151
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Mazzilli R, Rucci C, Vaiarelli A, Cimadomo D, Ubaldi FM, Foresta C, Ferlin A. Male factor infertility and assisted reproductive technologies: indications, minimum access criteria and outcomes. J Endocrinol Invest 2023; 46:1079-1085. [PMID: 36633791 DOI: 10.1007/s40618-022-02000-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023]
Abstract
BACKGROUND Infertility, which is defined as the inability to conceive after at least 12 months of regular unprotected sexual intercourses, affects about 15-20% of couples worldwide and a male factor is involved in about half of the cases. The development of assisted reproductive technology (ART) made it possible to conceive also to individuals affected from severe oligospermia or azoospermia. However, the impact of the male factor on embryo development, implantation, prevalence of chromosomal abnormalities, genetic and epigenetic alterations, and clinical and obstetric outcomes is still controversial. PURPOSE This narrative review examines the indications, minimum access criteria, and outcomes by individual ART technique in relation to the male factor.
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Affiliation(s)
- R Mazzilli
- Andrology Unit, Department of Clinical and Molecular Medicine, Sant'Andrea Hospital, Sapienza University of Rome, Via Di Grottarossa, 1036-1039, 00100, Rome, Italy.
- GeneraLife IVF, Clinica Valle Giulia, Rome, Italy.
| | - C Rucci
- GeneraLife IVF, Clinica Valle Giulia, Rome, Italy
- Department of Surgical Sciences, Gynecologic Unit, University of Rome "TorVergata", Rome, Italy
| | - A Vaiarelli
- GeneraLife IVF, Clinica Valle Giulia, Rome, Italy
| | - D Cimadomo
- GeneraLife IVF, Clinica Valle Giulia, Rome, Italy
| | - F M Ubaldi
- GeneraLife IVF, Clinica Valle Giulia, Rome, Italy
| | - C Foresta
- Department of Medicine, Unit of Andrology and Reproductive Medicine, University of Padova, Padova, Italy
| | - A Ferlin
- Department of Medicine, Unit of Andrology and Reproductive Medicine, University of Padova, Padova, Italy
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152
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Wang RJ, Al-Saffar SI, Rogers J, Hahn MW. Human generation times across the past 250,000 years. SCIENCE ADVANCES 2023; 9:eabm7047. [PMID: 36608127 PMCID: PMC9821931 DOI: 10.1126/sciadv.abm7047] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The generation times of our recent ancestors can tell us about both the biology and social organization of prehistoric humans, placing human evolution on an absolute time scale. We present a method for predicting historical male and female generation times based on changes in the mutation spectrum. Our analyses of whole-genome data reveal an average generation time of 26.9 years across the past 250,000 years, with fathers consistently older (30.7 years) than mothers (23.2 years). Shifts in sex-averaged generation times have been driven primarily by changes to the age of paternity, although we report a substantial increase in female generation times in the recent past. We also find a large difference in generation times among populations, reaching back to a time when all humans occupied Africa.
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Affiliation(s)
- Richard J. Wang
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
- Corresponding author.
| | - Samer I. Al-Saffar
- Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew W. Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
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153
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Vado Y, Pereda A, Manero-Azua A, Perez de Nanclares G. Frequency of de novo variants and parental mosaicism in families with inactivating PTH/PTHrP signaling disorder type 2. Front Endocrinol (Lausanne) 2023; 13:1055431. [PMID: 36686455 PMCID: PMC9846528 DOI: 10.3389/fendo.2022.1055431] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023] Open
Abstract
Objective iPPSD2 (which includes PHP1A and PPHP/POH) is a rare inherited autosomal dominant endocrine disorder caused by inactivating GNAS pathogenic variants. A high percentage of de novo cases has been suggested. In rare cases, parental mosaicism has been described, but its real frequency is unknown. Design A retrospective study including a series of 95 genetically confirmed iPPSD2 probands. Methods The frequency of de novo cases was evaluated and the distribution of the type of variants was compared according to the type of inheritance. The putative involved allele was determined by reverse transcriptase PCR (RT-PCR) or allele specific oligonucleotide RT-PCR (ASO-RT-PCR). The possibility of GNAS mosaicism was studied by next-generation sequencing (NGS) on the corresponding parental DNA. Results In 41 patients the variant was of de novo origin and in 24 the origin could not be established. In both cases 66.67% of variants generated a truncated or absent protein whereas the rest of the variants were missense or in-frame deletion/duplication. Parental origin was studied in 45 of those patients and determined in 35. Curiously, the percentage of de novo variants at the paternal allele was higher than when paternally inherited (31.1% vs 6.67%). NGS detected mosaicism in three independent families: one from paternal DNA (allelic ratio 10%) and two from maternal DNA (allelic ratio 10% and 2%). Conclusion De novo pathogenic variants are frequent in iPPSD2 (around 45%). Parental mosaicism is infrequent (8.11%) but should be analyzed with NGS, taking into account its importance in genetic counselling.
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Affiliation(s)
| | | | | | | | - Guiomar Perez de Nanclares
- Rare Diseases Research Group, Molecular (Epi)Genetics Laboratory, Bioaraba Health Research Institute, Araba University Hospital-Txagorritxu, Vitoria-Gasteiz, Araba, Spain
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154
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Cutler R, Vijg J. A mechanism for inheriting radiation-induced DNA damage. Nature 2023; 613:249-250. [PMID: 36544004 PMCID: PMC10262177 DOI: 10.1038/d41586-022-04449-y] [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] [Indexed: 12/24/2022]
Abstract
Radiation-damaged paternal DNA has been found to cause embryos of the second generation of nematode worms, but not the first, to die. The proposed mechanisms help to explain the observed lack of such an effect in humans.
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155
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Shea A, Bartz J, Zhang L, Dong X. Predicting mutational function using machine learning. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 791:108457. [PMID: 36965820 PMCID: PMC10239318 DOI: 10.1016/j.mrrev.2023.108457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/11/2023] [Accepted: 03/20/2023] [Indexed: 03/27/2023]
Abstract
Genetic variations are one of the major causes of phenotypic variations between human individuals. Although beneficial as being the substrate of evolution, germline mutations may cause diseases, including Mendelian diseases and complex diseases such as diabetes and heart diseases. Mutations occurring in somatic cells are a main cause of cancer and likely cause age-related phenotypes and other age-related diseases. Because of the high abundance of genetic variations in the human genome, i.e., millions of germline variations per human subject and thousands of additional somatic mutations per cell, it is technically challenging to experimentally verify the function of every possible mutation and their interactions. Significant progress has been made to solve this problem using computational approaches, especially machine learning (ML). Here, we review the progress and achievements made in recent years in this field of research. We classify the computational models in two ways: one according to their prediction goals including protein structural alterations, gene expression changes, and disease risks, and the other according to their methodologies, including non-machine learning methods, classical machine learning methods, and deep neural network methods. For models in each category, we discuss their architecture, prediction accuracy, and potential limitations. This review provides new insights into the applications and future directions of computational approaches in understanding the role of mutations in aging and disease.
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Affiliation(s)
- Anthony Shea
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Josh Bartz
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA; Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lei Zhang
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Xiao Dong
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA.
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156
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Wang S, Meyer DH, Schumacher B. Inheritance of paternal DNA damage by histone-mediated repair restriction. Nature 2023; 613:365-374. [PMID: 36544019 PMCID: PMC9834056 DOI: 10.1038/s41586-022-05544-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 11/08/2022] [Indexed: 12/24/2022]
Abstract
How paternal exposure to ionizing radiation affects genetic inheritance and disease risk in the offspring has been a long-standing question in radiation biology. In humans, nearly 80% of transmitted mutations arise in the paternal germline1, but the transgenerational effects of ionizing radiation exposure has remained controversial and the mechanisms are unknown. Here we show that in sex-separated Caenorhabditis elegans strains, paternal, but not maternal, exposure to ionizing radiation leads to transgenerational embryonic lethality. The offspring of irradiated males displayed various genome instability phenotypes, including DNA fragmentation, chromosomal rearrangement and aneuploidy. Paternal DNA double strand breaks were repaired by maternally provided error-prone polymerase theta-mediated end joining. Mechanistically, we show that depletion of an orthologue of human histone H1.0, HIS-24, or the heterochromatin protein HPL-1, could significantly reverse the transgenerational embryonic lethality. Removal of HIS-24 or HPL-1 reduced histone 3 lysine 9 dimethylation and enabled error-free homologous recombination repair in the germline of the F1 generation from ionizing radiation-treated P0 males, consequently improving the viability of the F2 generation. This work establishes the mechanistic underpinnings of the heritable consequences of paternal radiation exposure on the health of offspring, which may lead to congenital disorders and cancer in humans.
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Affiliation(s)
- Siyao Wang
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University Hospital and University of Cologne, Cologne, Germany.
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| | - David H Meyer
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University Hospital and University of Cologne, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University Hospital and University of Cologne, Cologne, Germany.
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
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157
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Teefy BB, Adler A, Xu A, Hsu K, Singh PP, Benayoun BA. Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish. Genome Res 2023; 33:141-153. [PMID: 36577520 PMCID: PMC9977155 DOI: 10.1101/gr.277301.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/23/2022] [Indexed: 12/30/2022]
Abstract
Although germline cells are considered to be functionally "immortal," both the germline and supporting somatic cells in the gonad within an organism experience aging. With increased age at parenthood, the age-related decline in reproductive success has become an important biological issue for an aging population. However, molecular mechanisms underlying reproductive aging across sexes in vertebrates remain poorly understood. To decipher molecular drivers of vertebrate gonadal aging across sexes, we perform longitudinal characterization of the gonadal transcriptome throughout the lifespan in the naturally short-lived African turquoise killifish (Nothobranchius furzeri). By combining mRNA-seq and small RNA-seq from 26 individuals, we characterize the aging gonads of young-adult, middle-aged, and old female and male fish. We analyze changes in transcriptional patterns of genes, transposable elements (TEs), and piRNAs. We find that testes seem to undergo only marginal changes during aging. In contrast, in middle-aged ovaries, the time point associated with peak female fertility in this strain, PIWI pathway components are transiently down-regulated, TE transcription is elevated, and piRNA levels generally decrease, suggesting that egg quality may already be declining at middle-age. Furthermore, we show that piRNA ping-pong biogenesis declines steadily with age in ovaries, whereas it is maintained in aging testes. To our knowledge, this data set represents the most comprehensive transcriptomic data set for vertebrate gonadal aging. This resource also highlights important pathways that are regulated during reproductive aging in either ovaries or testes, which could ultimately be leveraged to help restore aspects of youthful reproductive function.
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Affiliation(s)
- Bryan B Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA
| | - Ari Adler
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA
| | - Alan Xu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA.,Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, California 90089, USA
| | - Katelyn Hsu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA.,Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, California 90089, USA
| | - Param Priya Singh
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA.,Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, California 90089, USA.,Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, California 90089, USA.,USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, California 90089, USA.,USC Stem Cell Initiative, Los Angeles, California 90089, USA
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158
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Lee TH, Kim DS, Kim DK, Shin DH, Oh M, Lee WH, Song SH. Effect of male age on reproductive function: A comparison of young and middle-aged men. Investig Clin Urol 2023; 64:51-55. [PMID: 36629065 PMCID: PMC9834564 DOI: 10.4111/icu.20220302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/18/2022] [Accepted: 11/30/2022] [Indexed: 12/28/2022] Open
Abstract
PURPOSE There have been concerns regarding potential effects of older paternal age on male reproductive function. However, currently available data on this topic are insufficient and controversy exists. We analyzed semen characteristics and reproductive hormones in young men and middle-aged men to investigate the effect of age on male reproductive function. MATERIALS AND METHODS This study examined healthy males of reproductive age who visited a single infertility center from January 2016 to July 2021. The young group consisted of men who were less than 35 years-old, and the middle-age group consisted of men who were more than 45 years-old. RESULTS The two groups had no significant differences in sperm concentration ([89.9±59.4]×106/mL vs. [104.4±82.1]×106/mL, p=0.108) or sperm morphology (normal forms: 3.6%±1.5% vs. 3.4%±1.6%, p=0.131). However, the middle-age group had a smaller semen volume (3.2±1.5 mL vs. 2.5±1.4 mL, p<0.001), lower sperm motility (42.3%±9.8% vs. 31.2%±12.4%, p<0.001), lower progressive sperm motility (39.2%±10.3% vs. 28.4%±12.6%, p<0.001), and a higher serum follicle-stimulating hormone level. CONCLUSIONS Our results suggest that advanced male age might have a negative effect on fertility potential, as in women. This finding has important clinical implications because more couples are choosing to have children when they are older. Further studies on this issue, especially those that examine reproductive outcome, are warranted.
