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Waldvogel SM, Posey JE, Goodell MA. Human embryonic genetic mosaicism and its effects on development and disease. Nat Rev Genet 2024; 25:698-714. [PMID: 38605218 PMCID: PMC11408116 DOI: 10.1038/s41576-024-00715-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2024] [Indexed: 04/13/2024]
Abstract
Nearly every mammalian cell division is accompanied by a mutational event that becomes fixed in a daughter cell. When carried forward to additional cell progeny, a clone of variant cells can emerge. As a result, mammals are complex mosaics of clones that are genetically distinct from one another. Recent high-throughput sequencing studies have revealed that mosaicism is common, clone sizes often increase with age and specific variants can affect tissue function and disease development. Variants that are acquired during early embryogenesis are shared by multiple cell types and can affect numerous tissues. Within tissues, variant clones compete, which can result in their expansion or elimination. Embryonic mosaicism has clinical implications for genetic disease severity and transmission but is likely an under-recognized phenomenon. To better understand its implications for mosaic individuals, it is essential to leverage research tools that can elucidate the mechanisms by which expanded embryonic variants influence development and disease.
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Affiliation(s)
- Sarah M Waldvogel
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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2
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Wood KA, Tong RS, Motta M, Cordeddu V, Scimone ER, Bush SJ, Maxwell DW, Giannoulatou E, Caputo V, Traversa A, Mancini C, Ferrero GB, Benedicenti F, Grammatico P, Melis D, Steindl K, Brunetti-Pierri N, Trevisson E, Wilkie AO, Lin AE, Cormier-Daire V, Twigg SR, Tartaglia M, Goriely A. SMAD4 mutations causing Myhre syndrome are under positive selection in the male germline. Am J Hum Genet 2024; 111:1953-1969. [PMID: 39116879 DOI: 10.1016/j.ajhg.2024.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 08/10/2024] Open
Abstract
While it is widely thought that de novo mutations (DNMs) occur randomly, we previously showed that some DNMs are enriched because they are positively selected in the testes of aging men. These "selfish" mutations cause disorders with a shared presentation of features, including exclusive paternal origin, significant increase of the father's age, and high apparent germline mutation rate. To date, all known selfish mutations cluster within the components of the RTK-RAS-MAPK signaling pathway, a critical modulator of testicular homeostasis. Here, we demonstrate the selfish nature of the SMAD4 DNMs causing Myhre syndrome (MYHRS). By analyzing 16 informative trios, we show that MYHRS-causing DNMs originated on the paternally derived allele in all cases. We document a statistically significant epidemiological paternal age effect of 6.3 years excess for fathers of MYHRS probands. We developed an ultra-sensitive assay to quantify spontaneous MYHRS-causing SMAD4 variants in sperm and show that pathogenic variants at codon 500 are found at elevated level in sperm of most men and exhibit a strong positive correlation with donor's age, indicative of a high apparent germline mutation rate. Finally, we performed in vitro assays to validate the peculiar functional behavior of the clonally selected DNMs and explored the basis of the pathophysiology of the different SMAD4 sperm-enriched variants. Taken together, these data provide compelling evidence that SMAD4, a gene operating outside the canonical RAS-MAPK signaling pathway, is associated with selfish spermatogonial selection and raises the possibility that other genes/pathways are under positive selection in the aging human testis.
