024; 25:bbae323. [PMID: 38966948 PMCID: PMC11224609 DOI: 10.1093/bib/bbae323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 07/06/2024] Open
Abstract
Variants in cis-regulatory elements link the noncoding genome to human pathology; however, detailed analytic tools for understanding the association between cell-level brain pathology and noncoding variants are lacking. CWAS-Plus, adapted from a Python package for category-wide association testing (CWAS), enhances noncoding variant analysis by integrating both whole-genome sequencing (WGS) and user-provided functional data. With simplified parameter settings and an efficient multiple testing correction method, CWAS-Plus conducts the CWAS workflow 50 times faster than CWAS, making it more accessible and user-friendly for researchers. Here, we used a single-nuclei assay for transposase-accessible chromatin with sequencing to facilitate CWAS-guided noncoding variant analysis at cell-type-specific enhancers and promoters. Examining autism spectrum disorder WGS data (n = 7280), CWAS-Plus identified noncoding de novo variant associations in transcription factor binding sites within conserved loci. Independently, in Alzheimer's disease WGS data (n = 1087), CWAS-Plus detected rare noncoding variant associations in microglia-specific regulatory elements. These findings highlight CWAS-Plus's utility in genomic disorders and scalability for processing large-scale WGS data and in multiple-testing corrections. CWAS-Plus and its user manual are available at https://github.com/joonan-lab/cwas/ and https://cwas-plus.readthedocs.io/en/latest/, respectively.
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Affiliation(s)
- Yujin Kim
- Department of Integrated Biomedical and Life Science, Korea University, 145 Anam-ro, Seongbuk-ku, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seongbuk-ku, Seoul 02841, Republic of Korea
| | - Minwoo Jeong
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, 145 Anam-ro, Seongbuk-ku, Seoul 02841, Republic of Korea
| | - In Gyeong Koh
- Department of Integrated Biomedical and Life Science, Korea University, 145 Anam-ro, Seongbuk-ku, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seongbuk-ku, Seoul 02841, Republic of Korea
| | - Chanhee Kim
- Department of Integrated Biomedical and Life Science, Korea University, 145 Anam-ro, Seongbuk-ku, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seongbuk-ku, Seoul 02841, Republic of Korea
| | - Hyeji Lee
- Department of Integrated Biomedical and Life Science, Korea University, 145 Anam-ro, Seongbuk-ku, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seongbuk-ku, Seoul 02841, Republic of Korea
| | - Jae Hyun Kim
- Department of Integrated Biomedical and Life Science, Korea University, 145 Anam-ro, Seongbuk-ku, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seongbuk-ku, Seoul 02841, Republic of Korea
| | - Ronald Yurko
- Department of Statistics and Data Science, Carnegie Mellon University, 5000 Forbes Avenue, Squirrel Hill North, Pittsburgh, PA 15213, United States
| | - Il Bin Kim
- Department of Psychiatry, CHA Gangnam Medical Center, CHA University School of Medicine, 566 Nonhyon-ro, Gangnam-gu, Seoul 06135, Republic of Korea
| | - Jeongbin Park
- School of Biomedical Convergence Engineering, Pusan National University, 49 Busandaehak-ro, Mulgeum-eup, Yangsan-si, Gyeongsangnam-do, 50612, Republic of Korea
| | - Donna M Werling
- Laboratory of Genetics, University of Wisconsin-Madison, 425-g Henry Mall, Madison, WI 53706, Unite States
| | - Stephan J Sanders
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine, University of Oxford, Old Road Campus, Roosevelt Dr, Headington, Oxford OX3 7TY, United Kingdom
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, 1651 4th Street, San Francisco, CA 94158, United States
| | - Joon-Yong An
- Department of Integrated Biomedical and Life Science, Korea University, 145 Anam-ro, Seongbuk-ku, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seongbuk-ku, Seoul 02841, Republic of Korea
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, 145 Anam-ro, Seongbuk-ku, Seoul 02841, Republic of Korea
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22
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杨 晓. [Sperm Mosaic Variants and Their Influence on the Offspring]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2024; 55:535-541. [PMID: 38948294 PMCID: PMC11211766 DOI: 10.12182/20240560507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Indexed: 07/02/2024]
Abstract
Genomic mosaicism arising from mosaic variants is a phenomenon that describes the presence of a cell or cell populations with different genome compositions from the germline cells of an individual. It comprises all types of genetic variants. A large proportion of childhood genetic disorders are defined as being de novo, meaning that the disease-causing mutations are only detected in the proband, not in any of the parents. Population studies show that 80% of the de novo mutations arise from the paternal haplotype, that is, from paternal sperm mosaicism. This review provides a summary of the types and detection strategies of sperm mosaicism. In addition, it provides discussions on how recent studies demonstrated that genomic mosaic mutations in parents, especially those in the paternal sperms, could be inherited by the offspring and cause childhood disorders. According to the previous findings of the author's research team, sperm mosaicism derived from early embryogenesis and primordial germ cell stages can explain 5% to 20% of the de novo mutations related to clinical phenotypes and can serve as an important predictor of both rare and complex disorders. Sperm mosaicism shows great potential for clinical genetic diagnosis and consultations. Based on the published literature, the author suggests that, large-scale screening for de novo sperm mosaic mutations and population-based genetic screening should be conducted in future studies, which will greatly enhance the risk assessment in the offspring and effectively improve the genetic health at the population level. Implementation of direct sperm detection for de novo mutations will significantly increase the efficiency of the stratification of patient cohorts and improve recurrence risk assessment for future births. Future research in the field should be focused on the impact of environmental and lifestyle factors on the health of the offspring through sperms and their modeling of mutation signatures. In addition, targeted in vitro modeling of sperm mutations will also be a promising direction.
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Affiliation(s)
- 晓旭 杨
- 犹他大学 (盐湖城 UT 84112)University of Utah, Salt Lake City, UT 84112, USA
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23
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Xia QQ, Singh A, Wang J, Xuan ZX, Singer JD, Powell CM. Autism risk gene Cul3 alters neuronal morphology via caspase-3 activity in mouse hippocampal neurons. Front Cell Neurosci 2024; 18:1320784. [PMID: 38803442 PMCID: PMC11129687 DOI: 10.3389/fncel.2024.1320784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 04/15/2024] [Indexed: 05/29/2024] Open
Abstract
Autism Spectrum Disorders (ASDs) are neurodevelopmental disorders (NDDs) in which children display differences in social interaction/communication and repetitive stereotyped behaviors along with variable associated features. Cul3, a gene linked to ASD, encodes CUL3 (CULLIN-3), a protein that serves as a key component of a ubiquitin ligase complex with unclear function in neurons. Cul3 homozygous deletion in mice is embryonic lethal; thus, we examine the role of Cul3 deletion in early synapse development and neuronal morphology in hippocampal primary neuronal cultures. Homozygous deletion of Cul3 significantly decreased dendritic complexity and dendritic length, as well as axon formation. Synaptic spine density significantly increased, mainly in thin and stubby spines along with decreased average spine volume in Cul3 knockouts. Both heterozygous and homozygous knockout of Cul3 caused significant reductions in the density and colocalization of gephyrin/vGAT puncta, providing evidence of decreased inhibitory synapse number, while excitatory synaptic puncta vGulT1/PSD95 density remained unchanged. Based on previous studies implicating elevated caspase-3 after Cul3 deletion, we demonstrated increased caspase-3 in our neuronal cultures and decreased neuronal cell viability. We then examined the efficacy of the caspase-3 inhibitor Z-DEVD-FMK to rescue the decrease in neuronal cell viability, demonstrating reversal of the cell viability phenotype with caspase-3 inhibition. Studies have also implicated caspase-3 in neuronal morphological changes. We found that caspase-3 inhibition largely reversed the dendrite, axon, and spine morphological changes along with the inhibitory synaptic puncta changes. Overall, these data provide additional evidence that Cul3 regulates the formation or maintenance of cell morphology, GABAergic synaptic puncta, and neuronal viability in developing hippocampal neurons in culture.