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Affiliation(s)
- Tae Ho Lee
- Department of Urology, CHA Fertility Center Gangnam, CHA Gangnam Medical Center, CHA University, Seoul, Korea
| | - Dong Suk Kim
- Department of Urology, CHA Fertility Center Gangnam, CHA Gangnam Medical Center, CHA University, Seoul, Korea
| | - Dae Keun Kim
- Department of Urology, CHA Fertility Center, Seoul Station, CHA University, Seoul, Korea
| | - Dong Hyuk Shin
- CHA Fertility Center Gangnam, CHA University, Seoul, Korea
| | - Mihee Oh
- CHA Fertility Center Gangnam, CHA University, Seoul, Korea
| | - Won Hee Lee
- CHA Fertility Center Gangnam, CHA University, Seoul, Korea
| | - Seung-Hun Song
- Department of Urology, CHA Fertility Center Gangnam, CHA Gangnam Medical Center, CHA University, Seoul, Korea
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159
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Hall MB, Willis DE, Rodriguez EL, Schwarz JM. Maternal immune activation as an epidemiological risk factor for neurodevelopmental disorders: Considerations of timing, severity, individual differences, and sex in human and rodent studies. Front Neurosci 2023; 17:1135559. [PMID: 37123361 PMCID: PMC10133487 DOI: 10.3389/fnins.2023.1135559] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 03/13/2023] [Indexed: 05/02/2023] Open
Abstract
Epidemiological evidence suggests that one's risk of being diagnosed with a neurodevelopmental disorder (NDD)-such as autism, ADHD, or schizophrenia-increases significantly if their mother had a viral or bacterial infection during the first or second trimester of pregnancy. Despite this well-known data, little is known about how developing neural systems are perturbed by events such as early-life immune activation. One theory is that the maternal immune response disrupts neural processes important for typical fetal and postnatal development, which can subsequently result in specific and overlapping behavioral phenotypes in offspring, characteristic of NDDs. As such, rodent models of maternal immune activation (MIA) have been useful in elucidating neural mechanisms that may become dysregulated by MIA. This review will start with an up-to-date and in-depth, critical summary of epidemiological data in humans, examining the association between different types of MIA and NDD outcomes in offspring. Thereafter, we will summarize common rodent models of MIA and discuss their relevance to the human epidemiological data. Finally, we will highlight other factors that may interact with or impact MIA and its associated risk for NDDs, and emphasize the importance for researchers to consider these when designing future human and rodent studies. These points to consider include: the sex of the offspring, the developmental timing of the immune challenge, and other factors that may contribute to individual variability in neural and behavioral responses to MIA, such as genetics, parental age, the gut microbiome, prenatal stress, and placental buffering.
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160
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Bethune J, Kleppe A, Besenbacher S. A method to build extended sequence context models of point mutations and indels. Nat Commun 2022; 13:7884. [PMID: 36550134 PMCID: PMC9780256 DOI: 10.1038/s41467-022-35596-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
The mutation rate of a specific position in the human genome depends on the sequence context surrounding it. Modeling the mutation rate by estimating a rate for each possible k-mer, however, only works for small values of k since the data becomes too sparse for larger values of k. Here we propose a new method that solves this problem by grouping similar k-mers. We refer to the method as k-mer pattern partition and have implemented it in a software package called kmerPaPa. We use a large set of human de novo mutations to show that this new method leads to improved prediction of mutation rates and makes it possible to create models using wider sequence contexts than previous studies. As the first method of its kind, it does not only predict rates for point mutations but also insertions and deletions. We have additionally created a software package called Genovo that, given a k-mer pattern partition model, predicts the expected number of synonymous, missense, and other functional mutation types for each gene. Using this software, we show that the created mutation rate models increase the statistical power to detect genes containing disease-causing variants and to identify genes under strong selective constraint.
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Affiliation(s)
- Jörn Bethune
- grid.154185.c0000 0004 0512 597XDepartment of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - April Kleppe
- grid.154185.c0000 0004 0512 597XDepartment of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Søren Besenbacher
- grid.154185.c0000 0004 0512 597XDepartment of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722Department of Clinical Medicine, Aarhus University, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
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161
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Steely CJ, Watkins WS, Baird L, Jorde LB. The mutational dynamics of short tandem repeats in large, multigenerational families. Genome Biol 2022; 23:253. [PMID: 36510265 PMCID: PMC9743774 DOI: 10.1186/s13059-022-02818-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Short tandem repeats (STRs) compose approximately 3% of the genome, and mutations at STR loci have been linked to dozens of human diseases including amyotrophic lateral sclerosis, Friedreich ataxia, Huntington disease, and fragile X syndrome. Improving our understanding of these mutations would increase our knowledge of the mutational dynamics of the genome and may uncover additional loci that contribute to disease. To estimate the genome-wide pattern of mutations at STR loci, we analyze blood-derived whole-genome sequencing data for 544 individuals from 29 three-generation CEPH pedigrees. These pedigrees contain both sets of grandparents, the parents, and an average of 9 grandchildren per family. RESULTS We use HipSTR to identify de novo STR mutations in the 2nd generation of these pedigrees and require transmission to the third generation for validation. Analyzing approximately 1.6 million STR loci, we estimate the empirical de novo STR mutation rate to be 5.24 × 10-5 mutations per locus per generation. Perfect repeats mutate about 2 × more often than imperfect repeats. De novo STRs are significantly enriched in Alu elements. CONCLUSIONS Approximately 30% of new STR mutations occur within Alu elements, which compose only 11% of the genome, but only 10% are found in LINE-1 insertions, which compose 17% of the genome. Phasing these mutations to the parent of origin shows that parental transmission biases vary among families. We estimate the average number of de novo genome-wide STR mutations per individual to be approximately 85, which is similar to the average number of observed de novo single nucleotide variants.
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Affiliation(s)
- Cody J. Steely
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
| | - W. Scott Watkins
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
| | - Lisa Baird
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
| | - Lynn B. Jorde
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
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162
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Evo-devo perspectives on cancer. Essays Biochem 2022; 66:797-815. [PMID: 36250956 DOI: 10.1042/ebc20220041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 12/13/2022]
Abstract
The integration of evolutionary and developmental approaches into the field of evolutionary developmental biology has opened new areas of inquiry- from understanding the evolution of development and its underlying genetic and molecular mechanisms to addressing the role of development in evolution. For the last several decades, the terms 'evolution' and 'development' have been increasingly linked to cancer, in many different frameworks and contexts. This mini-review, as part of a special issue on Evolutionary Developmental Biology, discusses the main areas in cancer research that have been addressed through the lenses of both evolutionary and developmental biology, though not always fully or explicitly integrated in an evo-devo framework. First, it briefly introduces the current views on carcinogenesis that invoke evolutionary and/or developmental perspectives. Then, it discusses the main mechanisms proposed to have specifically evolved to suppress cancer during the evolution of multicellularity. Lastly, it considers whether the evolution of multicellularity and development was shaped by the threat of cancer (a cancer-evo-devo perspective), and/or whether the evolution of developmental programs and life history traits can shape cancer resistance/risk in various lineages (an evo-devo-cancer perspective). A proper evolutionary developmental framework for cancer, both as a disease and in terms of its natural history (in the context of the evolution of multicellularity and development as well as life history traits), could bridge the currently disparate evolutionary and developmental perspectives and uncover aspects that will provide new insights for cancer prevention and treatment.
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163
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Meunier L, Sorci G, Abi Hussein H, Hingrat Y, Rehspringer N, Saint-Jalme M, Lesobre L, Torres Carreira J. Pre-but not post-meiotic senescence affects sperm quality and reproductive success in the North African houbara bustard. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.977184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Age-dependent reduction in reproductive success can arise due to multiple factors including a deterioration of reproductive physiology. Senescing males have been shown to produce ejaculates with poor sperm quality, which impinges on male reproductive success. In addition to individual age, gamete age can also affect male reproductive success. Accordingly, variance in male reproductive success can be due to pre-meiotic (referring to individual age) and post-meiotic senescence (sperm age). Here, we tested whether male senescence and sperm cell aging have additive or interactive effects on male reproductive success in a bird with a promiscuous mating system, the North African houbara bustard. To assess the effect of pre-meiotic aging, we compared male reproductive success between two age classes (3-6- and 12–16-year-old). To infer the effect of post-meiotic aging, male ejaculates were collected at three-time intervals following a common initial collection (day 1, 5, and 10). Therefore, day 1 ejaculates are supposed to contain younger sperm than day 5 and 10 ejaculates. Following controlled artificial inseminations, reproductive success was assessed using three fitness-linked traits (hatching success, chick growth rate and survival). In addition to reproductive output, we also assessed whether pre- and post-meiotic aging affected a wide range of sperm and ejaculate traits. In agreement with previous reports, we found that males in the older age class produced less sperm with poorer motility compared to young individuals. However, contrary to the prediction, we found that ejaculates collected at day 5 and 10 tended to have better sperm traits such as motility and velocity. The results on sperm traits were generally mirrored in the effect on reproductive success since young males produced offspring that grew faster and had better survival during the first month of life, and eggs fertilized by sperm collected at day 5 had the highest hatching success. In any of the models, there was evidence for interactive effects of male and sperm age. Overall, these results confirm the role of pre-meiotic aging on male reproductive success. The lack of evidence for sperm aging could come from the experimental design but might also reflect the pattern of mating frequency in a species with a lek-based mating system.
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164
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Jimbo M, Kunisaki J, Ghaed M, Yu V, Flores HA, Hotaling JM. Fertility in the aging male: a systematic review. Fertil Steril 2022; 118:1022-1034. [PMID: 36509505 PMCID: PMC10914128 DOI: 10.1016/j.fertnstert.2022.10.035] [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: 08/12/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 12/14/2022]
Abstract
The negative effect of advanced female age on fertility and offspring health is well understood. In comparison, much less is known about the implications of male age on fertility, with many studies showing conflicting results. Nevertheless, increasing evidence suggests that advanced paternal age has negative effects on sperm parameters, reproductive success, and offspring health. Herein, we summarize the current body of knowledge on this controversial topic, with the belief that this review will serve as a resource for the clinicians providing fertility counseling to couples with older male partners.
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Affiliation(s)
- Masaya Jimbo
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah
| | - Jason Kunisaki
- Department of Human Genetics, University of Utah, Salt Lake City, Utah
| | - Mohammadali Ghaed
- Urology Department, Rasool Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Victor Yu
- University of Nevada Reno School of Medicine, Reno, Nevada
| | - Hunter A Flores
- Scott Department of Urology, Baylor College of Medicine, Houston, Texas
| | - James M Hotaling
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah.