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Affiliation(s)
- Katherine A Wood
- MRC Weatherall Institute of Molecular Medicine, Oxford OX39DS, UK; Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX39DS, UK; NIHR Oxford Biomedical Research Centre, Oxford OX39DU, UK
| | - R Spencer Tong
- MRC Weatherall Institute of Molecular Medicine, Oxford OX39DS, UK; Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX39DS, UK; NIHR Oxford Biomedical Research Centre, Oxford OX39DU, UK
| | - Marialetizia Motta
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Viviana Cordeddu
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Eleanor R Scimone
- Medical Genetics, Mass General Brigham, Harvard Medical School, Harvard University, Boston, MA 02114, USA
| | - Stephen J Bush
- MRC Weatherall Institute of Molecular Medicine, Oxford OX39DS, UK; Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX39DS, UK; NIHR Oxford Biomedical Research Centre, Oxford OX39DU, UK
| | - Dale W Maxwell
- MRC Weatherall Institute of Molecular Medicine, Oxford OX39DS, UK; Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX39DS, UK; NIHR Oxford Biomedical Research Centre, Oxford OX39DU, UK
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, NSW 2010, Australia; School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Viviana Caputo
- Department of Experimental Medicine, Sapienza University, 00161 Rome, Italy
| | - Alice Traversa
- Department of Experimental Medicine, Sapienza University, 00161 Rome, Italy
| | - Cecilia Mancini
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Giovanni B Ferrero
- Department of Clinical and Biological Science, University of Torino, 10126 Turin, Italy
| | | | - Paola Grammatico
- Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, 00152 Rome, Italy
| | - Daniela Melis
- Department of Medicine, Surgery and Dentistry, University of Salerno, 84081 Salerno, Italy
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University, 80131 Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine Program, University of Naples Federico II, Naples, Italy
| | - Eva Trevisson
- Department of Women's and Children's Health, University of Padova, 35128 Padua, Italy
| | - Andrew Om Wilkie
- MRC Weatherall Institute of Molecular Medicine, Oxford OX39DS, UK; Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX39DS, UK; NIHR Oxford Biomedical Research Centre, Oxford OX39DU, UK
| | - Angela E Lin
- Medical Genetics, Mass General Brigham, Harvard Medical School, Harvard University, Boston, MA 02114, USA
| | - Valerie Cormier-Daire
- Université Paris Cité, Service de Médecine Génomique des Maladies Rares, INSERM UMR 1163, Institut Imagine, Hôpital Necker-Enfants Malades, 75015 Paris, France
| | - Stephen Rf Twigg
- MRC Weatherall Institute of Molecular Medicine, Oxford OX39DS, UK; Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX39DS, UK; NIHR Oxford Biomedical Research Centre, Oxford OX39DU, UK
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy.
| | - Anne Goriely
- MRC Weatherall Institute of Molecular Medicine, Oxford OX39DS, UK; Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX39DS, UK; NIHR Oxford Biomedical Research Centre, Oxford OX39DU, UK.
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杨 晓. [Sperm Mosaic Variants and Their Influence on the Offspring]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2024; 55:535-541. [PMID: 38948294 PMCID: PMC11211766 DOI: 10.12182/20240560507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Indexed: 07/02/2024]
Abstract
Genomic mosaicism arising from mosaic variants is a phenomenon that describes the presence of a cell or cell populations with different genome compositions from the germline cells of an individual. It comprises all types of genetic variants. A large proportion of childhood genetic disorders are defined as being de novo, meaning that the disease-causing mutations are only detected in the proband, not in any of the parents. Population studies show that 80% of the de novo mutations arise from the paternal haplotype, that is, from paternal sperm mosaicism. This review provides a summary of the types and detection strategies of sperm mosaicism. In addition, it provides discussions on how recent studies demonstrated that genomic mosaic mutations in parents, especially those in the paternal sperms, could be inherited by the offspring and cause childhood disorders. According to the previous findings of the author's research team, sperm mosaicism derived from early embryogenesis and primordial germ cell stages can explain 5% to 20% of the de novo mutations related to clinical phenotypes and can serve as an important predictor of both rare and complex disorders. Sperm mosaicism shows great potential for clinical genetic diagnosis and consultations. Based on the published literature, the author suggests that, large-scale screening for de novo sperm mosaic mutations and population-based genetic screening should be conducted in future studies, which will greatly enhance the risk assessment in the offspring and effectively improve the genetic health at the population level. Implementation of direct sperm detection for de novo mutations will significantly increase the efficiency of the stratification of patient cohorts and improve recurrence risk assessment for future births. Future research in the field should be focused on the impact of environmental and lifestyle factors on the health of the offspring through sperms and their modeling of mutation signatures. In addition, targeted in vitro modeling of sperm mutations will also be a promising direction.