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Affiliation(s)
- Qiang-qiang Xia
- Department of Neurobiology, Marnix E. Heersink School of Medicine & Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Anju Singh
- Department of Neurobiology, Marnix E. Heersink School of Medicine & Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jing Wang
- Department of Neurobiology, Marnix E. Heersink School of Medicine & Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Zhong Xin Xuan
- Department of Neurobiology, Marnix E. Heersink School of Medicine & Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jeffrey D. Singer
- Department of Biology, Portland State University, Portland, OR, United States
| | - Craig M. Powell
- Department of Neurobiology, Marnix E. Heersink School of Medicine & Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
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24
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Matharu N, Zhao J, Sohota A, Deng L, Hung Y, Li Z, Sims J, Rattanasopha S, Meyer J, Carbone L, Kircher M, Ahituv N. Massively parallel jumping assay decodes Alu retrotransposition activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589814. [PMID: 38659854 PMCID: PMC11042287 DOI: 10.1101/2024.04.16.589814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The human genome contains millions of retrotransposons, several of which could become active due to somatic mutations having phenotypic consequences, including disease. However, it is not thoroughly understood how nucleotide changes in retrotransposons affect their jumping activity. Here, we developed a novel massively parallel jumping assay (MPJA) that can test the jumping potential of thousands of transposons en masse. We generated nucleotide variant library of selected four Alu retrotransposons containing 165,087 different haplotypes and tested them for their jumping ability using MPJA. We found 66,821 unique jumping haplotypes, allowing us to pinpoint domains and variants vital for transposition. Mapping these variants to the Alu-RNA secondary structure revealed stem-loop features that contribute to jumping potential. Combined, our work provides a novel high-throughput assay that assesses the ability of retrotransposons to jump and identifies nucleotide changes that have the potential to reactivate them in the human genome.
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Affiliation(s)
- Navneet Matharu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Jingjing Zhao
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Ajuni Sohota
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Linbei Deng
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Yan Hung
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Zizheng Li
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Jasmine Sims
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Sawitree Rattanasopha
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Josh Meyer
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
| | - Martin Kircher
- Berlin Institute of Health of Health at Charité - Universitätsmedizin Berlin, 10178, Berlin, Germany
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
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25
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Chu C, Ljungström V, Tran A, Jin H, Park PJ. Contribution of de novo retroelements to birth defects and childhood cancers. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.15.24305733. [PMID: 38699361 PMCID: PMC11065029 DOI: 10.1101/2024.04.15.24305733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Insertion of active retroelements-L1s, Alus, and SVAs-can disrupt proper genome function and lead to various disorders including cancer. However, the role of de novo retroelements (DNRTs) in birth defects and childhood cancers has not been well characterized due to the lack of adequate data and efficient computational tools. Here, we examine whole-genome sequencing data of 3,244 trios from 12 birth defect and childhood cancer cohorts in the Gabriella Miller Kids First Pediatric Research Program. Using an improved version of our tool xTea (x-Transposable element analyzer) that incorporates a deep-learning module, we identified 162 DNRTs, as well as 2 pseudogene insertions. Several variants are likely to be causal, such as a de novo Alu insertion that led to the ablation of a whole exon in the NF1 gene in a proband with brain tumor. We observe a high de novo SVA insertion burden in both high-intolerance loss-of-function genes and exons as well as more frequent de novo Alu insertions of paternal origin. We also identify potential mosaic DNRTs from embryonic stages. Our study reveals the important roles of DNRTs in causing birth defects and predisposition to childhood cancers.
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Affiliation(s)
- Chong Chu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Viktor Ljungström
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Antuan Tran
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Hu Jin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Peter J. Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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26
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Goldberg ME, Noyes MD, Eichler EE, Quinlan AR, Harris K. Effects of parental age and polymer composition on short tandem repeat de novo mutation rates. Genetics 2024; 226:iyae013. [PMID: 38298127 PMCID: PMC10990422 DOI: 10.1093/genetics/iyae013] [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: 08/11/2023] [Revised: 08/11/2023] [Accepted: 01/05/2024] [Indexed: 02/02/2024] Open
Abstract
Short tandem repeats (STRs) are hotspots of genomic variability in the human germline because of their high mutation rates, which have long been attributed largely to polymerase slippage during DNA replication. This model suggests that STR mutation rates should scale linearly with a father's age, as progenitor cells continually divide after puberty. In contrast, it suggests that STR mutation rates should not scale with a mother's age at her child's conception, since oocytes spend a mother's reproductive years arrested in meiosis II and undergo a fixed number of cell divisions that are independent of the age at ovulation. Yet, mirroring recent findings, we find that STR mutation rates covary with paternal and maternal age, implying that some STR mutations are caused by DNA damage in quiescent cells rather than polymerase slippage in replicating progenitor cells. These results echo the recent finding that DNA damage in oocytes is a significant source of de novo single nucleotide variants and corroborate evidence of STR expansion in postmitotic cells. However, we find that the maternal age effect is not confined to known hotspots of oocyte mutagenesis, nor are postzygotic mutations likely to contribute significantly. STR nucleotide composition demonstrates divergent effects on de novo mutation (DNM) rates between sexes. Unlike the paternal lineage, maternally derived DNMs at A/T STRs display a significantly greater association with maternal age than DNMs at G/C-containing STRs. These observations may suggest the mechanism and developmental timing of certain STR mutations and contradict prior attribution of replication slippage as the primary mechanism of STR mutagenesis.
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Affiliation(s)
- Michael E Goldberg
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Departments of Human Genetics and Biomedical Informatics, University of Utah, Salt Lake City, UT 84112, USA
| | - Michelle D Noyes
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Aaron R Quinlan
- Departments of Human Genetics and Biomedical Informatics, University of Utah, Salt Lake City, UT 84112, USA
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Computational Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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27
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Ren P, Zhang J, Vijg J. Somatic mutations in aging and disease. GeroScience 2024:10.1007/s11357-024-01113-3. [PMID: 38488948 DOI: 10.1007/s11357-024-01113-3] [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: 10/11/2023] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
Time always leaves its mark, and our genome is no exception. Mutations in the genome of somatic cells were first hypothesized to be the cause of aging in the 1950s, shortly after the molecular structure of DNA had been described. Somatic mutation theories of aging are based on the fact that mutations in DNA as the ultimate template for all cellular functions are irreversible. However, it took until the 1990s to develop the methods to test if DNA mutations accumulate with age in different organs and tissues and estimate the severity of the problem. By now, numerous studies have documented the accumulation of somatic mutations with age in normal cells and tissues of mice, humans, and other animals, showing clock-like mutational signatures that provide information on the underlying causes of the mutations. In this review, we will first briefly discuss the recent advances in next-generation sequencing that now allow quantitative analysis of somatic mutations. Second, we will provide evidence that the mutation rate differs between cell types, with a focus on differences between germline and somatic mutation rate. Third, we will discuss somatic mutational signatures as measures of aging, environmental exposure, and activities of DNA repair processes. Fourth, we will explain the concept of clonally amplified somatic mutations, with a focus on clonal hematopoiesis. Fifth, we will briefly discuss somatic mutations in the transcriptome and in our other genome, i.e., the genome of mitochondria. We will end with a brief discussion of a possible causal contribution of somatic mutations to the aging process.
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Affiliation(s)
- Peijun Ren
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jie Zhang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jan Vijg
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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28
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Gao Y, Zhang X, Chen H, Lu Y, Ma S, Yang Y, Zhang M, Xu S. Reconstructing the ancestral gene pool to uncover the origins and genetic links of Hmong-Mien speakers. BMC Biol 2024; 22:59. [PMID: 38475771 PMCID: PMC10935854 DOI: 10.1186/s12915-024-01838-9] [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: 10/10/2023] [Accepted: 02/01/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Hmong-Mien (HM) speakers are linguistically related and live primarily in China, but little is known about their ancestral origins or the evolutionary mechanism shaping their genomic diversity. In particular, the lack of whole-genome sequencing data on the Yao population has prevented a full investigation of the origins and evolutionary history of HM speakers. As such, their origins are debatable. RESULTS Here, we made a deep sequencing effort of 80 Yao genomes, and our analysis together with 28 East Asian populations and 968 ancient Asian genomes suggested that there is a strong genetic basis for the formation of the HM language family. We estimated that the most recent common ancestor dates to 5800 years ago, while the genetic divergence between the HM and Tai-Kadai speakers was estimated to be 8200 years ago. We proposed that HM speakers originated from the Yangtze River Basin and spread with agricultural civilization. We identified highly differentiated variants between HM and Han Chinese, in particular, a deafness-related missense variant (rs72474224) in the GJB2 gene is in a higher frequency in HM speakers than in others. CONCLUSIONS Our results indicated complex gene flow and medically relevant variants involved in the HM speakers' evolution history.
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Affiliation(s)
- Yang Gao
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xiaoxi Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Hao Chen
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Sen Ma
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yajun Yang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Menghan Zhang
- Institute of Modern Languages and Linguistics, and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China.