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165
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Wood KA, Goriely A. The impact of paternal age on new mutations and disease in the next generation. Fertil Steril 2022; 118:1001-1012. [PMID: 36351856 PMCID: PMC10909733 DOI: 10.1016/j.fertnstert.2022.10.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022]
Abstract
Advanced paternal age is associated with an increased risk of fathering children with genetic disorders and other adverse reproductive consequences. However, the mechanisms underlying this phenomenon remain largely unexplored. In this review, we focus on the impact of paternal age on de novo mutations that are an important contributor to genetic disease and can be studied both indirectly through large-scale sequencing studies and directly in the tissue in which they predominantly arise-the aging testis. We discuss the recent data that have helped establish the origins and frequency of de novo mutations, and highlight experimental evidence about the close link between new mutations, parental age, and genetic disease. We then focus on a small group of rare genetic conditions, the so-called "paternal age effect" disorders that show a strong association between paternal age and disease prevalence, and discuss the underlying mechanism ("selfish selection") and implications of this process in more detail. More broadly, understanding the causes and consequences of paternal age on genetic risk has important implications both for individual couples and for public health advice given that the average age of fatherhood is steadily increasing in many developed nations.
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Affiliation(s)
- Katherine A Wood
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Anne Goriely
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Oxford, United Kingdom.
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166
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Mo A, Saffari A, Kellner M, Döbler-Neumann M, Jordan C, Srivastava S, Zhang B, Sahin M, Fink JK, Smith L, Posey JE, Alter KE, Toro C, Blackstone C, Soldatos AG, Christie M, Schüle R, Ebrahimi-Fakhari D. Early-Onset and Severe Complex Hereditary Spastic Paraplegia Caused by De Novo Variants in SPAST. Mov Disord 2022; 37:2440-2446. [PMID: 36103453 PMCID: PMC10062395 DOI: 10.1002/mds.29225] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/13/2022] [Accepted: 08/26/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Familial hereditary spastic paraplegia (HSP)-SPAST (SPG4) typically presents with a pure HSP phenotype. OBJECTIVE The aim of this study was to delineate the genotypic and phenotypic spectrum of children with de novo HSP-SPAST. METHODS This study used a systematic cross-sectional analysis of clinical and molecular features. RESULTS We report the clinical and molecular spectrum of 40 patients with heterozygous pathogenic de novo variants in SPAST (age range: 2.2-27.7 years). We identified 19 unique variants (16/40 carried the same recurrent variant, p.Arg499His). Symptom onset was in early childhood (median: 11.0 months, interquartile range: 6.0 months) with significant motor and speech delay, followed by progressive ascending spasticity, dystonia, neurogenic bladder dysfunction, gastrointestinal dysmotility, and epilepsy. The mean Spastic Paraplegia Rating Scale score was 32.8 ± 9.7 (standard deviation). CONCLUSIONS These results confirm that de novo variants in SPAST lead to a severe and complex form of HSP that differs from classic familial pure HSP-SPAST. Clinicians should be aware of this syndrome in the differential diagnosis for cerebral palsy. © 2022 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Alisa Mo
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Afshin Saffari
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Melanie Kellner
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Marion Döbler-Neumann
- Department of Pediatric Neurology, University Children’s Hospital, Tübingen, Germany
| | - Catherine Jordan
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Siddharth Srivastava
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Bo Zhang
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- ICCTR Biostatistics and Research Design Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA
| | - Mustafa Sahin
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - John K. Fink
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Linsley Smith
- Department of Neurology and Rehabilitation Medicine, Texas Scottish Rite Hospital, University of Texas Southwestern Medical Center, Dallas, TX, 75219, USA
| | - Jennifer E. Posey
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Katharine E. Alter
- Functional and Applied Biomechanics Section, Department of Rehabilitation Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Camilo Toro
- Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA
| | - Craig Blackstone
- Movement Disorders Division, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ariane G. Soldatos
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Michelle Christie
- Department of Neurology and Rehabilitation Medicine, Texas Scottish Rite Hospital, University of Texas Southwestern Medical Center, Dallas, TX, 75219, USA
| | - Rebecca Schüle
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Darius Ebrahimi-Fakhari
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Movement Disorders Program, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, USA
- Intellectual and Developmental Disabilities Research Center, Boston Children’s Hospital, Boston, MA, USA
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167
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Wang SH, Wu CS, Hsu LY, Lin MC, Chen PC, Thompson WK, Fan CC. Paternal age and 13 psychiatric disorders in the offspring: a population-based cohort study of 7 million children in Taiwan. Mol Psychiatry 2022; 27:5244-5254. [PMID: 36042285 PMCID: PMC11285795 DOI: 10.1038/s41380-022-01753-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/02/2022] [Accepted: 08/12/2022] [Indexed: 01/14/2023]
Abstract
Although paternal age has been linked to certain psychiatric disorders, the nature of any causal relationship remains elusive. Here, we aimed to comprehensively assess the magnitude of a wide range of offspring's psychiatric risk conferred by paternal age, leveraging a pedigree inferred from covered-insurance relationship (accuracy >98%) in Taiwan's single-payer compulsory insurance program. We also examined whether there is an independent role of paternal age and explored the potential effect of parental age difference. A total cohort of 7,264,788 individuals born between 1980 and 2018 were included; 5,572,232 with sibling(s) were selected for sibling-comparison analyses and 1,368,942 and 1,044,420 children with information of paternal-grandparents and maternal-grandparents, respectively, were selected for multi-generation analyses. Using inpatient/outpatient claims data (1997-2018), we identified schizophrenia, autism, bipolar disorder (BPD), attention deficit-hyperactivity disorder (ADHD), major depressive disorder (MDD), eating disorder (ED), substance use disorder (SUD), mental retardation (MR), tic disorder, obsessive-compulsive disorder (OCD), anxiety, and somatoform disorder. We identified suicides using death certificates. Logistic regression analysis was used to estimate the paternal/maternal/grand-paternal age association with psychiatric risk in the offspring. The total cohort and sibling-comparison cohort resulted in similar estimates. Paternal age had a U-shaped relationship with offspring's MDD, ED, SUD, and anxiety. A very young maternal age (<20 years) was associated with markedly higher risk in offspring's SUD, MR, and suicide. Older paternal age (>25 years) was linearly associated with offspring's schizophrenia, autism, BPD, ADHD, MDD, ED, SUD, MR, OCD, anxiety, and suicide. Older grand-paternal age was linearly associated with offspring's schizophrenia, autism, ADHD, and MR. Dissimilar parental age was positively associated with offspring's ADHD, MDD, SUD, MR, anxiety, and suicide, and negatively associated with offspring's OCD. This comprehensive assessment provides solid evidence for the independent role of paternal age in psychiatric risk in the offspring and clarifies the significance of both early parenthood and delayed paternity.
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Affiliation(s)
- Shi-Heng Wang
- Department of Occupational Safety and Health, College of Public Health, China Medical University, Taichung, Taiwan.
- Department of Public Health, College of Public Health, China Medical University, Taichung, Taiwan.
- Interdisciplinary Freshmen Program of Public Health, College of Public Health, China Medical University, Taichung, Taiwan.
| | - Chi-Shin Wu
- National Center for Geriatrics and Welfare Research, National Health Research Institutes, Miaoli, Taiwan
- Department of Psychiatry, National Taiwan University Hospital, Yunlin branch, Douliu, Taiwan
| | - Le-Yin Hsu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
- Graduate Program of Data Science, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Mei-Chen Lin
- Department of Occupational Safety and Health, College of Public Health, China Medical University, Taichung, Taiwan
- Interdisciplinary Freshmen Program of Public Health, College of Public Health, China Medical University, Taichung, Taiwan
| | - Pei-Chun Chen
- Department of Public Health, College of Public Health, China Medical University, Taichung, 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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168
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Mansouri S, Gogoi H, Patel S, Katikaneni DS, Singh A, Aybar-Torres A, de Lartigue G, Jin L. MPYS Modulates Fatty Acid Metabolism and Immune Tolerance at Homeostasis Independent of Type I IFNs. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:2114-2132. [PMID: 36261171 PMCID: PMC9679991 DOI: 10.4049/jimmunol.2200158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/15/2022] [Indexed: 01/04/2023]
Abstract
MPYS/STING (stimulator of IFN genes) senses cyclic dinucleotides (CDNs), generates type I IFNs, and plays a critical role in infection, inflammation, and cancer. In this study, analyzing genotype and haplotype data from the 1000 Genomes Project, we found that the R71H-G230A-R293Q (HAQ) MPYS allele frequency increased 57-fold in East Asians compared with sub-Saharan Africans. Meanwhile, the G230A-R293Q (AQ) allele frequency decreased by 98% in East Asians compared with sub-Saharan Africans. We propose that the HAQ and AQ alleles underwent a natural selection during the out-of-Africa migration. We used mouse models of HAQ and AQ to investigate the underlying mechanism. We found that the mice carrying the AQ allele, which disappeared in East Asians, had normal CDN-type I IFN responses. Adult AQ mice, however, had less fat mass than did HAQ or wild-type mice on a chow diet. AQ epididymal adipose tissue had increased regulatory T cells and M2 macrophages with protein expression associated with enhanced fatty acid oxidation. Conditional knockout mice and adoptive cell transfer indicate a macrophage and regulatory T cell-intrinsic role of MPYS in fatty acid metabolism. Mechanistically, AQ/IFNAR1-/- mice had a similar lean phenotype as for the AQ mice. MPYS intrinsic tryptophan fluorescence revealed that the R71H change increased MPYS hydrophilicity. Lastly, we found that the second transmembrane (TM) and the TM2-TM3 linker region of MPYS interact with activated fatty acid, fatty acyl-CoA. In summary, studying the evolution of the human MPYS gene revealed an MPYS function in modulating fatty acid metabolism that may be critical during the out-of-Africa migration.
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Affiliation(s)
- Samira Mansouri
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL
| | - Himanshu Gogoi
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL
| | - Seema Patel
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL
| | - Divya S. Katikaneni
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL
| | - Arashdeep Singh
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL; and
- Center for Integrative Cardiovascular and Metabolic Disease, University of Florida, Gainesville, FL
| | - Alexandra Aybar-Torres
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL
| | - Guillaume de Lartigue
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL; and
- Center for Integrative Cardiovascular and Metabolic Disease, University of Florida, Gainesville, FL
| | - Lei Jin
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL
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169
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Sun Y, Yuan F, Wang L, Dai D, Zhang Z, Liang F, Liu N, Long J, Zhao X, Xi Y. Recombination and mutation shape variations in the major histocompatibility complex. J Genet Genomics 2022; 49:1151-1161. [PMID: 35358716 DOI: 10.1016/j.jgg.2022.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 01/14/2023]
Abstract
The major histocompatibility complex (MHC) is closely associated with numerous diseases, but its high degree of polymorphism complicates the discovery of disease-associated variants. In principle, recombination and de novo mutations are two critical factors responsible for MHC polymorphisms. However, direct evidence for this hypothesis is lacking. Here, we report the generation of fine-scale MHC recombination and de novo mutation maps of ∼5 Mb by deep sequencing (> 100×) of the MHC genome for 17 MHC recombination and 30 non-recombination Han Chinese families (a total of 190 individuals). Recombination hotspots and Han-specific breakpoints are located in close proximity at haplotype block boundaries. The average MHC de novo mutation rate is higher than the genome-wide de novo mutation rate, particularly in MHC recombinant individuals. Notably, mutation and recombination generated polymorphisms are located within and outside linkage disequilibrium regions of the MHC, respectively, and evolution of the MHC locus was mainly controlled by positive selection. These findings provide insights on the evolutionary causes of the MHC diversity and may facilitate the identification of disease-associated genetic variants.