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Affiliation(s)
- 晓旭 杨
- 犹他大学 (盐湖城 UT 84112)University of Utah, Salt Lake City, UT 84112, USA
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Juchnewitsch AG, Pomm K, Dutta A, Tamp E, Valkna A, Lillepea K, Mahyari E, Tjagur S, Belova G, Kübarsepp V, Castillo-Madeen H, Riera-Escamilla A, Põlluaas L, Nagirnaja L, Poolamets O, Vihljajev V, Sütt M, Versbraegen N, Papadimitriou S, McLachlan RI, Jarvi KA, Schlegel PN, Tennisberg S, Korrovits P, Vigh-Conrad K, O’Bryan MK, Aston KI, Lenaerts T, Conrad DF, Kasak L, Punab M, Laan M. Undiagnosed RASopathies in infertile men. Front Endocrinol (Lausanne) 2024; 15:1312357. [PMID: 38654924 PMCID: PMC11035881 DOI: 10.3389/fendo.2024.1312357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/11/2024] [Indexed: 04/26/2024] Open
Abstract
RASopathies are syndromes caused by congenital defects in the Ras/mitogen-activated protein kinase (MAPK) pathway genes, with a population prevalence of 1 in 1,000. Patients are typically identified in childhood based on diverse characteristic features, including cryptorchidism (CR) in >50% of affected men. As CR predisposes to spermatogenic failure (SPGF; total sperm count per ejaculate 0-39 million), we hypothesized that men seeking infertility management include cases with undiagnosed RASopathies. Likely pathogenic or pathogenic (LP/P) variants in 22 RASopathy-linked genes were screened in 521 idiopathic SPGF patients (including 155 CR cases) and 323 normozoospermic controls using exome sequencing. All 844 men were recruited to the ESTonian ANDrology (ESTAND) cohort and underwent identical andrological phenotyping. RASopathy-specific variant interpretation guidelines were used for pathogenicity assessment. LP/P variants were identified in PTPN11 (two), SOS1 (three), SOS2 (one), LZTR1 (one), SPRED1 (one), NF1 (one), and MAP2K1 (one). The findings affected six of 155 cases with CR and SPGF, three of 366 men with SPGF only, and one (of 323) normozoospermic subfertile man. The subgroup "CR and SPGF" had over 13-fold enrichment of findings compared to controls (3.9% vs. 0.3%; Fisher's exact test, p = 5.5 × 10-3). All ESTAND subjects with LP/P variants in the Ras/MAPK pathway genes presented congenital genitourinary anomalies, skeletal and joint conditions, and other RASopathy-linked health concerns. Rare forms of malignancies (schwannomatosis and pancreatic and testicular cancer) were reported on four occasions. The Genetics of Male Infertility Initiative (GEMINI) cohort (1,416 SPGF cases and 317 fertile men) was used to validate the outcome. LP/P variants in PTPN11 (three), LZTR1 (three), and MRAS (one) were identified in six SPGF cases (including 4/31 GEMINI cases with CR) and one normozoospermic man. Undiagnosed RASopathies were detected in total for 17 ESTAND and GEMINI subjects, 15 SPGF patients (10 with CR), and two fertile men. Affected RASopathy genes showed high expression in spermatogenic and testicular somatic cells. In conclusion, congenital defects in the Ras/MAPK pathway genes represent a new congenital etiology of syndromic male infertility. Undiagnosed RASopathies were especially enriched among patients with a history of cryptorchidism. Given the relationship between RASopathies and other conditions, infertile men found to have this molecular diagnosis should be evaluated for known RASopathy-linked health concerns, including specific rare malignancies.