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29
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Lecoquierre F, Cassinari K, Drouot N, May A, Fourneaux S, Charbonnier F, Derambure C, Coutant S, Saugier-Veber P, Hoischen A, Charbonnier C, Nicolas G. Assessment of parental mosaicism rates in neurodevelopmental disorders caused by apparent de novo pathogenic variants using deep sequencing. Sci Rep 2024; 14:5289. [PMID: 38438430 PMCID: PMC10912112 DOI: 10.1038/s41598-024-53358-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/31/2024] [Indexed: 03/06/2024] Open
Abstract
While de novo variants (DNV) are overall at low risk of recurrence in subsequent pregnancies, a subset is at high risk due to parental mosaicism. Accurately identifying cases of parental mosaicism is therefore important for genetic counseling in clinical care. Some studies have investigated the rate of parental mosaics, but most were either limited by the sensitivity of the techniques (i.e. exome or genome sequencing), or focused on specific types of disease such as epileptic syndromes. This study aimed to determine the proportion of parental mosaicism among the DNV causing neurodevelopmental disorders (NDDs) in a series not enriched in epilepsy syndromes. We collected 189 patients with NDD-associated DNV. We applied a smMIP enrichment method and sequenced parental blood DNA samples to an average depth of 7000x. Power simulation indicated that mosaicism with an allelic fraction of 0.5% would have been detected for 87% of positions with 90% power. We observed seven parental mosaic variants (3.7% of families), of which four (2.1% of families) had an allelic fraction of less than 1%. In total, our study identifies a relatively low proportion of parental mosaicism in NDD-associated DNVs and raises the question of a biological mechanism behind the higher rates of parental mosaicism detected in other studies, particularly those focusing on epileptic syndromes.
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Affiliation(s)
- François Lecoquierre
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France.
- Centre de Ressources Biologiques institutionnel du CHU de Rouen - Biothèque filière génétique, Rouen, France.
| | - Kévin Cassinari
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Nathalie Drouot
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Angèle May
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Steeve Fourneaux
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Francoise Charbonnier
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Celine Derambure
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Sophie Coutant
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Camille Charbonnier
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Gaël Nicolas
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
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Giannubilo SR, Marzioni D, Tossetta G, Montironi R, Meccariello ML, Ciavattini A. The "Bad Father": Paternal Role in Biology of Pregnancy and in Birth Outcome. BIOLOGY 2024; 13:165. [PMID: 38534435 DOI: 10.3390/biology13030165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/21/2024] [Accepted: 02/29/2024] [Indexed: 03/28/2024]
Abstract
Pregnancy is generally studied as a biological interaction between a mother and a fetus; however, the father, with his characteristics, lifestyle, genetics, and living environment, is by no means unrelated to the outcome of pregnancy. The half of the fetal genetic heritage of paternal derivation can be decisive in cases of inherited chromosomal disorders, and can be the result of de novo genetic alterations. In addition to the strictly pathological aspects, paternal genetics may transmit thrombophilic traits that affect the implantation and vascular construction of the feto-placental unit, lead to placenta-mediated diseases such as pre-eclampsia and fetal growth retardation, and contribute to the multifactorial genesis of preterm delivery. Biological aspects of immunological tolerance to paternal antigens also appear to be crucial for these pathologies. Finally, this review describes the biological findings by which the environment, exposure to pathogens, lifestyle, and nutritional style of the father affect fetal pathophysiological and epigenetic definition.
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Affiliation(s)
- Stefano Raffaele Giannubilo
- Clinic of Obstetrics and Gynaecology, Department of Clinical Sciences, Università Politecnica Delle Marche, 60123 Ancona, Italy
| | - Daniela Marzioni
- Department of Experimental and Clinical Medicine, Università Politecnica Delle Marche, 60126 Ancona, Italy
| | - Giovanni Tossetta
- Department of Experimental and Clinical Medicine, Università Politecnica Delle Marche, 60126 Ancona, Italy
| | - Ramona Montironi
- Clinic of Obstetrics and Gynaecology, Department of Clinical Sciences, Università Politecnica Delle Marche, 60123 Ancona, Italy
| | - Maria Liberata Meccariello
- Clinic of Obstetrics and Gynaecology, Department of Clinical Sciences, Università Politecnica Delle Marche, 60123 Ancona, Italy
| | - Andrea Ciavattini
- Clinic of Obstetrics and Gynaecology, Department of Clinical Sciences, Università Politecnica Delle Marche, 60123 Ancona, Italy
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Yin S, Zhou Y, Zhao C, Yang J, Yuan P, Zhao Y, Qi H, Wei Y. Association of Paternal Age Alone and Combined with Maternal Age with Perinatal Outcomes: A Prospective Multicenter Cohort Study in China. J Epidemiol Glob Health 2024; 14:120-130. [PMID: 38190051 PMCID: PMC11043302 DOI: 10.1007/s44197-023-00175-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/30/2023] [Indexed: 01/09/2024] Open
Abstract
Maternal and paternal age at birth is increasing globally. Maternal age may affect perinatal outcomes, but the effect of paternal age and its joint effect with maternal age are not well established. This prospective, multicenter, cohort analysis used data from the University Hospital Advanced Age Pregnant Cohort Study in China from 2016 to 2021, to investigate the separate association of paternal age and joint association of paternal and maternal age with adverse perinatal outcomes. Of 16,114 singleton deliveries, mean paternal and maternal age (± SD) was 38.0 ± 5.3 years and 36.0 ± 4.1 years. In unadjusted analyses, older paternal age was associated with increased risks of gestational diabetes mellitus (GDM), hypertensive disorders of pregnancy, preeclampsia, placenta accreta spectrum disorders, placenta previa, cesarean delivery (CD), and postpartum hemorrhage, preterm birth (PTB), large-for-gestational-age, macrosomia, and congenital anomaly, except for small-for-gestational-age. In multivariable analyses, the associations turned to null for most outcomes, and attenuated but still significant for GDM, CD, PTB, and macrosomia. As compare to paternal age of < 30 years, the risks in older paternal age groups increased by 31-45% for GDM, 17-33% for CD, 32-36% for PTB, and 28-31% for macrosomia. The predicted probabilities of GDM, placenta previa, and CD increased rapidly with paternal age up to thresholds of 36.4-40.3 years, and then plateaued or decelerated. The risks of GDM, CD, and PTB were much greater for pregnancies with younger paternal and older maternal age, despite no statistical interaction between the associations related to paternal and maternal age. Our findings support the advocation that paternal age, besides maternal age, should be considered during preconception counseling.Trial Registration NCT03220750, Registered July 18, 2017-Retrospectively registered, https://classic.clinicaltrials.gov/ct2/show/NCT03220750 .
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Affiliation(s)
- Shaohua Yin
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrical and Gynecology, National Center for Healthcare Quality Management in Obstetrics, Peking University Third Hospital, Haidian District, 49 North Garden Rd., Beijing, 100191, China
- National Clinical Research Center for Obstetrical and Gynecology, Peking University Third Hospital, Beijing, 100191, China
| | - Yubo Zhou
- Institute of Reproductive and Child Health/National Health Commission Key Laboratory of Reproductive Health, Peking University Health Science Center, Beijing, 100191, China
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, 100191, China
| | - Cheng Zhao
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrical and Gynecology, National Center for Healthcare Quality Management in Obstetrics, Peking University Third Hospital, Haidian District, 49 North Garden Rd., Beijing, 100191, China
- National Clinical Research Center for Obstetrical and Gynecology, Peking University Third Hospital, Beijing, 100191, China
| | - Jing Yang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrical and Gynecology, National Center for Healthcare Quality Management in Obstetrics, Peking University Third Hospital, Haidian District, 49 North Garden Rd., Beijing, 100191, China
- National Clinical Research Center for Obstetrical and Gynecology, Peking University Third Hospital, Beijing, 100191, China
| | - Pengbo Yuan
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrical and Gynecology, National Center for Healthcare Quality Management in Obstetrics, Peking University Third Hospital, Haidian District, 49 North Garden Rd., Beijing, 100191, China
- National Clinical Research Center for Obstetrical and Gynecology, Peking University Third Hospital, Beijing, 100191, China
| | - Yangyu Zhao
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrical and Gynecology, National Center for Healthcare Quality Management in Obstetrics, Peking University Third Hospital, Haidian District, 49 North Garden Rd., Beijing, 100191, China
- National Clinical Research Center for Obstetrical and Gynecology, Peking University Third Hospital, Beijing, 100191, China
| | - Hongbo Qi
- Department of Obstetrics, Women and Children's Hospital of Chongqing Medical University, No. 120 Longshan Road, Yubei District, Chongqing, 400021, China.
| | - Yuan Wei
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrical and Gynecology, National Center for Healthcare Quality Management in Obstetrics, Peking University Third Hospital, Haidian District, 49 North Garden Rd., Beijing, 100191, China.
- National Clinical Research Center for Obstetrical and Gynecology, Peking University Third Hospital, Beijing, 100191, China.