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Affiliation(s)
- Yuying Sun
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Institute of Beijing 307 Hospital, Anhui Medical University, Hefei, Anhui 230032, China.
| | - Fang Yuan
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Ling Wang
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Institute of Beijing 307 Hospital, Anhui Medical University, Hefei, Anhui 230032, China
| | - Dongfa Dai
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Institute of Beijing 307 Hospital, Anhui Medical University, Hefei, Anhui 230032, China
| | - Zhijian Zhang
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Institute of Beijing 307 Hospital, Anhui Medical University, Hefei, Anhui 230032, China
| | - Fei Liang
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Nan Liu
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Juan Long
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Xiao Zhao
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Yongzhi Xi
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China.
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170
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Estimating the genome-wide mutation rate from thousands of unrelated individuals. Am J Hum Genet 2022; 109:2178-2184. [PMID: 36370709 PMCID: PMC9748258 DOI: 10.1016/j.ajhg.2022.10.015] [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: 07/11/2022] [Accepted: 10/15/2022] [Indexed: 11/13/2022] Open
Abstract
We provide a method for estimating the genome-wide mutation rate from sequence data on unrelated individuals by using segments of identity by descent (IBD). The length of an IBD segment indicates the time to shared ancestor of the segment, and mutations that have occurred since the shared ancestor result in discordances between the two IBD haplotypes. Previous methods for IBD-based estimation of mutation rate have required the use of family data for accurate phasing of the genotypes. This has limited the scope of application of IBD-based mutation rate estimation. Here, we develop an IBD-based method for mutation rate estimation from population data, and we apply it to whole-genome sequence data on 4,166 European American individuals from the TOPMed Framingham Heart Study, 2,996 European American individuals from the TOPMed My Life, Our Future study, and 1,586 African American individuals from the TOPMed Hypertension Genetic Epidemiology Network study. Although mutation rates may differ between populations as a result of genetic factors, demographic factors such as average parental age, and environmental exposures, our results are consistent with equal genome-wide average mutation rates across these three populations. Our overall estimate of the average genome-wide mutation rate per 108 base pairs per generation for single-nucleotide variants is 1.24 (95% CI 1.18-1.33).
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171
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Pokrovac I, Pezer Ž. Recent advances and current challenges in population genomics of structural variation in animals and plants. Front Genet 2022; 13:1060898. [PMID: 36523759 PMCID: PMC9745067 DOI: 10.3389/fgene.2022.1060898] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/15/2022] [Indexed: 05/02/2024] Open
Abstract
The field of population genomics has seen a surge of studies on genomic structural variation over the past two decades. These studies witnessed that structural variation is taxonomically ubiquitous and represent a dominant form of genetic variation within species. Recent advances in technology, especially the development of long-read sequencing platforms, have enabled the discovery of structural variants (SVs) in previously inaccessible genomic regions which unlocked additional structural variation for population studies and revealed that more SVs contribute to evolution than previously perceived. An increasing number of studies suggest that SVs of all types and sizes may have a large effect on phenotype and consequently major impact on rapid adaptation, population divergence, and speciation. However, the functional effect of the vast majority of SVs is unknown and the field generally lacks evidence on the phenotypic consequences of most SVs that are suggested to have adaptive potential. Non-human genomes are heavily under-represented in population-scale studies of SVs. We argue that more research on other species is needed to objectively estimate the contribution of SVs to evolution. We discuss technical challenges associated with SV detection and outline the most recent advances towards more representative reference genomes, which opens a new era in population-scale studies of structural variation.
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Affiliation(s)
| | - Željka Pezer
- Laboratory for Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
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172
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Ren X, Liu Y, Zhao Y, Li B, Bai D, Bou G, Zhang X, Du M, Wang X, Bou T, Shen Y, Dugarjaviin M. Analysis of the Whole-Genome Sequences from an Equus Parent-Offspring Trio Provides Insight into the Genomic Incompatibilities in the Hybrid Mule. Genes (Basel) 2022; 13:genes13122188. [PMID: 36553455 PMCID: PMC9778318 DOI: 10.3390/genes13122188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/07/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Interspecific hybridization often shows negative effects on hybrids. However, only a few multicellular species, limited to a handful of plants and animals, have shown partial genetic mechanisms by which hybridization leads to low fitness in hybrids. Here, to explore the outcome of combining the two genomes of a horse and donkey, we analyzed the whole-genome sequences from an Equus parent-offspring trio using Illumina platforms. We generated 41.39× and 46.21× coverage sequences for the horse and mule, respectively. For the donkey, a 40.38× coverage sequence was generated and stored in our laboratory. Approximately 24.86 million alleles were discovered that varied from the reference genome. Single nucleotide polymorphisms were used as polymorphic markers for assigning alleles to their parental genomic inheritance. We identified 25,703 Mendelian inheritance error single nucleotide polymorphisms in the mule genome that were not inherited from the parents through Mendelian inheritance. A total of 555 de novo single nucleotide polymorphisms were also identified. The rate of de novo single nucleotide polymorphisms was 2.21 × 10-7 in the mule from the Equus parent-offspring trio. This rate is obviously higher than the natural mutation rate for Equus, which is also consistent with the previous hypothesis that interracial crosses may have a high mutation rate. The genes associated with these single nucleotide polymorphisms are mainly involved in immune processes, DNA repair, and cancer processes. The results of the analysis of three genomes from an Equus parent-offspring trio improved our knowledge of the consequences of the integration of parental genomes in mules.
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173
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Rosenkjær D, Skytte AB, Kroløkke C. Investigation of motivations for depositing sperm during the COVID-19 pandemic. HUM FERTIL 2022:1-7. [DOI: 10.1080/14647273.2022.2142857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Daniel Rosenkjær
- Cryos International Sperm and Egg bank, Vesterbro Torv 3, Aarhus C, Denmark
| | - Anne-Bine Skytte
- Cryos International Sperm and Egg bank, Vesterbro Torv 3, Aarhus C, Denmark
| | - Charlotte Kroløkke
- Department for the Study of Culture, University of Southern Denmark, Odense M, Denmark
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174
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Caporali L, Fiorini C, Palombo F, Romagnoli M, Baccari F, Zenesini C, Visconti P, Posar A, Scaduto MC, Ormanbekova D, Battaglia A, Tancredi R, Cameli C, Viggiano M, Olivieri A, Torroni A, Maestrini E, Rochat MJ, Bacchelli E, Carelli V, Maresca A. Dissecting the multifaceted contribution of the mitochondrial genome to autism spectrum disorder. Front Genet 2022; 13:953762. [PMID: 36419830 PMCID: PMC9676943 DOI: 10.3389/fgene.2022.953762] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/12/2022] [Indexed: 11/15/2023] Open
Abstract
Autism spectrum disorder (ASD) is a clinically heterogeneous class of neurodevelopmental conditions with a strong, albeit complex, genetic basis. The genetic architecture of ASD includes different genetic models, from monogenic transmission at one end, to polygenic risk given by thousands of common variants with small effects at the other end. The mitochondrial DNA (mtDNA) was also proposed as a genetic modifier for ASD, mostly focusing on maternal mtDNA, since the paternal mitogenome is not transmitted to offspring. We extensively studied the potential contribution of mtDNA in ASD pathogenesis and risk through deep next generation sequencing and quantitative PCR in a cohort of 98 families. While the maternally-inherited mtDNA did not seem to predispose to ASD, neither for haplogroups nor for the presence of pathogenic mutations, an unexpected influence of paternal mtDNA, apparently centered on haplogroup U, came from the Italian families extrapolated from the test cohort (n = 74) when compared to the control population. However, this result was not replicated in an independent Italian cohort of 127 families and it is likely due to the elevated paternal age at time of conception. In addition, ASD probands showed a reduced mtDNA content when compared to their unaffected siblings. Multivariable regression analyses indicated that variants with 15%-5% heteroplasmy in probands are associated to a greater severity of ASD based on ADOS-2 criteria, whereas paternal super-haplogroups H and JT were associated with milder phenotypes. In conclusion, our results suggest that the mtDNA impacts on ASD, significantly modifying the phenotypic expression in the Italian population. The unexpected finding of protection induced by paternal mitogenome in term of severity may derive from a role of mtDNA in influencing the accumulation of nuclear de novo mutations or epigenetic alterations in fathers' germinal cells, affecting the neurodevelopment in the offspring. This result remains preliminary and needs further confirmation in independent cohorts of larger size. If confirmed, it potentially opens a different perspective on how paternal non-inherited mtDNA may predispose or modulate other complex diseases.
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Affiliation(s)
- Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Claudio Fiorini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Flavia Palombo
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Martina Romagnoli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Flavia Baccari
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Epidemiologia e Statistica, Bologna, Italy
| | - Corrado Zenesini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Epidemiologia e Statistica, Bologna, Italy
| | - Paola Visconti
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
| | - Annio Posar
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Maria Cristina Scaduto
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
| | - Danara Ormanbekova
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Agatino Battaglia
- IRCCS Stella Maris Foundation, Department of Developmental Neuroscience, Pisa, Italy
| | - Raffaella Tancredi
- IRCCS Stella Maris Foundation, Department of Developmental Neuroscience, Pisa, Italy
| | - Cinzia Cameli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Marta Viggiano
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Antonio Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Elena Maestrini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Magali Jane Rochat
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma Diagnostica Funzionale Neuroradiologica, Bologna, Italy
| | - Elena Bacchelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Alessandra Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
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175
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Schlichta F, Moinet A, Peischl S, Excoffier L. The Impact of Genetic Surfing on Neutral Genomic Diversity. Mol Biol Evol 2022; 39:msac249. [PMID: 36403964 PMCID: PMC9703594 DOI: 10.1093/molbev/msac249] [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] [Indexed: 11/22/2022] Open
Abstract
Range expansions have been common in the history of most species. Serial founder effects and subsequent population growth at expansion fronts typically lead to a loss of genomic diversity along the expansion axis. A frequent consequence is the phenomenon of "gene surfing," where variants located near the expanding front can reach high frequencies or even fix in newly colonized territories. Although gene surfing events have been characterized thoroughly for a specific locus, their effects on linked genomic regions and the overall patterns of genomic diversity have been little investigated. In this study, we simulated the evolution of whole genomes during several types of 1D and 2D range expansions differing by the extent of migration, founder events, and recombination rates. We focused on the characterization of local dips of diversity, or "troughs," taken as a proxy for surfing events. We find that, for a given recombination rate, once we consider the amount of diversity lost since the beginning of the expansion, it is possible to predict the initial evolution of trough density and their average width irrespective of the expansion condition. Furthermore, when recombination rates vary across the genome, we find that troughs are over-represented in regions of low recombination. Therefore, range expansions can leave local and global genomic signatures often interpreted as evidence of past selective events. Given the generality of our results, they could be used as a null model for species having gone through recent expansions, and thus be helpful to correctly interpret many evolutionary biology studies.
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Affiliation(s)
- Flávia Schlichta
- Computational and Molecular Population Genetics lab, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Antoine Moinet
- Computational and Molecular Population Genetics lab, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Interfaculty Bioinformatics Unit, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Stephan Peischl
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Interfaculty Bioinformatics Unit, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Laurent Excoffier
- Computational and Molecular Population Genetics lab, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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176
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Holt GS, Batty LE, Alobaidi BKS, Smith HE, Oud MS, Ramos L, Xavier MJ, Veltman JA. Phasing of de novo mutations using a scaled-up multiple amplicon long-read sequencing approach. Hum Mutat 2022; 43:1545-1556. [PMID: 36047340 PMCID: PMC9826063 DOI: 10.1002/humu.24450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/11/2022] [Accepted: 08/18/2022] [Indexed: 01/11/2023]
Abstract
De novo mutations (DNMs) play an important role in severe genetic disorders that reduce fitness. To better understand their role in disease, it is important to determine the parent-of-origin and timing of mutational events that give rise to these mutations, especially in sex-specific developmental disorders such as male infertility. However, currently available short-read sequencing approaches are not ideally suited for phasing, as this requires long continuous DNA strands that span both the DNM and one or more informative single-nucleotide polymorphisms. To overcome these challenges, we optimized and implemented a multiplexed long-read sequencing approach using Oxford Nanopore technologies MinION platform. We focused on improving target amplification, integrating long-read sequenced data with high-quality short-read sequence data, and developing an anchored phasing computational method. This approach handled the inherent phasing challenges of long-range target amplification and the normal accumulation of sequencing error associated with long-read sequencing. In total, 77 of 109 DNMs (71%) were successfully phased and parent-of-origin identified. The majority of phased DNMs were prezygotic (90%), the accuracy of which is highlighted by an average mutant allele frequency of 49.6% and standard error of 0.84%. This study demonstrates the benefits of employing an integrated short-read and long-read sequencing approach for large-scale DNM phasing.