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Affiliation(s)
- Anna-Grete Juchnewitsch
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Kristjan Pomm
- Andrology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Avirup Dutta
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Erik Tamp
- Centre of Pathology, East Tallinn Central Hospital, Tallinn, Estonia
| | - Anu Valkna
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Kristiina Lillepea
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Eisa Mahyari
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | | | - Galina Belova
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Viljo Kübarsepp
- Department of Surgery, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Pediatric Surgery, Clinic of Surgery, Tartu University Hospital, Tartu, Estonia
| | - Helen Castillo-Madeen
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Antoni Riera-Escamilla
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Lisanna Põlluaas
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Liina Nagirnaja
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Olev Poolamets
- Andrology Clinic, Tartu University Hospital, Tartu, Estonia
| | | | - Mailis Sütt
- Andrology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Nassim Versbraegen
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
| | - Sofia Papadimitriou
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Science, Ghent University, Ghent, Belgium
| | - Robert I. McLachlan
- Hudson Institute of Medical Research and the Department of Obstetrics and Gynecology, Monash University, Clayton, VIC, Australia
| | - Keith A. Jarvi
- Division of Urology, Department of Surgery, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Peter N. Schlegel
- Department of Urology, Weill Cornell Medical College, New York, NY, United States
| | | | - Paul Korrovits
- Andrology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Katinka Vigh-Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Moira K. O’Bryan
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Kenneth I. Aston
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Brussels, Belgium
| | - Donald F. Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
- Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Beaverton, OR, United States
| | - Laura Kasak
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Margus Punab
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Andrology Clinic, Tartu University Hospital, Tartu, Estonia
- Department of Surgery, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Maris Laan
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
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Chatsirisupachai K, de Magalhães JP. Somatic mutations in human ageing: New insights from DNA sequencing and inherited mutations. Ageing Res Rev 2024; 96:102268. [PMID: 38490496 DOI: 10.1016/j.arr.2024.102268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 02/19/2024] [Accepted: 03/06/2024] [Indexed: 03/17/2024]
Abstract
The accumulation of somatic mutations is a driver of cancer and has long been associated with ageing. Due to limitations in quantifying mutation burden with age in non-cancerous tissues, the impact of somatic mutations in other ageing phenotypes is unclear. Recent advances in DNA sequencing technologies have allowed the large-scale quantification of somatic mutations in ageing tissues. These studies have revealed a gradual accumulation of mutations in normal tissues with age as well as a substantial clonal expansion driven mostly by cancer-related mutations. Nevertheless, it is difficult to envision how the burden and stochastic nature of age-related somatic mutations identified so far can explain most ageing phenotypes that develop gradually. Studies across species have also found that longer-lived species have lower somatic mutation rates, though these could be due to selective pressures acting on other phenotypes such as perhaps cancer. Recent studies in patients with higher somatic mutation burden and no signs of accelerated ageing further question the role of somatic mutations in ageing. Overall, with a few exceptions like cancer, recent DNA sequencing studies and inherited mutations do not support the idea that somatic mutations accumulating with age drive ageing phenotypes, and the phenotypic role, if any, of somatic mutations in ageing remains unclear.
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Affiliation(s)
- Kasit Chatsirisupachai
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK; Institute of Inflammation and Ageing, University of Birmingham, Queen Elizabeth Hospital, Mindelsohn Way, Birmingham, UK.