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Eskelinen S, Halt AH, Hakko H, Riipinen P, Riala K. The association of family size and birth order in adolescence to the likelihood of developing psychotic disorders in young adulthood: A follow-up study of former adolescent inpatients. Psychiatry Res 2024; 333:115719. [PMID: 38219349 DOI: 10.1016/j.psychres.2024.115719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/14/2023] [Accepted: 01/03/2024] [Indexed: 01/16/2024]
Abstract
This is a clinical follow-up study of 508 former adolescent psychiatric inpatients admitted to hospital between 2001 and 2006 in Northern Finland. The participants were interviewed using the K-SADS-PL and the EuropASI instruments. Until 2016, the national Finnish Care Register for Health Care provided data on psychiatric diagnoses. Using logistic regression analysis, we examined how birth order and childhood family size affected the incidence of schizophrenia spectrum disorder (SSD) and other psychotic disorders by young adulthood. Participants were separated into three diagnostic subgroups 1) participants with SSD (n = 76), 2) participants with a psychotic disorder other than SSD (n = 107) and 3) participants with only one nonpsychotic depressive episode (n = 118). The main conclusions were that large family size in adolescence (six or more children), male sex and father having psychiatric problems or being unemployed, were significantly associated with a higher likelihood of SSD among study participants. Large family size also associated to a higher likelihood of developing other psychotic disorders. Being the first born or an only child reduced the likelihood of psychotic disorders other than SSD. When diagnosing and treating children and teenagers with psychotic symptoms, information regarding their family size and sibling position may be relevant.
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Affiliation(s)
- Siiri Eskelinen
- Research Unit of Clinical Medicine, Psychiatry, University of Oulu, P.O.BOX 5000, 90014, Oulu, Finland
| | - Anu-Helmi Halt
- Research Unit of Clinical Medicine, Psychiatry, University of Oulu, P.O.BOX 5000, 90014, Oulu, Finland; Department of Psychiatry, Oulu University Hospital, Oulu, P.O.BOX 26, 90029 Oulu, Finland
| | - Helinä Hakko
- Department of Psychiatry, Oulu University Hospital, Oulu, P.O.BOX 26, 90029 Oulu, Finland
| | - Pirkko Riipinen
- Research Unit of Clinical Medicine, Psychiatry, University of Oulu, P.O.BOX 5000, 90014, Oulu, Finland; Department of Psychiatry, Oulu University Hospital, Oulu, P.O.BOX 26, 90029 Oulu, Finland
| | - Kaisa Riala
- Research Unit of Clinical Medicine, Psychiatry, University of Oulu, P.O.BOX 5000, 90014, Oulu, Finland.
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Guan J, Wu X, Zhang J, Li J, Wang H, Wang Q. Global research landscape on the contribution of de novo mutations to human genetic diseases over the past 20 years: bibliometric analysis. J Neurogenet 2024; 38:9-18. [PMID: 38647210 DOI: 10.1080/01677063.2024.2335171] [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: 01/12/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
As the contribution of de novo mutations (DNMs) to human genetic diseases has been gradually uncovered, analyzing the global research landscape over the past 20 years is essential. Because of the large and rapidly increasing number of publications in this field, understanding the current landscape of the contribution of DNMs in the human genome to genetic diseases remains a challenge. Bibliometric analysis provides an approach for visualizing these studies using information in published records in a specific field. This study aimed to illustrate the current global research status and explore trends in the field of DNMs underlying genetic diseases. Bibliometric analyses were performed using the Bibliometrix Package based on the R language version 4.1.3 and CiteSpace version 6.1.R2 software for publications from 2000 to 2021 indexed under the Web of Science Core Collection (WoSCC) about DNMs underlying genetic diseases on 17 September 2022. We identified 3435 records, which were published in 731 journals by 26,538 authors from 6052 institutes in 66 countries. There was an upward trend in the number of publications since 2013. The USA, China, and Germany contributed the majority of the records included. The University of Washington, Columbia University, and Baylor College of Medicine were the top-producing institutions. Evan E Eichler of the University of Washington, Stephan J Sanders of the Yale University School of Medicine, and Ingrid E Scheffer of the University of Melbourne were the most high-ranked authors. Keyword co-occurrence analysis suggested that DNMs in neurodevelopmental disorders and intellectual disabilities were research hotspots and trends. In conclusion, our data show that DNMs have a significant effect on human genetic diseases, with a noticeable increase in annual publications over the last 5 years. Furthermore, potential hotspots are shifting toward understanding the causative role and clinical interpretation of newly identified or low-frequency DNMs observed in patients.
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Affiliation(s)
- Jing Guan
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Xiaonan Wu
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Jiao Zhang
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Jin Li
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Hongyang Wang
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Qiuju Wang
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
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La Rocca LA, Frank J, Bentzen HB, Pantel JT, Gerischer K, Bovier A, Krawitz PM. Understanding recessive disease risk in multi-ethnic populations with different degrees of consanguinity. Am J Med Genet A 2024; 194:e63452. [PMID: 37921563 DOI: 10.1002/ajmg.a.63452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023]
Abstract
Population medical genetics aims at translating clinically relevant findings from recent studies of large cohorts into healthcare for individuals. Genetic counseling concerning reproductive risks and options is still mainly based on family history, and consanguinity is viewed to increase the risk for recessive diseases regardless of the demographics. However, in an increasingly multi-ethnic society with diverse approaches to partner selection, healthcare professionals should also sharpen their intuition for the influence of different mating schemes in non-equilibrium dynamics. We, therefore, revisited the so-called out-of-Africa model and studied in forward simulations with discrete and not overlapping generations the effect of inbreeding on the average number of recessive lethals in the genome. We were able to reproduce in both frameworks the drop in the incidence of recessive disorders, which is a transient phenomenon during and after the growth phase of a population, and therefore showed their equivalence. With the simulation frameworks, we also provide the means to study and visualize the effect of different kin sizes and mating schemes on these parameters for educational purposes.
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Affiliation(s)
- Luis A La Rocca
- Institute for Applied Mathematics, University of Bonn, Bonn, Germany
| | - Julia Frank
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Heidi Beate Bentzen
- Centre for Medical Ethics, Faculty of Medicine, Univeristy of Oslo, Oslo, Norway
| | - Jean Tori Pantel
- Department of Digitalization and General Practice, University Hospital RWTH Aachen, Aachen, Germany
| | - Konrad Gerischer
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Anton Bovier
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Peter M Krawitz
- Institute for Applied Mathematics, University of Bonn, Bonn, Germany
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Buffalo V, Kern AD. A quantitative genetic model of background selection in humans. PLoS Genet 2024; 20:e1011144. [PMID: 38507461 PMCID: PMC10984650 DOI: 10.1371/journal.pgen.1011144] [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: 09/17/2023] [Revised: 04/01/2024] [Accepted: 01/19/2024] [Indexed: 03/22/2024] Open
Abstract
Across the human genome, there are large-scale fluctuations in genetic diversity caused by the indirect effects of selection. This "linked selection signal" reflects the impact of selection according to the physical placement of functional regions and recombination rates along chromosomes. Previous work has shown that purifying selection acting against the steady influx of new deleterious mutations at functional portions of the genome shapes patterns of genomic variation. To date, statistical efforts to estimate purifying selection parameters from linked selection models have relied on classic Background Selection theory, which is only applicable when new mutations are so deleterious that they cannot fix in the population. Here, we develop a statistical method based on a quantitative genetics view of linked selection, that models how polygenic additive fitness variance distributed along the genome increases the rate of stochastic allele frequency change. By jointly predicting the equilibrium fitness variance and substitution rate due to both strong and weakly deleterious mutations, we estimate the distribution of fitness effects (DFE) and mutation rate across three geographically distinct human samples. While our model can accommodate weaker selection, we find evidence of strong selection operating similarly across all human samples. Although our quantitative genetic model of linked selection fits better than previous models, substitution rates of the most constrained sites disagree with observed divergence levels. We find that a model incorporating selective interference better predicts observed divergence in conserved regions, but overall our results suggest uncertainty remains about the processes generating fitness variation in humans.
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Affiliation(s)
- Vince Buffalo
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
- Institute of Ecology and Evolution and Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Andrew D. Kern
- Institute of Ecology and Evolution and Department of Biology, University of Oregon, Eugene, Oregon, United States of America
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Lopes-Marques M, Mort M, Carneiro J, Azevedo A, Amaro AP, Cooper DN, Azevedo L. Meta-analysis of 46,000 germline de novo mutations linked to human inherited disease. Hum Genomics 2024; 18:20. [PMID: 38395944 PMCID: PMC10885371 DOI: 10.1186/s40246-024-00587-8] [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: 11/10/2023] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND De novo mutations (DNMs) are variants that occur anew in the offspring of noncarrier parents. They are not inherited from either parent but rather result from endogenous mutational processes involving errors of DNA repair/replication. These spontaneous errors play a significant role in the causation of genetic disorders, and their importance in the context of molecular diagnostic medicine has become steadily more apparent as more DNMs have been reported in the literature. In this study, we examined 46,489 disease-associated DNMs annotated by the Human Gene Mutation Database (HGMD) to ascertain their distribution across gene and disease categories. RESULTS Most disease-associated DNMs reported to date are found to be associated with developmental and psychiatric disorders, a reflection of the focus of sequencing efforts over the last decade. Of the 13,277 human genes in which DNMs have so far been found, the top-10 genes with the highest proportions of DNM relative to gene size were H3-3 A, DDX3X, CSNK2B, PURA, ZC4H2, STXBP1, SCN1A, SATB2, H3-3B and TUBA1A. The distribution of CADD and REVEL scores for both disease-associated DNMs and those mutations not reported to be de novo revealed a trend towards higher deleteriousness for DNMs, consistent with the likely lower selection pressure impacting them. This contrasts with the non-DNMs, which are presumed to have been subject to continuous negative selection over multiple generations. CONCLUSION This meta-analysis provides important information on the occurrence and distribution of disease-associated DNMs in association with heritable disease and should make a significant contribution to our understanding of this major type of mutation.