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Affiliation(s)
- Giles S. Holt
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Lois E. Batty
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Bilal K. S. Alobaidi
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Hannah E. Smith
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Manon S. Oud
- Department of Human Genetics, Donders Institute for BrainCognition and Behaviour, RadboudumcNijmegenThe Netherlands
| | - Liliana Ramos
- Department of Obstetrics and Gynecology, Division of Reproductive MedicineRadboudumcNijmegenThe Netherlands
| | - Miguel J. Xavier
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Joris A. Veltman
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
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177
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Cope H, Ivimey-Cook ER, Moorad J. Triparental ageing in a laboratory population of an insect with maternal care. Behav Ecol 2022; 33:1123-1132. [PMID: 36518633 PMCID: PMC9735237 DOI: 10.1093/beheco/arac078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 07/13/2022] [Accepted: 08/08/2022] [Indexed: 09/10/2024] Open
Abstract
Parental age at reproduction influences offspring size and survival by affecting prenatal and postnatal conditions in a wide variety of species, including humans. However, most investigations into this manifestation of ageing focus upon maternal age effects; the effects of paternal age and interactions between maternal and paternal age are often neglected. Furthermore, even when maternal age effects are studied, pre- and post-natal effects are often confounded. Using a cross-fostered experimental design, we investigated the joint effects of pre-natal paternal and maternal and post-natal maternal ages on five traits related to offspring outcomes in a laboratory population of a species of burying beetle, Nicrophorus vespilloides. We found a significant positive effect of the age of the egg producer on larval survival to dispersal. We found more statistical evidence for interaction effects, which acted on larval survival and egg length. Both interaction effects were negative and involved the age of the egg-producer, indicating that age-related pre-natal maternal improvements were mitigated by increasing age in fathers and foster mothers. These results agree with an early study that found little evidence for maternal senescence, but it emphasizes that parental age interactions may be an important contributor to ageing patterns. We discuss how the peculiar life history of this species may promote selection to resist the evolution of parental age effects, and how this might have influenced our ability to detect senescence.
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Affiliation(s)
- Hilary Cope
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Edward R Ivimey-Cook
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jacob Moorad
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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178
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Maleszka R, Kucharski R. Without mechanisms, theories and models in insect epigenetics remain a black box. Trends Genet 2022; 38:1108-1111. [PMID: 35623905 DOI: 10.1016/j.tig.2022.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 01/24/2023]
Abstract
Insect epigenetics must confront the remarkable diversity of epigenomic systems in various lineages and use mechanistic approaches to move beyond vague functional explanations based on predictions and inferences. To accelerate progress, what is required now is a convergence of genomic data with biochemical and single-cell-type analyses in selected species representing contrasting evolutionary solutions in epigenetics.
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Affiliation(s)
- Ryszard Maleszka
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia.
| | - Robert Kucharski
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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179
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Characteristics and treatment patterns of autism spectrum disorder in China, 2020. Psychiatry Res 2022; 317:114879. [PMID: 36215776 DOI: 10.1016/j.psychres.2022.114879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/20/2022] [Accepted: 10/01/2022] [Indexed: 01/05/2023]
Abstract
This study aimed to investigate the characteristics of children diagnosed with ASD in China and to estimate ASD treatment patterns in 2020. This study used data from the 2020 Survey on Family Circumstance and Demand Support and Resources among Autistic Children in China. The study sample included 4,557 children diagnosed with ASD aged 2-16 years old. Data were collected through questionnaires completed by parents. Of the 4,557 children with ASD, there was a male-to-female ratio of 5.75:1, and the average age when ASD risk symptoms were first reported was 27.97(SD=10.83) months. Higher proportions of families with highly educated parents (college and above; around 58%) and advanced parental age at childbirth (≥35 years; over 50%) were found among autistic children. Additionally, about 41.05% of autistic children had an immediate family member diagnosed with mental/intellectual disorders. In terms of the treatment patterns for autistic children, 84.82% had received behavioral and developmental treatments and 77.74% had received therapy-based treatments, whereas 3% children had not received any treatment. Higher odds of non-treatment were found among children who were male (OR=1.69, 95% CI: 1.01,3.03) and had ASD diagnosed later on (OR= 1.02, 95% CI:1.01,1.03), as compared to their counterparts. Future studies will need to explore the etiology of the disparities of ASD, and policy efforts are critically needed to understand and address the barriers for children with ASD to receive appropriate treatments.
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180
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Kim IB, Lee T, Lee J, Kim J, Lee S, Koh IG, Kim JH, An JY, Lee H, Kim WK, Ju YS, Cho Y, Yu SJ, Kim SA, Oh M, Han DW, Kim E, Choi JK, Yoo HJ, Lee JH. Non-coding de novo mutations in chromatin interactions are implicated in autism spectrum disorder. Mol Psychiatry 2022; 27:4680-4694. [PMID: 35840799 DOI: 10.1038/s41380-022-01697-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 06/27/2022] [Accepted: 07/01/2022] [Indexed: 12/14/2022]
Abstract
Three-dimensional chromatin interactions regulate gene expressions. The significance of de novo mutations (DNMs) in chromatin interactions remains poorly understood for autism spectrum disorder (ASD). We generated 813 whole-genome sequences from 242 Korean simplex families to detect DNMs, and identified target genes which were putatively affected by non-coding DNMs in chromatin interactions. Non-coding DNMs in chromatin interactions were significantly involved in transcriptional dysregulations related to ASD risk. Correspondingly, target genes showed spatiotemporal expressions relevant to ASD in developing brains and enrichment in biological pathways implicated in ASD, such as histone modification. Regarding clinical features of ASD, non-coding DNMs in chromatin interactions particularly contributed to low intelligence quotient levels in ASD probands. We further validated our findings using two replication cohorts, Simons Simplex Collection (SSC) and MSSNG, and showed the consistent enrichment of non-coding DNM-disrupted chromatin interactions in ASD probands. Generating human induced pluripotent stem cells in two ASD families, we were able to demonstrate that non-coding DNMs in chromatin interactions alter the expression of target genes at the stage of early neural development. Taken together, our findings indicate that non-coding DNMs in ASD probands lead to early neurodevelopmental disruption implicated in ASD risk via chromatin interactions.
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Affiliation(s)
- Il Bin Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Department of Psychiatry, Hanyang University Guri Hospital, Guri, 11923, Republic of Korea
| | - Taeyeop Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Department of Psychiatry, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Junehawk Lee
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Jonghun Kim
- Department of Genetics, Yale Stem Cell Center, Yale Child Study Center, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Suho Lee
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, 34141, Republic of Korea
| | - In Gyeong Koh
- Industry-University Cooperation Foundation, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jae Hyun Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea.,BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea.,School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea
| | - Joon-Yong An
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea.,BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea.,School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea
| | - Hyunseong Lee
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul, 05030, Republic of Korea
| | - Woo Kyeong Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yongseong Cho
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Seok Jong Yu
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Soon Ae Kim
- Department of Pharmacology, Eulji University, Daejeon, 13135, Republic of Korea
| | - Miae Oh
- Department of Psychiatry, Kyung Hee University Hospital, Seoul, 02447, Republic of Korea
| | - Dong Wook Han
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China.,Organoid sciences, Ltd., Bundang-gu, Seongnam, 13488, Republic of Korea
| | - Eunjoon Kim
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, 34141, Republic of Korea. .,Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
| | - Hee Jeong Yoo
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea. .,Department of Psychiatry, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| | - Jeong Ho Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea. .,Sovargen Co. Ltd., Daejeon, 34051, Republic of Korea.
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181
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Du H, Jolly A, Grochowski CM, Yuan B, Dawood M, Jhangiani SN, Li H, Muzny D, Fatih JM, Coban-Akdemir Z, Carlin ME, Scheuerle AE, Witzl K, Posey JE, Pendleton M, Harrington E, Juul S, Hastings PJ, Bi W, Gibbs RA, Sedlazeck FJ, Lupski JR, Carvalho CMB, Liu P. The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation. Genome Med 2022; 14:122. [PMID: 36303224 PMCID: PMC9609164 DOI: 10.1186/s13073-022-01123-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 10/10/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The multiple de novo copy number variant (MdnCNV) phenotype is described by having four or more constitutional de novo CNVs (dnCNVs) arising independently throughout the human genome within one generation. It is a rare peri-zygotic mutational event, previously reported to be seen once in every 12,000 individuals referred for genome-wide chromosomal microarray analysis due to congenital abnormalities. These rare families provide a unique opportunity to understand the genetic factors of peri-zygotic genome instability and the impact of dnCNV on human diseases. METHODS Chromosomal microarray analysis (CMA), array-based comparative genomic hybridization, short- and long-read genome sequencing (GS) were performed on the newly identified MdnCNV family to identify de novo mutations including dnCNVs, de novo single-nucleotide variants (dnSNVs), and indels. Short-read GS was performed on four previously published MdnCNV families for dnSNV analysis. Trio-based rare variant analysis was performed on the newly identified individual and four previously published MdnCNV families to identify potential genetic etiologies contributing to the peri-zygotic genomic instability. Lin semantic similarity scores informed quantitative human phenotype ontology analysis on three MdnCNV families to identify gene(s) driving or contributing to the clinical phenotype. RESULTS In the newly identified MdnCNV case, we revealed eight de novo tandem duplications, each ~ 1 Mb, with microhomology at 6/8 breakpoint junctions. Enrichment of de novo single-nucleotide variants (SNV; 6/79) and de novo indels (1/12) was found within 4 Mb of the dnCNV genomic regions. An elevated post-zygotic SNV mutation rate was observed in MdnCNV families. Maternal rare variant analyses identified three genes in distinct families that may contribute to the MdnCNV phenomenon. Phenotype analysis suggests that gene(s) within dnCNV regions contribute to the observed proband phenotype in 3/3 cases. CNVs in two cases, a contiguous gene duplication encompassing PMP22 and RAI1 and another duplication affecting NSD1 and SMARCC2, contribute to the clinically observed phenotypic manifestations. CONCLUSIONS Characteristic features of dnCNVs reported here are consistent with a microhomology-mediated break-induced replication (MMBIR)-driven mechanism during the peri-zygotic period. Maternal genetic variants in DNA repair genes potentially contribute to peri-zygotic genomic instability. Variable phenotypic features were observed across a cohort of three MdnCNV probands, and computational quantitative phenotyping revealed that two out of three had evidence for the contribution of more than one genetic locus to the proband's phenotype supporting the hypothesis of de novo multilocus pathogenic variation (MPV) in those families.
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Affiliation(s)
- Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christopher M Grochowski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics Laboratory, Houston, TX, 77021, USA
- Seattle Children's Hospital, Seattle, WA, 98105, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - He Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Mary Esther Carlin
- Division of Genetics and Metabolism, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Angela E Scheuerle
- Division of Genetics and Metabolism, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Division of Genetics Diagnostics, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Karin Witzl
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, 1000, Ljubljana, Slovenia
- Medical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | | | | | - Sissel Juul
- Oxford Nanopore Technologies Inc, New York, NY, 10013, USA
| | - P J Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, BCM, Houston, TX, 77030, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics Laboratory, Houston, TX, 77021, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Fritz J Sedlazeck
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Texas Children's Hospital, Houston, TX, 77030, USA.