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Giannubilo SR, Marzioni D, Tossetta G, Montironi R, Meccariello ML, Ciavattini A. The "Bad Father": Paternal Role in Biology of Pregnancy and in Birth Outcome. BIOLOGY 2024; 13:165. [PMID: 38534435 DOI: 10.3390/biology13030165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/21/2024] [Accepted: 02/29/2024] [Indexed: 03/28/2024]
Abstract
Pregnancy is generally studied as a biological interaction between a mother and a fetus; however, the father, with his characteristics, lifestyle, genetics, and living environment, is by no means unrelated to the outcome of pregnancy. The half of the fetal genetic heritage of paternal derivation can be decisive in cases of inherited chromosomal disorders, and can be the result of de novo genetic alterations. In addition to the strictly pathological aspects, paternal genetics may transmit thrombophilic traits that affect the implantation and vascular construction of the feto-placental unit, lead to placenta-mediated diseases such as pre-eclampsia and fetal growth retardation, and contribute to the multifactorial genesis of preterm delivery. Biological aspects of immunological tolerance to paternal antigens also appear to be crucial for these pathologies. Finally, this review describes the biological findings by which the environment, exposure to pathogens, lifestyle, and nutritional style of the father affect fetal pathophysiological and epigenetic definition.
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Affiliation(s)
- Stefano Raffaele Giannubilo
- Clinic of Obstetrics and Gynaecology, Department of Clinical Sciences, Università Politecnica Delle Marche, 60123 Ancona, Italy
| | - Daniela Marzioni
- Department of Experimental and Clinical Medicine, Università Politecnica Delle Marche, 60126 Ancona, Italy
| | - Giovanni Tossetta
- Department of Experimental and Clinical Medicine, Università Politecnica Delle Marche, 60126 Ancona, Italy
| | - Ramona Montironi
- Clinic of Obstetrics and Gynaecology, Department of Clinical Sciences, Università Politecnica Delle Marche, 60123 Ancona, Italy
| | - Maria Liberata Meccariello
- Clinic of Obstetrics and Gynaecology, Department of Clinical Sciences, Università Politecnica Delle Marche, 60123 Ancona, Italy
| | - Andrea Ciavattini
- Clinic of Obstetrics and Gynaecology, Department of Clinical Sciences, Università Politecnica Delle Marche, 60123 Ancona, Italy
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Lv MQ, Yang YQ, Li YX, Zhou L, Ge P, Sun RF, Zhang J, Gao JC, Qu LQ, Jing QY, Li PC, Yan YJ, Wang HX, Li HC, Zhou DX. A detection model of testis-derived circular RNAs in serum for predicting testicular sperm retrieval rate in non-obstructive azoospermia patients. Andrology 2024. [PMID: 38421140 DOI: 10.1111/andr.13617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 01/18/2024] [Accepted: 02/12/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND Microdissection testicular sperm extraction is an effective method to retrieve sperm from non-obstructive azoospermia patients. However, its successful rate is less than 50%. OBJECTIVES To identify the predictive value of circular RNAs in serum for sperm retrieval rate in non-obstructive azoospermia patients. MATERIALS AND METHODS 180 non-obstructive azoospermia patients were recruited in this study, including 84 individuals with successful sperm retrieval and 96 individuals with failed sperm retrieval. Our study contained two phases. First, 20 patients, selected from the 180 patients, were included in screening cohort. In this cohort, the top 20 circular RNAs from our previous testicular circRNA profiles were verified between successful and failed sperm retrieval groups using real-time polymerase chain reaction. Six circular RNAs with the most significantly different expressions were selected for further verification. Second, the 180 patients were included as discovery cohort to verify the six circular RNAs. Circular RNAs were extracted from serum in each participant. Logistic regression analysis was further performed to identify the predictive value and the area under the curve analysis was used to evaluate diagnostic efficiency, sensitivity, and specificity. RESULTS Six circular RNAs including hsa_circ_0058058, hsa_circ_0008045, hsa_circ_0084789, hsa_circ_0000550, hsa_circ_0007422, and hsa_circ_0004099 showed aberrant expressions between the successful and failed sperm retrieval group. In addition, both single-circular RNA panels and multi-circular RNA panels were finally verified to be significant in predicting sperm retrieval rate. Notably, multi-circular RNAs panels demonstrated better predictive abilities compared with single-circRNA panels, and the combined panel of six-circular RNAs (risk score = 1.094×hsa_circ_0058058+0.697×hsa_circ_0008045+0.718×hsa_circ_0084789-0.591×hsa_circ_0000550-0.435×hsa_circ_0007422-1.017×hsa_circ_0004099-1.561) exhibited the best predictive ability in the present study with an AUC of 0.977, a sensitivity of 91.7% and a specificity of 86.5%. A higher risk score indicated a higher risk of failure in sperm retrieval. DISCUSSION AND CONCLUSION Our study was the first to report that testis-derived circular RNAs in serum have the ability to predict sperm retrieval rate in non-obstructive azoospermia patients, whether it is a single-circular RNA or a combination of multi-circular RNAs.