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Affiliation(s)
- Mónica Lopes-Marques
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - João Carneiro
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - António Azevedo
- CHUdSA-Centro Hospitalar Universitário de Santo António, Porto, Portugal
- UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - Andreia P Amaro
- UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Luísa Azevedo
- UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal.
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal.
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Nakamura T, Ueda J, Mizuno S, Honda K, Kazuno AA, Yamamoto H, Hara T, Takata A. Topologically associating domains define the impact of de novo promoter variants on autism spectrum disorder risk. CELL GENOMICS 2024; 4:100488. [PMID: 38280381 PMCID: PMC10879036 DOI: 10.1016/j.xgen.2024.100488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/24/2023] [Accepted: 01/02/2024] [Indexed: 01/29/2024]
Abstract
Whole-genome sequencing (WGS) studies of autism spectrum disorder (ASD) have demonstrated the roles of rare promoter de novo variants (DNVs). However, most promoter DNVs in ASD are not located immediately upstream of known ASD genes. In this study analyzing WGS data of 5,044 ASD probands, 4,095 unaffected siblings, and their parents, we show that promoter DNVs within topologically associating domains (TADs) containing ASD genes are significantly and specifically associated with ASD. An analysis considering TADs as functional units identified specific TADs enriched for promoter DNVs in ASD and indicated that common variants in these regions also confer ASD heritability. Experimental validation using human induced pluripotent stem cells (iPSCs) showed that likely deleterious promoter DNVs in ASD can influence multiple genes within the same TAD, resulting in overall dysregulation of ASD-associated genes. These results highlight the importance of TADs and gene-regulatory mechanisms in better understanding the genetic architecture of ASD.
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Affiliation(s)
- Takumi Nakamura
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Junko Ueda
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Shota Mizuno
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kurara Honda
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - An-A Kazuno
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hirona Yamamoto
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Tomonori Hara
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Organ Anatomy, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Atsushi Takata
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan.
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Lin I, Wei A, Gebo TA, Boutros PC, Flanagan M, Kucine N, Cunniff C, Arboleda VA, Chang VY. Increased Frequency of Clonal Hematopoiesis of Indeterminate Potential in Bloom Syndrome Probands and Carriers. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.02.24302163. [PMID: 38370823 PMCID: PMC10871368 DOI: 10.1101/2024.02.02.24302163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Background Bloom Syndrome (BSyn) is an autosomal recessive disorder caused by biallelic germline variants in BLM, which functions to maintain genomic stability. BSyn patients have poor growth, immune defects, insulin resistance, and a significantly increased risk of malignancies, most commonly hematologic. The malignancy risk in carriers of pathogenic variants in BLM (BLM variant carriers) remains understudied. Clonal hematopoiesis of indeterminate potential (CHIP) is defined by presence of somatic mutations in leukemia-related genes in blood of individuals without leukemia and is associated with increased risk of leukemia. We hypothesize that somatic mutations driving clonal expansion may be an underlying mechanism leading to increased cancer risk in BSyn patients and BLM variant carriers. Methods To determine whether de novo or somatic variation is increased in BSyn patients or carriers, we performed and analyzed exome sequencing on BSyn and control trios. Results We discovered that both BSyn patients and carriers had increased numbers of low-frequency, putative somatic variants in CHIP genes compared to controls. Furthermore, BLM variant carriers had increased numbers of somatic variants in DNA methylation genes compared to controls. There was no statistical difference in the numbers of de novo variants in BSyn probands compared to control probands. Conclusion Our findings of increased CHIP in BSyn probands and carriers suggest that one or two germline pathogenic variants in BLM could be sufficient to increase the risk of clonal hematopoiesis. These findings warrant further studies in larger cohorts to determine the significance of CHIP as a potential biomarker of aging, cancer, cardiovascular disease, morbidity and mortality.
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Affiliation(s)
- Isabella Lin
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA
| | - Angela Wei
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA
- Interdepartmental BioInformatics Program, UCLA
| | - Tsumugi A Gebo
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA
- Institute for Precision Health, University of California Los Angeles, Los Angeles, CA
| | - P C Boutros
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Interdepartmental BioInformatics Program, UCLA
- Department of Urology, University of California Los Angeles, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA
- Institute for Precision Health, University of California Los Angeles, Los Angeles, CA
- Molecular Biology Institute, University of California, Los Angeles, CA
| | - Maeve Flanagan
- Department of Pediatrics, Weill Cornell Medicine, New York, NY
| | - Nicole Kucine
- Department of Pediatrics, Weill Cornell Medicine, New York, NY
| | - C Cunniff
- Department of Pediatrics, Weill Cornell Medicine, New York, NY
| | - V A Arboleda
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA
- Interdepartmental BioInformatics Program, UCLA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA
- Institute for Precision Health, University of California Los Angeles, Los Angeles, CA
- Molecular Biology Institute, University of California, Los Angeles, CA
| | - V Y Chang
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA
- Institute for Precision Health, University of California Los Angeles, Los Angeles, CA
- Division of Pediatric Hematology/Oncology, UCLA, Los Angeles, CA
- Children's Discovery and Innovation Institute, UCLA, Los Angeles, CA
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Brignola C, Volorio S, De Vecchi G, Zaffaroni D, Dall’Olio V, Mariette F, Sardella D, Capra F, Signoroni S, Rausa E, Vitellaro M, Pensotti V, Ricci MT. De novo germline pathogenic variant in Lynch Syndrome: A rare event or the tip of the iceberg? TUMORI JOURNAL 2024; 110:69-73. [PMID: 37691472 PMCID: PMC10851626 DOI: 10.1177/03008916231197113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/28/2023] [Accepted: 08/08/2023] [Indexed: 09/12/2023]
Abstract
Lynch Syndrome is an autosomal dominant cancer predisposition syndrome caused by germline pathogenic variants or epimutation in one of the DNA mismatch repair genes. De novo pathogenic variants in mismatch repair genes have been described as a rare event in Lynch Syndrome (1-5%), although the prevalence of de novo pathogenic variants in Lynch Syndrome is probably underestimated. The de novo pathogenic variant was identified in a 26-year-old woman diagnosed with an adenocarcinoma of the caecum with mismatch repair protein deficiency at immunohistochemistry and a synchronous neuroendocrine tumor of the appendix with normal expression of mismatch repair proteins. DNA testing revealed deletion of exon 6 of the MLH1 gene. It appeared to be a de novo event, as the deletion was not detected in the patient's parents. The presence of a mosaicism in the patient was excluded and haplotype analysis demonstrated the paternal origin of the chromosome harboring the deletion. The de novo deletion probably originated either from a very early postzygotic or a single prezygotic mutational event, or from a gonadal mosaicism. In conclusion, the identification of de novo pathogenic variants is crucial to allow proper genetic counseling and appropriate management of the patient's family.