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Pacific Northwest Research Institute, 720 Broadway, Seattle, WA, 98122, USA.
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Baylor Genetics Laboratory, Houston, TX, 77021, USA.
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182
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Hanson HE, Liebl AL. The Mutagenic Consequences of DNA Methylation within and across Generations. EPIGENOMES 2022; 6:33. [PMID: 36278679 PMCID: PMC9624357 DOI: 10.3390/epigenomes6040033] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 12/28/2022] Open
Abstract
DNA methylation is an epigenetic modification with wide-ranging consequences across the life of an organism. This modification can be stable, persisting through development despite changing environmental conditions. However, in other contexts, DNA methylation can also be flexible, underlying organismal phenotypic plasticity. One underappreciated aspect of DNA methylation is that it is a potent mutagen; methylated cytosines mutate at a much faster rate than other genetic motifs. This mutagenic property of DNA methylation has been largely ignored in eco-evolutionary literature, despite its prevalence. Here, we explore how DNA methylation induced by environmental and other factors could promote mutation and lead to evolutionary change at a more rapid rate and in a more directed manner than through stochastic genetic mutations alone. We argue for future research on the evolutionary implications of DNA methylation driven mutations both within the lifetime of organisms, as well as across timescales.
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Affiliation(s)
- Haley E. Hanson
- Global and Planetary Health, University of South Florida, Tampa, FL 33620, USA
| | - Andrea L. Liebl
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
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183
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Sharman P, Young AJ, Wilson AJ. Evidence of maternal and paternal age effects on speed in thoroughbred racehorses. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220691. [PMID: 36249332 DOI: 10.5061/dryad.qbzkh18m0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/16/2022] [Indexed: 05/25/2023]
Abstract
Effects of parental age on offspring viability have been reported in a wide range of species. However, to what extent parental age influences offspring traits beyond viability remains unclear. Moreover, previous research has primarily focused on maternal age effects. The purpose of this study was to test for paternal and maternal age effects on offspring speed in thoroughbred racehorses. We analysed over 900 000 race performances by over 100 000 horses on British racecourses between 1996 and 2019. With knowledge of the age of all 41 107 dams and 2 887 sires at offspring conception, we jointly modelled maternal and paternal age effects using a 'within-individual centring' approach. Within-parents, we identified a significant effect of maternal age on offspring speed of -0.017 yards s-1 yr-1 and a corresponding paternal age effect of -0.011 yards s-1 yr-1. Although maternal age effects were stronger (more negative), the existence and magnitude of paternal effects is particularly noteworthy, given thoroughbred sires have no involvement in parental care. Our results also suggest that the selective disappearance of both sires and dams is ongoing. These findings could potentially be used to optimize thoroughbred racehorse breeding decisions, and more generally, add to the increasing body of evidence that both maternal and paternal age affect a range of offspring characteristics.
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Affiliation(s)
- Patrick Sharman
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
| | - Andrew J Young
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
| | - Alastair J Wilson
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
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184
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Sharman P, Young AJ, Wilson AJ. Evidence of maternal and paternal age effects on speed in thoroughbred racehorses. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220691. [PMID: 36249332 PMCID: PMC9532991 DOI: 10.1098/rsos.220691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/16/2022] [Indexed: 05/10/2023]
Abstract
Effects of parental age on offspring viability have been reported in a wide range of species. However, to what extent parental age influences offspring traits beyond viability remains unclear. Moreover, previous research has primarily focused on maternal age effects. The purpose of this study was to test for paternal and maternal age effects on offspring speed in thoroughbred racehorses. We analysed over 900 000 race performances by over 100 000 horses on British racecourses between 1996 and 2019. With knowledge of the age of all 41 107 dams and 2 887 sires at offspring conception, we jointly modelled maternal and paternal age effects using a 'within-individual centring' approach. Within-parents, we identified a significant effect of maternal age on offspring speed of -0.017 yards s-1 yr-1 and a corresponding paternal age effect of -0.011 yards s-1 yr-1. Although maternal age effects were stronger (more negative), the existence and magnitude of paternal effects is particularly noteworthy, given thoroughbred sires have no involvement in parental care. Our results also suggest that the selective disappearance of both sires and dams is ongoing. These findings could potentially be used to optimize thoroughbred racehorse breeding decisions, and more generally, add to the increasing body of evidence that both maternal and paternal age affect a range of offspring characteristics.
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Affiliation(s)
- Patrick Sharman
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
| | - Andrew J. Young
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
| | - Alastair J. Wilson
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
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185
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Sharman P, Young AJ, Wilson AJ. Evidence of maternal and paternal age effects on speed in thoroughbred racehorses. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220691. [PMID: 36249332 DOI: 10.6084/m9.figshare.c.6228607] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/16/2022] [Indexed: 05/25/2023]
Abstract
Effects of parental age on offspring viability have been reported in a wide range of species. However, to what extent parental age influences offspring traits beyond viability remains unclear. Moreover, previous research has primarily focused on maternal age effects. The purpose of this study was to test for paternal and maternal age effects on offspring speed in thoroughbred racehorses. We analysed over 900 000 race performances by over 100 000 horses on British racecourses between 1996 and 2019. With knowledge of the age of all 41 107 dams and 2 887 sires at offspring conception, we jointly modelled maternal and paternal age effects using a 'within-individual centring' approach. Within-parents, we identified a significant effect of maternal age on offspring speed of -0.017 yards s-1 yr-1 and a corresponding paternal age effect of -0.011 yards s-1 yr-1. Although maternal age effects were stronger (more negative), the existence and magnitude of paternal effects is particularly noteworthy, given thoroughbred sires have no involvement in parental care. Our results also suggest that the selective disappearance of both sires and dams is ongoing. These findings could potentially be used to optimize thoroughbred racehorse breeding decisions, and more generally, add to the increasing body of evidence that both maternal and paternal age affect a range of offspring characteristics.
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Affiliation(s)
- Patrick Sharman
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
| | - Andrew J Young
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
| | - Alastair J Wilson
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
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186
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Mohiuddin M, Kooy RF, Pearson CE. De novo mutations, genetic mosaicism and human disease. Front Genet 2022; 13:983668. [PMID: 36226191 PMCID: PMC9550265 DOI: 10.3389/fgene.2022.983668] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022] Open
Abstract
Mosaicism—the existence of genetically distinct populations of cells in a particular organism—is an important cause of genetic disease. Mosaicism can appear as de novo DNA mutations, epigenetic alterations of DNA, and chromosomal abnormalities. Neurodevelopmental or neuropsychiatric diseases, including autism—often arise by de novo mutations that usually not present in either of the parents. De novo mutations might occur as early as in the parental germline, during embryonic, fetal development, and/or post-natally, through ageing and life. Mutation timing could lead to mutation burden of less than heterozygosity to approaching homozygosity. Developmental timing of somatic mutation attainment will affect the mutation load and distribution throughout the body. In this review, we discuss the timing of de novo mutations, spanning from mutations in the germ lineage (all ages), to post-zygotic, embryonic, fetal, and post-natal events, through aging to death. These factors can determine the tissue specific distribution and load of de novo mutations, which can affect disease. The disease threshold burden of somatic de novo mutations of a particular gene in any tissue will be important to define.
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Affiliation(s)
- Mohiuddin Mohiuddin
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
| | - R. Frank Kooy
- Department of Medical Genetics, University of Antwerp, Edegem, Belgium
| | - Christopher E. Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
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187
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Gau CC, Lee HJ, Lu HY, Wu CY, Huang HY, Tsai HJ, Yao TC. Association of advanced paternal age with lung function at school age. Respir Res 2022; 23:259. [PMID: 36127724 PMCID: PMC9487029 DOI: 10.1186/s12931-022-02178-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Epidemiological studies suggest that advanced paternal age impact offspring health, but its impact on respiratory health is unclear. This study aimed to investigate the association of paternal age with lung function and fraction of exhaled nitric oxide (FeNO) in children. METHODS We analyzed data from 1330 single-born children (576 girls, 43.3%; mean age, 6.4 years), who participated in the Longitudinal Investigation of Global Health in Taiwanese Schoolchildren (LIGHTS) cohort and received measurements of lung function and FeNO at 6-year follow-up visits. Covariate-adjusted regression analyses were applied. RESULTS Every 5-year increase in paternal age at birth was associated with 0.51% decrease in FEV1/FVC ratio (95% CI - 0.86 to - 0.15; p = 0.005) and 19.86 mL/s decrease in FEF75 (95% CI: - 34.07 to - 5.65; p = 0.006). Stratified analyses revealed that increasing paternal age at birth was associated with decreasing FEV1/FVC ratio and FEF75 only among children with prenatal exposure to environmental tobacco smoke (ETS) or not being breastfed. Sensitivity analyses using paternal age as a categorical variable found decreasing FEV1/FVC ratio and FEF75 in the groups of paternal age 35-39 and ≥ 40 years. There was no association of paternal age at birth with FeNO. CONCLUSION Our findings provide novel evidence linking advanced paternal age at birth with decreasing lung function in children at school age. Children with prenatal exposure to ETS or not being breastfed are more vulnerable to the adverse effect of advanced paternal age on childhood lung function. Further studies are warranted to confirm this novel adverse effect of advanced paternal age.
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Affiliation(s)
- Chun-Chun Gau
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, 5 Fu-Hsin Street, Kweishan, Taoyuan, Taiwan
- School of Medicine, Chang Gung University College of Medicine, Taoyuan, Taiwan
- Division of Pediatric General Medicine, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Pediatrics, New Taipei Municipal TuCheng Hospital, New Taipei, Taiwan
| | - Hsin-Ju Lee
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, 5 Fu-Hsin Street, Kweishan, Taoyuan, Taiwan
| | - Hung-Yi Lu
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, 5 Fu-Hsin Street, Kweishan, Taoyuan, Taiwan
| | - Chao-Yi Wu
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, 5 Fu-Hsin Street, Kweishan, Taoyuan, Taiwan
- School of Medicine, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Hsin-Yi Huang
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, 5 Fu-Hsin Street, Kweishan, Taoyuan, Taiwan
| | - Hui-Ju Tsai
- Institute of Population Health Sciences, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County, 35053, Taiwan.
| | - Tsung-Chieh Yao
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, 5 Fu-Hsin Street, Kweishan, Taoyuan, Taiwan.
- School of Medicine, Chang Gung University College of Medicine, Taoyuan, Taiwan.
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188
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Zhou M, Yao T, Li J, Hui H, Fan W, Guan Y, Zhang A, Xu B. Preliminary prediction of semen quality based on modifiable lifestyle factors by using the XGBoost algorithm. Front Med (Lausanne) 2022; 9:811890. [PMID: 36177329 PMCID: PMC9514383 DOI: 10.3389/fmed.2022.811890] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 08/01/2022] [Indexed: 11/17/2022] Open
Abstract
Introduction Semen quality has decreased gradually in recent years, and lifestyle changes are among the primary causes for this issue. Thus far, the specific lifestyle factors affecting semen quality remain to be elucidated. Materials and methods In this study, data on the following factors were collected from 5,109 men examined at our reproductive medicine center: 10 lifestyle factors that potentially affect semen quality (smoking status, alcohol consumption, staying up late, sleeplessness, consumption of pungent food, intensity of sports activity, sedentary lifestyle, working in hot conditions, sauna use in the last 3 months, and exposure to radioactivity); general factors including age, abstinence period, and season of semen examination; and comprehensive semen parameters [semen volume, sperm concentration, progressive and total sperm motility, sperm morphology, and DNA fragmentation index (DFI)]. Then, machine learning with the XGBoost algorithm was applied to establish a primary prediction model by using the collected data. Furthermore, the accuracy of the model was verified via multiple logistic regression following k-fold cross-validation analyses. Results The results indicated that for semen volume, sperm concentration, progressive and total sperm motility, and DFI, the area under the curve (AUC) values ranged from 0.648 to 0.697, while the AUC for sperm morphology was only 0.506. Among the 13 factors, smoking status was the major factor affecting semen volume, sperm concentration, and progressive and total sperm motility. Age was the most important factor affecting DFI. Logistic combined with cross-validation analysis revealed similar results. Furthermore, it showed that heavy smoking (>20 cigarettes/day) had an overall negative effect on semen volume and sperm concentration and progressive and total sperm motility (OR = 4.69, 6.97, 11.16, and 10.35, respectively), while age of >35 years was associated with increased DFI (OR = 5.47). Conclusion The preliminary lifestyle-based model developed for semen quality prediction by using the XGBoost algorithm showed potential for clinical application and further optimization with larger training datasets.