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Affiliation(s)
- Mo-Qi Lv
- Department of Pathology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
- Institute of Genetics and Development, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, China
| | - Yan-Qi Yang
- Department of Pathology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
- Institute of Genetics and Development, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, China
| | - Yi-Xin Li
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Liang Zhou
- Assisted Reproduction Center, Northwest Women's and Children's Hospital, Xi'an, China
- Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Pan Ge
- Department of Pathology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
- Institute of Genetics and Development, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, China
| | - Rui-Fang Sun
- Department of Pathology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
- Institute of Genetics and Development, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, China
| | - Jian Zhang
- Department of Pathology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
- Institute of Genetics and Development, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, China
| | - Jun-Cheng Gao
- School of Humanities and Social Development, Northwest A&F University, Xianyang, China
| | - Liu-Qing Qu
- Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Qi-Ya Jing
- Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Pin-Cheng Li
- Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yu-Jia Yan
- Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Hai-Xu Wang
- Assisted Reproduction Center, Xijing Hospital of Air Force Medical University (the former the Fourth Military Medical University), Xi'an, China
| | - He-Cheng Li
- Department of Urology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Dang-Xia Zhou
- Department of Pathology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
- Institute of Genetics and Development, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, China
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8
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Moura S, Hartl I, Brumovska V, Calabrese PP, Yasari A, Striedner Y, Bishara M, Mair T, Ebner T, Schütz GJ, Sevcsik E, Tiemann-Boege I. Exploring FGFR3 Mutations in the Male Germline: Implications for Clonal Germline Expansions and Paternal Age-Related Dysplasias. Genome Biol Evol 2024; 16:evae015. [PMID: 38411226 PMCID: PMC10898338 DOI: 10.1093/gbe/evae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2024] [Indexed: 02/28/2024] Open
Abstract
Delayed fatherhood results in a higher risk of inheriting a new germline mutation that might result in a congenital disorder in the offspring. In particular, some FGFR3 mutations increase in frequency with age, but there are still a large number of uncharacterized FGFR3 mutations that could be expanding in the male germline with potentially early- or late-onset effects in the offspring. Here, we used digital polymerase chain reaction to assess the frequency and spatial distribution of 10 different FGFR3 missense substitutions in the sexually mature male germline. Our functional assessment of the receptor signaling of the variants with biophysical methods showed that 9 of these variants resulted in a higher activation of the receptor´s downstream signaling, resulting in 2 different expansion behaviors. Variants that form larger subclonal expansions in a dissected postmortem testis also showed a positive correlation of the substitution frequency with the sperm donor's age, and a high and ligand-independent FGFR3 activation. In contrast, variants that measured high FGFR3 signaling and elevated substitution frequencies independent of the donor's age did not result in measurable subclonal expansions in the testis. This suggests that promiscuous signal activation might also result in an accumulation of mutations before the sexual maturation of the male gonad with clones staying relatively constant in size throughout time. Collectively, these results provide novel insights into our understanding of the mutagenesis of driver mutations and their resulting mosaicism in the male germline with important consequences for the transmission and recurrence of associated disorders.