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Affiliation(s)
- Clorinda Brignola
- Unit of Hereditary Digestive Tract Tumors, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sara Volorio
- Cancer Genetics Test Laboratory, Cogentech s.r.l. Società Benefit a Socio Unico, Milan, Italy
| | - Giovanna De Vecchi
- Cancer Genetics Test Laboratory, Cogentech s.r.l. Società Benefit a Socio Unico, Milan, Italy
| | - Daniela Zaffaroni
- Unit of Hereditary Digestive Tract Tumors, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Valentina Dall’Olio
- Cancer Genetics Test Laboratory, Cogentech s.r.l. Società Benefit a Socio Unico, Milan, Italy
| | - Frederique Mariette
- Cancer Genetics Test Laboratory, Cogentech s.r.l. Società Benefit a Socio Unico, Milan, Italy
| | - Domenico Sardella
- Cancer Genetics Test Laboratory, Cogentech s.r.l. Società Benefit a Socio Unico, Milan, Italy
| | - Fabio Capra
- Cancer Genetics Test Laboratory, Cogentech s.r.l. Società Benefit a Socio Unico, Milan, Italy
| | - Stefano Signoroni
- Unit of Hereditary Digestive Tract Tumors, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Emanuele Rausa
- Unit of Hereditary Digestive Tract Tumors, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Marco Vitellaro
- Unit of Hereditary Digestive Tract Tumors, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Valeria Pensotti
- Cancer Genetics Test Laboratory, Cogentech s.r.l. Società Benefit a Socio Unico, Milan, Italy
| | - Maria Teresa Ricci
- Unit of Hereditary Digestive Tract Tumors, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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Wang SH, Lin MC, Wu CS, Chen PC, Thompson WK, Fan CC. Familial factors rather than paternal age contribute to the aetiology of epilepsy. Int J Epidemiol 2024; 53:dyad191. [PMID: 38199793 DOI: 10.1093/ije/dyad191] [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: 02/04/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Whether paternal age associated with offspring's epilepsy risk is a cause of de novo mutation as men age, or just an association due to confounding factors, is still unclear. METHODS We performed a population-based, multi-generation and sibling comparison study in Taiwan, which included 2 751 232 singletons born in 2001-17 who were followed until 2020. Of these, 819 371/826 087 with information on paternal/maternal grandparents were selected for multi-generation analyses and 1 748 382 with sibling(s) were selected for sibling comparison. Cox proportional hazard regression was used to estimate the hazard ratio (HR) and 95% confidence interval (CI). RESULTS In the total cohort, there was an increased risk of epilepsy in individuals with advanced paternal age, e.g. the HR for paternal age ≥50 was1.36 (95% CI: 1.15-1.61) compared with paternal age 25-29, and fathers older than mothers, e.g. the HR for parental age difference ≥15 years was 1.29 (95% CI: 1.16-1.43). When accounting for parental age difference, the association between paternal age and epilepsy in offspring was attenuated (HR for paternal age ≥50 was 1.11, 95% CI: 0.93-1.34). Multi-generation analyses did not support the association of advanced grand-paternal age at childbirth of the parent with offspring's risk of epilepsy. Sibling comparison analyses did not support the association of older paternal age with increased risk of epilepsy (HR was 0.96 for per year increase in paternal age, 95% CI: 0.96-0.97). CONCLUSIONS These results do not support the hypothesis that advanced paternal age is associated with epilepsy in offspring. Instead, familial factors may explain the observed paternal age association with the offspring's risk of epilepsy.
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Affiliation(s)
- Shi-Heng Wang
- National Center for Geriatrics and Welfare Research, National Health Research Institutes, Zhunan, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Mei-Chen Lin
- National Center for Geriatrics and Welfare Research, National Health Research Institutes, Zhunan, Taiwan
| | - Chi-Shin Wu
- National Center for Geriatrics and Welfare Research, National Health Research Institutes, Zhunan, Taiwan
- Department of Psychiatry, National Taiwan University Hospital, Yunlin Branch, Douliu, Taiwan
| | - Pei-Chun Chen
- National Center for Geriatrics and Welfare Research, National Health Research Institutes, Zhunan, Taiwan
| | - Wesley K Thompson
- Center for Population Neuroscience and Genetics, Laureate Institute for Brain Research, Tulsa, OK, USA
| | - Chun-Chieh Fan
- Center for Population Neuroscience and Genetics, Laureate Institute for Brain Research, Tulsa, OK, USA
- Department of Radiology, School of Medicine, University of California San Diego, La Jolla, CA, USA
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Moura S, Hartl I, Brumovska V, Calabrese PP, Yasari A, Striedner Y, Bishara M, Mair T, Ebner T, Schütz GJ, Sevcsik E, Tiemann-Boege I. Exploring FGFR3 Mutations in the Male Germline: Implications for Clonal Germline Expansions and Paternal Age-Related Dysplasias. Genome Biol Evol 2024; 16:evae015. [PMID: 38411226 PMCID: PMC10898338 DOI: 10.1093/gbe/evae015] [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: 01/19/2024] [Indexed: 02/28/2024] Open
Abstract
Delayed fatherhood results in a higher risk of inheriting a new germline mutation that might result in a congenital disorder in the offspring. In particular, some FGFR3 mutations increase in frequency with age, but there are still a large number of uncharacterized FGFR3 mutations that could be expanding in the male germline with potentially early- or late-onset effects in the offspring. Here, we used digital polymerase chain reaction to assess the frequency and spatial distribution of 10 different FGFR3 missense substitutions in the sexually mature male germline. Our functional assessment of the receptor signaling of the variants with biophysical methods showed that 9 of these variants resulted in a higher activation of the receptor´s downstream signaling, resulting in 2 different expansion behaviors. Variants that form larger subclonal expansions in a dissected postmortem testis also showed a positive correlation of the substitution frequency with the sperm donor's age, and a high and ligand-independent FGFR3 activation. In contrast, variants that measured high FGFR3 signaling and elevated substitution frequencies independent of the donor's age did not result in measurable subclonal expansions in the testis. This suggests that promiscuous signal activation might also result in an accumulation of mutations before the sexual maturation of the male gonad with clones staying relatively constant in size throughout time. Collectively, these results provide novel insights into our understanding of the mutagenesis of driver mutations and their resulting mosaicism in the male germline with important consequences for the transmission and recurrence of associated disorders.
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Affiliation(s)
- Sofia Moura
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, USA
| | - Ingrid Hartl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | | | - Peter P Calabrese
- Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
| | - Atena Yasari
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Yasmin Striedner
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | | | - Theresa Mair
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Thomas Ebner
- Department of Gynecology, Obstetrics and Gynecological Endocrinology, Johannes Kepler University, 4020 Linz, Austria
| | | | - Eva Sevcsik
- Institute of Applied Physics, TU Wien, Vienna, Austria
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Kimmins S, Anderson RA, Barratt CLR, Behre HM, Catford SR, De Jonge CJ, Delbes G, Eisenberg ML, Garrido N, Houston BJ, Jørgensen N, Krausz C, Lismer A, McLachlan RI, Minhas S, Moss T, Pacey A, Priskorn L, Schlatt S, Trasler J, Trasande L, Tüttelmann F, Vazquez-Levin MH, Veltman JA, Zhang F, O'Bryan MK. Frequency, morbidity and equity - the case for increased research on male fertility. Nat Rev Urol 2024; 21:102-124. [PMID: 37828407 DOI: 10.1038/s41585-023-00820-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2023] [Indexed: 10/14/2023]
Abstract
Currently, most men with infertility cannot be given an aetiology, which reflects a lack of knowledge around gamete production and how it is affected by genetics and the environment. A failure to recognize the burden of male infertility and its potential as a biomarker for systemic illness exists. The absence of such knowledge results in patients generally being treated as a uniform group, for whom the strategy is to bypass the causality using medically assisted reproduction (MAR) techniques. In doing so, opportunities to prevent co-morbidity are missed and the burden of MAR is shifted to the woman. To advance understanding of men's reproductive health, longitudinal and multi-national centres for data and sample collection are essential. Such programmes must enable an integrated view of the consequences of genetics, epigenetics and environmental factors on fertility and offspring health. Definition and possible amelioration of the consequences of MAR for conceived children are needed. Inherent in this statement is the necessity to promote fertility restoration and/or use the least invasive MAR strategy available. To achieve this aim, protocols must be rigorously tested and the move towards personalized medicine encouraged. Equally, education of the public, governments and clinicians on the frequency and consequences of infertility is needed. Health options, including male contraceptives, must be expanded, and the opportunities encompassed in such investment understood. The pressing questions related to male reproductive health, spanning the spectrum of andrology are identified in the Expert Recommendation.
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Affiliation(s)
- Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- The Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
- The Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montreal, Quebec, Canada
| | - Richard A Anderson
- MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK
| | - Christopher L R Barratt
- Division of Systems Medicine, School of Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Hermann M Behre
- Center for Reproductive Medicine and Andrology, University Hospital, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Sarah R Catford
- Hudson Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Obstetrics and Gynaecology, The Royal Women's Hospital, Melbourne, Victoria, Australia
| | | | - Geraldine Delbes
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Sante Biotechnologie, Laval, Quebec, Canada
| | - Michael L Eisenberg
- Department of Urology and Obstetrics and Gynecology, Stanford University, Stanford, CA, USA
| | - Nicolas Garrido
- IVI Foundation, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - Brendan J Houston
- School of BioSciences and Bio21 Institute, The University of Melbourne, Parkville, Melbourne, Australia
| | - Niels Jørgensen
- Department of Growth and Reproduction, International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Csilla Krausz
- Department of Experimental and Clinical Biomedical Sciences, 'Mario Serio', University of Florence, University Hospital of Careggi Florence, Florence, Italy
| | - Ariane Lismer
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Robert I McLachlan
- Hudson Institute of Medical Research and the Department of Obstetrics and Gynaecology, Monash University, Melbourne, Australia
- Monash IVF Group, Richmond, Victoria, Australia
| | - Suks Minhas
- Department of Surgery and Cancer Imperial, London, UK
| | - Tim Moss
- Healthy Male and the Department of Obstetrics and Gynaecology, Monash University, Melbourne, Victoria, Australia
| | - Allan Pacey
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Lærke Priskorn
- Department of Growth and Reproduction, International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Stefan Schlatt
- Centre for Reproductive Medicine and Andrology, University of Münster, Münster, Germany
| | - Jacquetta Trasler
- Departments of Paediatrics, Human Genetics and Pharmacology & Therapeutics, McGill University and Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Leonardo Trasande
- Center for the Investigation of Environmental Hazards, Department of Paediatrics, NYU Grossman School of Medicine, New York, NY, USA
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Mónica Hebe Vazquez-Levin
- Instituto de Biología y Medicina Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Fundación IBYME, Buenos Aires, Argentina
| | - Joris A Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Moira K O'Bryan
- School of BioSciences and Bio21 Institute, The University of Melbourne, Parkville, Melbourne, Australia.