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Affiliation(s)
- Mingjuan Zhou
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianci Yao
- Shanghai National Engineering Research Center of Digital Television Co., Ltd., Shanghai, China
| | - Jian Li
- Clinical Research Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Hui
- Cooperative Medianet Innovation Center, Shanghai Jiao Tong University, Shanghai, China
| | - Weimin Fan
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunfeng Guan
- School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Yunfeng Guan
| | - Aijun Zhang
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Aijun Zhang
| | - Bufang Xu
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Bufang Xu
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189
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Vihinen M. Individual Genetic Heterogeneity. Genes (Basel) 2022; 13:1626. [PMID: 36140794 PMCID: PMC9498725 DOI: 10.3390/genes13091626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/25/2022] [Accepted: 09/08/2022] [Indexed: 11/28/2022] Open
Abstract
Genetic variation has been widely covered in literature, however, not from the perspective of an individual in any species. Here, a synthesis of genetic concepts and variations relevant for individual genetic constitution is provided. All the different levels of genetic information and variation are covered, ranging from whether an organism is unmixed or hybrid, has variations in genome, chromosomes, and more locally in DNA regions, to epigenetic variants or alterations in selfish genetic elements. Genetic constitution and heterogeneity of microbiota are highly relevant for health and wellbeing of an individual. Mutation rates vary widely for variation types, e.g., due to the sequence context. Genetic information guides numerous aspects in organisms. Types of inheritance, whether Mendelian or non-Mendelian, zygosity, sexual reproduction, and sex determination are covered. Functions of DNA and functional effects of variations are introduced, along with mechanism that reduce and modulate functional effects, including TARAR countermeasures and intraindividual genetic conflict. TARAR countermeasures for tolerance, avoidance, repair, attenuation, and resistance are essential for life, integrity of genetic information, and gene expression. The genetic composition, effects of variations, and their expression are considered also in diseases and personalized medicine. The text synthesizes knowledge and insight on individual genetic heterogeneity and organizes and systematizes the central concepts.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, BMC B13, Lund University, SE-22184 Lund, Sweden
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190
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Gondo Y. DETECTION OF TRANSGENERATIONAL GENETIC EFFECTS BASED ON WHOLE-GENOME SEQUENCING IN THE MOUSE MODEL. RADIATION PROTECTION DOSIMETRY 2022; 198:1137-1142. [PMID: 36083724 DOI: 10.1093/rpd/ncac079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
It has become feasible to detect de novo mutations in mammalian genomes by using whole-genome sequencing. The power to detect numbers of de novo mutations should provide a useful tool to assess the transgenerational genetic effects of radiations on living organisms. By reviewing the spontaneous mutations in the mouse as a model, an action plan is proposed to detect the induced mutations after accumulating mutations for several generations with continuous exposure to low-dose radiations. Some susceptibility differences against radiations between humans and model animals for the transgenerational effect have been suggested. The applicability of the mouse model for the assessment of low-dose radiation is also discussed.
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Affiliation(s)
- Yoichi Gondo
- Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimo-Kasuya, Isehara, Kanagawa 259-1193, Japan
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191
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Byrska-Bishop M, Evani US, Zhao X, Basile AO, Abel HJ, Regier AA, Corvelo A, Clarke WE, Musunuri R, Nagulapalli K, Fairley S, Runnels A, Winterkorn L, Lowy E, Paul Flicek, Germer S, Brand H, Hall IM, Talkowski ME, Narzisi G, Zody MC. High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios. Cell 2022; 185:3426-3440.e19. [PMID: 36055201 PMCID: PMC9439720 DOI: 10.1016/j.cell.2022.08.004] [Citation(s) in RCA: 296] [Impact Index Per Article: 148.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 06/21/2022] [Accepted: 08/03/2022] [Indexed: 01/05/2023]
Abstract
The 1000 Genomes Project (1kGP) is the largest fully open resource of whole-genome sequencing (WGS) data consented for public distribution without access or use restrictions. The final, phase 3 release of the 1kGP included 2,504 unrelated samples from 26 populations and was based primarily on low-coverage WGS. Here, we present a high-coverage 3,202-sample WGS 1kGP resource, which now includes 602 complete trios, sequenced to a depth of 30X using Illumina. We performed single-nucleotide variant (SNV) and short insertion and deletion (INDEL) discovery and generated a comprehensive set of structural variants (SVs) by integrating multiple analytic methods through a machine learning model. We show gains in sensitivity and precision of variant calls compared to phase 3, especially among rare SNVs as well as INDELs and SVs spanning frequency spectrum. We also generated an improved reference imputation panel, making variants discovered here accessible for association studies.
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Affiliation(s)
| | | | - Xuefang Zhao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | | | - Haley J Abel
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Allison A Regier
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Wayne E Clarke
- New York Genome Center, New York, NY 10013, USA; Outlier Informatics Inc., Saskatoon, SK S7H 1L4, Canada
| | | | | | - Susan Fairley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | | | - Ernesto Lowy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Harrison Brand
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ira M Hall
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Genomic Health, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Michael E Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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192
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Antaki D, Guevara J, Maihofer AX, Klein M, Gujral M, Grove J, Carey CE, Hong O, Arranz MJ, Hervas A, Corsello C, Vaux KK, Muotri AR, Iakoucheva LM, Courchesne E, Pierce K, Gleeson JG, Robinson EB, Nievergelt CM, Sebat J. A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex. Nat Genet 2022; 54:1284-1292. [PMID: 35654974 PMCID: PMC9474668 DOI: 10.1038/s41588-022-01064-5] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/28/2022] [Indexed: 01/21/2023]
Abstract
The genetic etiology of autism spectrum disorder (ASD) is multifactorial, but how combinations of genetic factors determine risk is unclear. In a large family sample, we show that genetic loads of rare and polygenic risk are inversely correlated in cases and greater in females than in males, consistent with a liability threshold that differs by sex. De novo mutations (DNMs), rare inherited variants and polygenic scores were associated with various dimensions of symptom severity in children and parents. Parental age effects on risk for ASD in offspring were attributable to a combination of genetic mechanisms, including DNMs that accumulate in the paternal germline and inherited risk that influences behavior in parents. Genes implicated by rare variants were enriched in excitatory and inhibitory neurons compared with genes implicated by common variants. Our results suggest that a phenotypic spectrum of ASD is attributable to a spectrum of genetic factors that impact different neurodevelopmental processes.
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Affiliation(s)
- Danny Antaki
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
- Beyster Center for Psychiatric Genomics, University of California San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - James Guevara
- Beyster Center for Psychiatric Genomics, University of California San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Adam X Maihofer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Marieke Klein
- Beyster Center for Psychiatric Genomics, University of California San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Madhusudan Gujral
- Beyster Center for Psychiatric Genomics, University of California San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Jakob Grove
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine and Center for Integrative Sequencing, iSEQ, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Caitlin E Carey
- Harvard T.H. Chan School of Public Health, Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Oanh Hong
- Beyster Center for Psychiatric Genomics, University of California San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Maria J Arranz
- Research Laboratory Unit, Fundacio Docencia i Recerca Mutua, Terrassa, Spain
| | - Amaia Hervas
- Child and Adolescent Mental Health Unit, Hospital Universitari Mútua de Terrassa, Barcelona, Spain
| | - Christina Corsello
- TEACCH Autism Program, University of North Carolina, Chapel Hill, NC, USA
| | | | - Alysson R Muotri
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics and Department of Cellular & Molecular Medicine, University of California San Diego, School of Medicine, Center for Academic Research and Training in Anthropogeny, Archealization Center, Kavli Institute for Brain and Mind, La Jolla, CA, USA
| | - Lilia M Iakoucheva
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Eric Courchesne
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Autism Center of Excellence, University of California San Diego, La Jolla, CA, USA
| | - Karen Pierce
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Autism Center of Excellence, University of California San Diego, La Jolla, CA, USA
| | - Joseph G Gleeson
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Elise B Robinson
- Harvard T.H. Chan School of Public Health, Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | | | - Jonathan Sebat
- Beyster Center for Psychiatric Genomics, University of California San Diego, La Jolla, CA, USA.
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
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193
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Omolaoye TS, El Shahawy O, Skosana BT, Boillat T, Loney T, du Plessis SS. The mutagenic effect of tobacco smoke on male fertility. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:62055-62066. [PMID: 34536221 PMCID: PMC9464177 DOI: 10.1007/s11356-021-16331-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 08/30/2021] [Indexed: 05/15/2023]
Abstract
Despite the association between tobacco use and the harmful effects on general health as well as male fertility parameters, smoking remains globally prevalent. The main content of tobacco smoke is nicotine and its metabolite cotinine. These compounds can pass the blood-testis barrier, which subsequently causes harm of diverse degree to the germ cells. Although controversial, smoking has been shown to cause not only a decrease in sperm motility, sperm concentration, and an increase in abnormal sperm morphology, but also genetic and epigenetic aberrations in spermatozoa. Both animal and human studies have highlighted the occurrence of sperm DNA-strand breaks (fragmentation), genome instability, genetic mutations, and the presence of aneuploids in the germline of animals and men exposed to tobacco smoke. The question to be asked at this point is, if smoking has the potential to cause all these genetic aberrations, what is the extent of damage? Hence, this review aimed to provide evidence that smoking has a mutagenic effect on sperm and how this subsequently affects male fertility. Additionally, the role of tobacco smoke as an aneugen will be explored. We furthermore aim to incorporate the epidemiological aspects of the aforementioned and provide a holistic approach to the topic.
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Affiliation(s)
- Temidayo S Omolaoye
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Omar El Shahawy
- Department of Population Health, New York University Grossman School of Medicine, New York City, NY, USA
| | - Bongekile T Skosana
- Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Thomas Boillat
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Tom Loney
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Stefan S du Plessis
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.
- Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
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Zhang C, Yan L, Qiao J. Effect of advanced parental age on pregnancy outcome and offspring health. J Assist Reprod Genet 2022; 39:1969-1986. [PMID: 35925538 PMCID: PMC9474958 DOI: 10.1007/s10815-022-02533-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/24/2021] [Indexed: 10/16/2022] Open
Abstract
PURPOSE Fertility at advanced age has become increasingly common, but the aging of parents may adversely affect the maturation of gametes and the development of embryos, and therefore the effects of aging are likely to be transmitted to the next generation. This article reviewed the studies in this field in recent years. METHODS We searched the relevant literature in recent years with the keywords of "advanced maternal/paternal age" combined with "adverse pregnancy outcome" or "birth defect" in the PubMed database and classified the effects of parental advanced age on pregnancy outcomes and birth defects. Related studies on the effect of advanced age on birth defects were classified as chromosomal abnormalities, neurological and psychiatric disorders, and other systemic diseases. The effect of assisted reproduction technology (ART) on fertility in advanced age was also discussed. RESULTS Differences in the definition of the range of advanced age and other confounding factors among studies were excluded, most studies believed that advanced parental age would affect pregnancy outcomes and birth defects in offspring. CONCLUSION To some extent, advanced parental age caused adverse pregnancy outcomes and birth defects. The occurrence of these results was related to the molecular genetic changes caused by aging, such as gene mutations, epigenetic variations, etc. Any etiology of adverse pregnancy outcomes and birth defects related to aging might be more than one. The detrimental effect of advanced age can be corrected to some extent by ART.