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Pouyan Mehr D, Faraji N, Rezaei S, Keshavarz P. Single-locus and Haplotype Associations of GRIN2B Gene with Autism Spectrum Disorders and the Demographic and Clinical Characteristics of Patients in Guilan, Iran. J Autism Dev Disord 2024; 54:607-614. [PMID: 36399225 DOI: 10.1007/s10803-022-05818-2] [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] [Accepted: 11/05/2022] [Indexed: 11/19/2022]
Abstract
Autism spectrum disorders (ASDs) are described as generalized developmental disorders, with an average age of onset of 36 months. Genetic and environmental factors may contribute to this multifactorial disorder. The present study aimed to investigate the association of three GRIN2B polymorphisms, including rs1019385, rs1024893, and rs3764028, with ASDs. Based on the results, there was a significant difference regarding the genotype frequency of rs3764028 polymorphism between the control and case (ASD) groups (P = 0.027). According to the recessive model, this variant was associated with ASDs (P = 0.23). None of the eight haplotype models with frequencies above 0.5 showed significant differences between the case and control groups in terms of allelic frequency. The present results showed that the rs376028 variant was directly related to the phenotypic symptoms of ASDs.
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Affiliation(s)
- Donya Pouyan Mehr
- Cellular and Molecular Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Niloofar Faraji
- Cellular and Molecular Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Sajjad Rezaei
- Department of Psychology, University of Guilan, Rasht, Iran
| | - Parvaneh Keshavarz
- Cellular and Molecular Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran.
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Gressel GM, Frey MK, Norquist B, Senter L, Blank SV, Urban RR. Germline and somatic testing for ovarian Cancer: An SGO clinical practice statement. Gynecol Oncol 2024; 181:170-178. [PMID: 38215513 DOI: 10.1016/j.ygyno.2023.12.010] [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: 09/29/2023] [Revised: 12/09/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Germline and somatic genetic testing have become critical components of care for people with ovarian cancer. The identification of germline and somatic pathogenic variants as well as homologous recombination deficiency can contribute to the prediction of treatment response, prognostic outcome, and suitability for targeted agents (e.g. poly (ADP-ribose) polymerase (PARP) inhibitors). Furthermore, identifying germline pathogenic variants can prompt cascade genetic testing for at-risk relatives. Despite the clinical benefits and consensus recommendations from several organizations calling for universal genetic testing in ovarian cancer, only about one third of patients complete germline or somatic genetic testing. The members of the Society of Gynecologic Oncology (SGO) Clinical Practice Committee have composed this statement to provide an overview of germline and somatic genetic testing for patients with epithelial ovarian cancer, focusing on available testing modalities and options for care delivery.
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Affiliation(s)
- G M Gressel
- Corewell Health Cancer Center, Division of Gynecologic Oncology, Michigan State University- College of Human Medicine, United States.
| | - M K Frey
- Weill Cornell Medicine, Division of Gynecologic Oncology, United States
| | - B Norquist
- University of Washington School of Medicine, Division of Gynecologic Oncology, United States
| | - L Senter
- The Ohio State University, Comprehensive Cancer Center,United States
| | - S V Blank
- Icahn School of Medicine at Mount Sinai, United States
| | - R R Urban
- University of Washington School of Medicine, Division of Gynecologic Oncology, United States
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45
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Panier S, Wang S, Schumacher B. Genome Instability and DNA Repair in Somatic and Reproductive Aging. ANNUAL REVIEW OF PATHOLOGY 2024; 19:261-290. [PMID: 37832947 DOI: 10.1146/annurev-pathmechdis-051122-093128] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Genetic material is constantly subjected to genotoxic insults and is critically dependent on DNA repair. Genome maintenance mechanisms differ in somatic and germ cells as the soma only requires maintenance during an individual's lifespan, while the germline indefinitely perpetuates its genetic information. DNA lesions are recognized and repaired by mechanistically highly diverse repair machineries. The DNA damage response impinges on a vast array of homeostatic processes and can ultimately result in cell fate changes such as apoptosis or cellular senescence. DNA damage causally contributes to the aging process and aging-associated diseases, most prominently cancer. By causing mutations, DNA damage in germ cells can lead to genetic diseases and impact the evolutionary trajectory of a species. The mechanisms ensuring tight control of germline DNA repair could be highly instructive in defining strategies for improved somatic DNA repair. They may provide future interventions to maintain health and prevent disease during aging.
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Affiliation(s)
- Stephanie Panier
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Siyao Wang
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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46
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Tener SJ, Lin Z, Park SJ, Oraedu K, Ulgherait M, Van Beek E, Martínez-Muñiz A, Pantalia M, Gatto JA, Volpi J, Stavropoulos N, Ja WW, Canman JC, Shirasu-Hiza M. Neuronal knockdown of Cullin3 as a Drosophila model of autism spectrum disorder. Sci Rep 2024; 14:1541. [PMID: 38233464 PMCID: PMC10794434 DOI: 10.1038/s41598-024-51657-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 01/06/2024] [Indexed: 01/19/2024] Open
Abstract
Mutations in Cullin-3 (Cul3), a conserved gene encoding a ubiquitin ligase, are strongly associated with autism spectrum disorder (ASD). Here, we characterize ASD-related pathologies caused by neuron-specific Cul3 knockdown in Drosophila. We confirmed that neuronal Cul3 knockdown causes short sleep, paralleling sleep disturbances in ASD. Because sleep defects and ASD are linked to metabolic dysregulation, we tested the starvation response of neuronal Cul3 knockdown flies; they starved faster and had lower triacylglyceride levels than controls, suggesting defects in metabolic homeostasis. ASD is also characterized by increased biomarkers of oxidative stress; we found that neuronal Cul3 knockdown increased sensitivity to hyperoxia, an exogenous oxidative stress. Additional hallmarks of ASD are deficits in social interactions and learning. Using a courtship suppression assay that measures social interactions and memory of prior courtship, we found that neuronal Cul3 knockdown reduced courtship and learning compared to controls. Finally, we found that neuronal Cul3 depletion alters the anatomy of the mushroom body, a brain region required for memory and sleep. Taken together, the ASD-related phenotypes of neuronal Cul3 knockdown flies establish these flies as a genetic model to study molecular and cellular mechanisms underlying ASD pathology, including metabolic and oxidative stress dysregulation and neurodevelopment.
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Affiliation(s)
- Samantha J Tener
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Zhi Lin
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Scarlet J Park
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Kairaluchi Oraedu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Matthew Ulgherait
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Emily Van Beek
- Waksman Institute, Rutgers University, Piscataway, NJ, 08854, USA
| | - Andrés Martínez-Muñiz
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Meghan Pantalia
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jared A Gatto
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Julia Volpi
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | | | - William W Ja
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Julie C Canman
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Mimi Shirasu-Hiza
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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Ng JK, Turner TN. HAT: de novo variant calling for highly accurate short-read and long-read sequencing data. Bioinformatics 2024; 40:btad775. [PMID: 38175776 PMCID: PMC10777354 DOI: 10.1093/bioinformatics/btad775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 12/05/2023] [Indexed: 01/06/2024] Open
Abstract
MOTIVATION de novo variants (DNVs) are variants that are present in offspring but not in their parents. DNVs are both important for examining mutation rates as well as in the identification of disease-related variation. While efforts have been made to call DNVs, calling of DNVs is still challenging from parent-child sequenced trio data. We developed Hare And Tortoise (HAT) as an automated DNV detection workflow for highly accurate short-read and long-read sequencing data. Reliable detection of DNVs is important for human genomics and HAT addresses this need. RESULTS HAT is a computational workflow that begins with aligned read data (i.e. CRAM or BAM) from a parent-child sequenced trio and outputs DNVs. HAT detects high-quality DNVs from Illumina short-read whole-exome sequencing, Illumina short-read whole-genome sequencing, and highly accurate PacBio HiFi long-read whole-genome sequencing data. The quality of these DNVs is high based on a series of quality metrics including number of DNVs per individual, percent of DNVs at CpG sites, and percent of DNVs phased to the paternal chromosome of origin. AVAILABILITY AND IMPLEMENTATION https://github.com/TNTurnerLab/HAT.
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Affiliation(s)
- Jeffrey K Ng
- Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Tychele N Turner
- Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
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Stendahl AM, Sanghvi R, Peterson S, Ray K, Lima AC, Rahbari R, Conrad DF. A naturally occurring variant of MBD4 causes maternal germline hypermutation in primates. Genome Res 2023; 33:2053-2059. [PMID: 37984997 PMCID: PMC10760519 DOI: 10.1101/gr.277977.123] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023]
Abstract
As part of an ongoing genome sequencing project at the Oregon National Primate Research Center, we identified a rhesus macaque with a rare homozygous frameshift mutation in the gene methyl-CpG binding domain 4, DNA glycosylase (MBD4). MBD4 is responsible for the repair of C > T deamination mutations at CpG dinucleotides and has been linked to somatic hypermutation and cancer predisposition in humans. We show here that MBD4-associated hypermutation also affects the germline: The six offspring of the MBD4-null dam have a fourfold to sixfold increase in de novo mutation burden. This excess burden was predominantly C > T mutations at CpG dinucleotides consistent with MBD4 loss of function in the dam. There was also a significant excess of C > T at CpA sites, indicating an important, unappreciated role for MBD4 to repair deamination in CpA contexts. The MBD4-null dam developed sustained eosinophilia later in life, but we saw no other signs of neoplastic processes associated with MBD4 loss of function in humans nor any obvious disease in the hypermutated offspring. This work provides the first evidence for a genetic factor causing hypermutation in the maternal germline of a mammal and adds to the very small list of naturally occurring variants known to modulate germline mutation rates in mammals.
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Affiliation(s)
- Alexandra M Stendahl
- Division of Genetics, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Rashesh Sanghvi
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Samuel Peterson
- Division of Genetics, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Karina Ray
- Division of Genetics, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Ana C Lima
- Division of Genetics, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Raheleh Rahbari
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Donald F Conrad
- Division of Genetics, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA;
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Goldberg ME, Noyes MD, Eichler EE, Quinlan AR, Harris K. Effects of parental age and polymer composition on short tandem repeat de novo mutation rates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.22.573131. [PMID: 38187618 PMCID: PMC10769404 DOI: 10.1101/2023.12.22.573131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Short tandem repeats (STRs) are hotspots of genomic variability in the human germline because of their high mutation rates, which have long been attributed largely to polymerase slippage during DNA replication. This model suggests that STR mutation rates should scale linearly with a father's age, as progenitor cells continually divide after puberty. In contrast, it suggests that STR mutation rates should not scale with a mother's age at her child's conception, since oocytes spend a mother's reproductive years arrested in meiosis II and undergo a fixed number of cell divisions that are independent of the age at ovulation. Yet, mirroring recent findings, we find that STR mutation rates covary with paternal and maternal age, implying that some STR mutations are caused by DNA damage in quiescent cells rather than the classical mechanism of polymerase slippage in replicating progenitor cells. These results also echo the recent finding that DNA damage in quiescent oocytes is a significant source of de novo SNVs and corroborate evidence of STR expansion in postmitotic cells. However, we find that the maternal age effect is not confined to previously discovered hotspots of oocyte mutagenesis, nor are post-zygotic mutations likely to contribute significantly. STR nucleotide composition demonstrates divergent effects on DNM rates between sexes. Unlike the paternal lineage, maternally derived DNMs at A/T STRs display a significantly greater association with maternal age than DNMs at GC-containing STRs. These observations may suggest the mechanism and developmental timing of certain STR mutations and are especially surprising considering the prior belief in replication slippage as the dominant mechanism of STR mutagenesis.
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Affiliation(s)
- Michael E. Goldberg
- Department of Genome Sciences, University of Washington, 3720 15 Ave NE, Seattle, WA, 98195
- Departments of Human Genetics and Biomedical Informatics, University of Utah, 15 S 2030 E, Salt Lake City, UT, 84112
| | - Michelle D. Noyes
- Department of Genome Sciences, University of Washington, 3720 15 Ave NE, Seattle, WA, 98195
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, 3720 15 Ave NE, Seattle, WA, 98195
- Howard Hughes Medical Institute, 3720 15 Ave NE, University of Washington, Seattle, WA, 98195
| | - Aaron R. Quinlan
- Departments of Human Genetics and Biomedical Informatics, University of Utah, 15 S 2030 E, Salt Lake City, UT, 84112
- These authors contributed equally to this work
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, 3720 15 Ave NE, Seattle, WA, 98195
- Computational Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109
- These authors contributed equally to this work
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50
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Pande S, Majethia P, Nair K, Rao LP, Mascarenhas S, Kaur N, do Rosario MC, Neethukrishna K, Chaurasia A, Hunakunti B, Jadhav N, Xavier S, Kumar J, Bhat V, Bhavani GS, Narayanan DL, Yatheesha BL, Patil SJ, Nampoothiri S, Kamath N, Aroor S, Bhat Y R, Lewis LE, Sharma S, Bajaj S, Sankhyan N, Siddiqui S, Nayak SS, Bielas S, Girisha KM, Shukla A. De novo variants underlying monogenic syndromes with intellectual disability in a neurodevelopmental cohort from India. Eur J Hum Genet 2023:10.1038/s41431-023-01513-7. [PMID: 38114583 DOI: 10.1038/s41431-023-01513-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/21/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023] Open
Abstract
The contribution of de novo variants as a cause of intellectual disability (ID) is well established in several cohorts reported from the developed world. However, the genetic landscape as well as the appropriate testing strategies for identification of de novo variants of these disorders remain largely unknown in low-and middle-income countries like India. In this study, we delineate the clinical and genotypic spectrum of 54 families (55 individuals) with syndromic ID harboring rare de novo variants. We also emphasize on the effectiveness of singleton exome sequencing as a valuable tool for diagnosing these disorders in resource limited settings. Overall, 46 distinct disorders were identified encompassing 46 genes with 51 single-nucleotide variants and/or indels and two copy-number variants. Pathogenic variants were identified in CREBBP, TSC2, KMT2D, MECP2, IDS, NIPBL, NSD1, RIT1, SOX10, BRWD3, FOXG1, BCL11A, KDM6B, KDM5C, SETD5, QRICH1, DCX, SMARCD1, ASXL1, ASXL3, AKT3, FBN2, TCF12, WASF1, BRAF, SMARCA4, SMARCA2, TUBG1, KMT2A, CTNNB1, DLG4, MEIS2, GATAD2B, FBXW7, ANKRD11, ARID1B, DYNC1H1, HIVEP2, NEXMIF, ZBTB18, SETD1B, DYRK1A, SRCAP, CASK, L1CAM, and KRAS. Twenty-four of these monogenic disorders have not been previously reported in the Indian population. Notably, 39 out of 53 (74%) disease-causing variants are novel. These variants were identified in the genes mainly encoding transcriptional and chromatin regulators, serine threonine kinases, lysosomal enzymes, molecular motors, synaptic proteins, neuronal migration machinery, adhesion molecules, structural proteins and signaling molecules.
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Affiliation(s)
- Shruti Pande
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Purvi Majethia
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Karthik Nair
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Lakshmi Priya Rao
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Selinda Mascarenhas
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Namanpreet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Michelle C do Rosario
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Kausthubham Neethukrishna
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ankur Chaurasia
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, United Kingdom
| | - Bhagesh Hunakunti
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Nalesh Jadhav
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Sruthy Xavier
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Jeevan Kumar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Vivekananda Bhat
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - B L Yatheesha
- Dheemahi Child Neurology and Development Center, Shivamogga, India
| | - Siddaramappa J Patil
- Division of Medical Genetics, Mazumdar Shaw Medical Center, Narayana Hrudayalaya Hospitals, Bangalore, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Cochin, India
| | - Nutan Kamath
- Department of Paediatrics, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India
| | - Shrikiran Aroor
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ramesh Bhat Y
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Leslie E Lewis
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Suvasini Sharma
- Neurology Division, Department of Pediatrics, Lady Hardinge Medical College and Associated Kalawati Saran Children's Hospital, New Delhi, India
| | | | - Naveen Sankhyan
- Pediatric Neurology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Shahyan Siddiqui
- Department of Neuro and Vascular Interventional Radiology, Yashoda Hospitals, Secunderabad, Hyderabad, India
| | - Shalini S Nayak
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States of America
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- Suma Genomics Private Limited, Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
- Department of Genetics, College of Medicine & Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
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