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Affiliation(s)
- Cong Zhang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North garden road, Haidian district, Beijing, 100191, People's Republic of China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest (Chinese Academy of Medical Sciences), Beijing, 100191, China
- Savid Medical College (University of Chinese Academy of Sciences), Beijing, 100049, China
| | - Liying Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North garden road, Haidian district, Beijing, 100191, People's Republic of China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest (Chinese Academy of Medical Sciences), Beijing, 100191, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North garden road, Haidian district, Beijing, 100191, People's Republic of China.
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest (Chinese Academy of Medical Sciences), Beijing, 100191, China.
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195
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Warrier V, Zhang X, Reed P, Havdahl A, Moore TM, Cliquet F, Leblond CS, Rolland T, Rosengren A, Rowitch DH, Hurles ME, Geschwind DH, Børglum AD, Robinson EB, Grove J, Martin HC, Bourgeron T, Baron-Cohen S. Genetic correlates of phenotypic heterogeneity in autism. Nat Genet 2022; 54:1293-1304. [PMID: 35654973 PMCID: PMC9470531 DOI: 10.1038/s41588-022-01072-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 04/01/2022] [Indexed: 12/27/2022]
Abstract
The substantial phenotypic heterogeneity in autism limits our understanding of its genetic etiology. To address this gap, here we investigated genetic differences between autistic individuals (nmax = 12,893) based on core and associated features of autism, co-occurring developmental disabilities and sex. We conducted a comprehensive factor analysis of core autism features in autistic individuals and identified six factors. Common genetic variants were associated with the core factors, but de novo variants were not. We found that higher autism polygenic scores (PGS) were associated with lower likelihood of co-occurring developmental disabilities in autistic individuals. Furthermore, in autistic individuals without co-occurring intellectual disability (ID), autism PGS are overinherited by autistic females compared to males. Finally, we observed higher SNP heritability for autistic males and for autistic individuals without ID. Deeper phenotypic characterization will be critical in determining how the complex underlying genetics shape cognition, behavior and co-occurring conditions in autism.
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Affiliation(s)
- Varun Warrier
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK.
| | - Xinhe Zhang
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Patrick Reed
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Alexandra Havdahl
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
- Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway
- PROMENTA Research Center, Department of Psychology, University of Oslo, Oslo, Norway
| | - Tyler M Moore
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Lifespan Brain Institute of the Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA, USA
| | - Freddy Cliquet
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris Cité, Paris, France
| | - Claire S Leblond
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris Cité, Paris, France
| | - Thomas Rolland
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris Cité, Paris, France
| | - Anders Rosengren
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Institute of Biological Psychiatry, MHC Sct Hans, Copenhagen University Hospital, Copenhagen, Denmark
| | - David H Rowitch
- Department of Paediatrics, Cambridge University Clinical School, Cambridge, UK
| | - Matthew E Hurles
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Daniel H Geschwind
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine (CGPM), Aarhus University, Aarhus, Denmark
- Department of Biomedicine (Human Genetics) and iSEQ Center, Aarhus University, Aarhus, Denmark
| | - Elise B Robinson
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine (CGPM), Aarhus University, Aarhus, Denmark
- Department of Biomedicine (Human Genetics) and iSEQ Center, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Hilary C Martin
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris Cité, Paris, France
| | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK.
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196
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Khachadourian V, Zaks N, Lin E, Reichenberg A, Janecka M. Reprint of: Advanced paternal age and risk of schizophrenia in offspring - Review of epidemiological findings and potential mechanisms. Schizophr Res 2022; 247:84-91. [PMID: 36085274 DOI: 10.1016/j.schres.2022.08.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 11/28/2022]
Abstract
A large number of studies have examined the association between advanced paternal age (APA) and risk of schizophrenia in offspring. Here we present an overview of epidemiological studies on this subject published since 2000, and systematically summarize their methodologies and results. Next, we discuss evidence to elucidate the potential mechanisms contributing to the association between APA and offspring schizophrenia, considering paternal psychiatric morbidity and genetic liability, maternal factors, and findings from family design studies. We propose that multiple mechanisms, including causal and non-causal pathways, contribute to the observed relationship between APA and schizophrenia in offspring, and conclude by highlighting the need for multi-disciplinary studies in disentangling these complex, non-mutually exclusive mechanisms.
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Affiliation(s)
- Vahe Khachadourian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America; Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America.
| | - Nina Zaks
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Emma Lin
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America; Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Abraham Reichenberg
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America; Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America; Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Magdalena Janecka
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America; Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
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197
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Abstract
Genetic diseases disrupt the functionality of an infant's genome during fetal-neonatal adaptation and represent a leading cause of neonatal and infant mortality in the United States. Due to disease acuity, gene locus and allelic heterogeneity, and overlapping and diverse clinical phenotypes, diagnostic genome sequencing in neonatal intensive care units has required the development of methods to shorten turnaround times and improve genomic interpretation. From 2012 to 2021, 31 clinical studies documented the diagnostic and clinical utility of first-tier rapid or ultrarapid whole-genome sequencing through cost-effective identification of pathogenic genomic variants that change medical management, suggest new therapeutic strategies, and refine prognoses. Genomic diagnosis also permits prediction of reproductive recurrence risk for parents and surviving probands. Using implementation science and quality improvement, deployment of a genomic learning healthcare system will contribute to a reduction of neonatal and infant mortality through the integration of genome sequencing into best-practice neonatal intensive care.
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Affiliation(s)
- Stephen F. Kingsmore
- Rady Children’s Hospital Institute for Genomic Medicine, Rady Children’s Hospital-San Diego
| | - F. Sessions Cole
- Division of Newborn Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine in St. Louis
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198
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Stolzenbach V, Woods DC, Tilly JL. Non-neutral clonal selection and its potential role in mammalian germline stem cell dysfunction with advancing age. Front Cell Dev Biol 2022; 10:942652. [PMID: 36081905 PMCID: PMC9445274 DOI: 10.3389/fcell.2022.942652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
The concept of natural selection, or "survival of the fittest", refers to an evolutionary process in nature whereby traits emerge in individuals of a population through random gene alterations that enable those individuals to better adapt to changing environmental conditions. This genetic variance allows certain members of the population to gain an advantage over others in the same population to survive and reproduce in greater numbers under new environmental pressures, with the perpetuation of those advantageous traits in future progeny. Here we present that the behavior of adult stem cells in a tissue over time can, in many respects, be viewed in the same manner as evolution, with each stem cell clone being representative of an individual within a population. As stem cells divide or are subjected to cumulative oxidative damage over the lifespan of the organism, random genetic alterations are introduced into each clone that create variance in the population. These changes may occur in parallel to, or in response to, aging-associated changes in microenvironmental cues perceived by the stem cell population. While many of these alterations will be neutral or silent in terms of affecting cell function, a small fraction of these changes will enable certain clones to respond differently to shifts in microenvironmental conditions that arise with advancing age. In some cases, the same advantageous genetic changes that support survival and expansion of certain clones over others in the population (viz. non-neutral competition) could be detrimental to the downstream function of the differentiated stem cell descendants. In the context of the germline, such a situation would be devastating to successful propagation of the species across generations. However, even within a single generation, the “evolution” of stem cell lineages in the body over time can manifest into aging-related organ dysfunction and failure, as well as lead to chronic inflammation, hyperplasia, and cancer. Increased research efforts to evaluate stem cells within a population as individual entities will improve our understanding of how organisms age and how certain diseases develop, which in turn may open new opportunities for clinical detection and management of diverse pathologies.
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199
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Mai L, Inada H, Kimura R, Kanno K, Matsuda T, Tachibana RO, Tucci V, Komaki F, Hiroi N, Osumi N. Advanced paternal age diversifies individual trajectories of vocalization patterns in neonatal mice. iScience 2022; 25:104834. [PMID: 36039363 PMCID: PMC9418688 DOI: 10.1016/j.isci.2022.104834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/27/2022] [Accepted: 07/20/2022] [Indexed: 10/25/2022] Open
Abstract
Infant crying is a communicative behavior impaired in neurodevelopmental disorders (NDDs). Because advanced paternal age is a risk factor for NDDs, we performed computational approaches to evaluate how paternal age affected vocal communication and body weight development in C57BL/6 mouse offspring from young and aged fathers. Analyses of ultrasonic vocalization (USV) consisting of syllables showed that advanced paternal age reduced the number and duration of syllables, altered the syllable composition, and caused lower body weight gain in pups. Pups born to young fathers had convergent vocal characteristics with a rich repertoire, whereas those born to aged fathers exhibited more divergent vocal patterns with limited repertoire. Additional analyses revealed that some pups from aged fathers displayed atypical USV trajectories. Thus, our study indicates that advanced paternal age has a significant effect on offspring's vocal development. Our computational analyses are effective in characterizing altered individual diversity.
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Affiliation(s)
- Lingling Mai
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Hitoshi Inada
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan.,Laboratory of Health and Sports Sciences, Division of Biomedical Engineering for Health and Welfare, Tohoku University Graduate School of Biomedical Engineering, Sendai 980-8575, Japan
| | - Ryuichi Kimura
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan.,Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Kouta Kanno
- Faculty of Law, Economics and Humanities, Kagoshima University, Kagoshima 890-0065, Japan
| | - Takeru Matsuda
- Statistical Mathematics Unit, RIKEN Center for Brain Science, Wako 351-0198, Japan
| | - Ryosuke O Tachibana
- Department of Life Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Valter Tucci
- Genetics and Epigenetics of Behavior (GEB) Laboratory, Istituto Italiano di Tecnologia, Genova 16163, Italy
| | - Fumiyasu Komaki
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo 113-8656, Japan.,Mathematical Informatics Collaboration Unit, RIKEN Center for Brain Science, Wako 351-0198, Japan
| | - Noboru Hiroi
- Department of Pharmacology, University of Texas Health Science Center at San Antonio, San Antonio 78229, USA.,Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio 78229, USA.,Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio 78229, USA
| | - Noriko Osumi
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
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200
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de Manuel M, Wu FL, Przeworski M. A paternal bias in germline mutation is widespread in amniotes and can arise independently of cell division numbers. eLife 2022; 11:e80008. [PMID: 35916372 PMCID: PMC9439683 DOI: 10.7554/elife.80008] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
In humans and other mammals, germline mutations are more likely to arise in fathers than in mothers. Although this sex bias has long been attributed to DNA replication errors in spermatogenesis, recent evidence from humans points to the importance of mutagenic processes that do not depend on cell division, calling into question our understanding of this basic phenomenon. Here, we infer the ratio of paternal-to-maternal mutations, α, in 42 species of amniotes, from putatively neutral substitution rates of sex chromosomes and autosomes. Despite marked differences in gametogenesis, physiologies and environments across species, fathers consistently contribute more mutations than mothers in all the species examined, including mammals, birds, and reptiles. In mammals, α is as high as 4 and correlates with generation times; in birds and snakes, α appears more stable around 2. These observations are consistent with a simple model, in which mutations accrue at equal rates in both sexes during early development and at a higher rate in the male germline after sexual differentiation, with a conserved paternal-to-maternal ratio across species. Thus, α may reflect the relative contributions of two or more developmental phases to total germline mutations, and is expected to depend on generation time even if mutations do not track cell divisions.
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Affiliation(s)
- Marc de Manuel
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Felix L Wu
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Molly Przeworski
- Department of Systems Biology, Columbia UniversityNew YorkUnited States
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