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Affiliation(s)
- Sofia Moura
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, USA
| | - Ingrid Hartl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | | | - Peter P Calabrese
- Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
| | - Atena Yasari
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Yasmin Striedner
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | | | - Theresa Mair
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Thomas Ebner
- Department of Gynecology, Obstetrics and Gynecological Endocrinology, Johannes Kepler University, 4020 Linz, Austria
| | | | - Eva Sevcsik
- Institute of Applied Physics, TU Wien, Vienna, Austria
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9
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Striedner Y, Arbeithuber B, Moura S, Nowak E, Reinhardt R, Muresan L, Salazar R, Ebner T, Tiemann-Boege I. Exploring the Micro-Mosaic Landscape of FGFR3 Mutations in the Ageing Male Germline and Their Potential Implications in Meiotic Differentiation. Genes (Basel) 2024; 15:191. [PMID: 38397181 PMCID: PMC10888257 DOI: 10.3390/genes15020191] [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: 01/03/2024] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/25/2024] Open
Abstract
Advanced paternal age increases the risk of transmitting de novo germline mutations, particularly missense mutations activating the receptor tyrosine kinase (RTK) signalling pathway, as exemplified by the FGFR3 mutation, which is linked to achondroplasia (ACH). This risk is attributed to the expansion of spermatogonial stem cells carrying the mutation, forming sub-clonal clusters in the ageing testis, thereby increasing the frequency of mutant sperm and the number of affected offspring from older fathers. While prior studies proposed a correlation between sub-clonal cluster expansion in the testis and elevated mutant sperm production in older donors, limited data exist on the universality of this phenomenon. Our study addresses this gap by examining the testis-expansion patterns, as well as the increases in mutations in sperm for two FGFR3 variants-c.1138G>A (p.G380R) and c.1948A>G (p.K650E)-which are associated with ACH or thanatophoric dysplasia (TDII), respectively. Unlike the ACH mutation, which showed sub-clonal expansion events in an aged testis and a significant increase in mutant sperm with the donor's age, as also reported in other studies, the TDII mutation showed focal mutation pockets in the testis but exhibited reduced transmission into sperm and no significant age-related increase. The mechanism behind this divergence remains unclear, suggesting potential pleiotropic effects of aberrant RTK signalling in the male germline, possibly hindering differentiation requiring meiosis. This study provides further insights into the transmission risks of micro-mosaics associated with advanced paternal age in the male germline.
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Affiliation(s)
- Yasmin Striedner
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
| | - Barbara Arbeithuber
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
- Department of Gynecology, Obstetrics and Gynecological Endocrinology, Johannes Kepler University, 4020 Linz, Austria;
| | - Sofia Moura
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Elisabeth Nowak
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
| | - Ronja Reinhardt
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
- Department of Structural and Computational Biology, Max Perutz Labs, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Leila Muresan
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 2EL, UK;
- Faculty of Science and Engineering, Anglia Ruskin University, Cambridge CB1 1PT, UK
| | - Renato Salazar
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
| | - Thomas Ebner
- Department of Gynecology, Obstetrics and Gynecological Endocrinology, Johannes Kepler University, 4020 Linz, Austria;
| | - Irene Tiemann-Boege
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
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10
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Hosseini Nami A, Kabiri M, Zafarghandi Motlagh F, Shirzadeh T, Bagherian H, Zeinali R, Karimi A, Zeinali S. Identification and in silico structural analysis for the first de novo mutation in the cystic fibrosis transmembrane conductance regulator protein in Iran: case report and developmental insight using microsatellite markers. Ther Adv Respir Dis 2024; 18:17534666241253990. [PMID: 38904297 PMCID: PMC11193346 DOI: 10.1177/17534666241253990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/19/2024] [Indexed: 06/22/2024] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease caused by the inheritance of two mutant cystic fibrosis transmembrane conductance regulator (CFTR) alleles, one from each parent. Autosomal recessive disorders are rarely associated with germline mutations or mosaicism. Here, we propose a case of paternal germline mutation causing CF. The subject also had an identifiable maternal mutant allele. We identified the compound heterozygous variants in the proband through Sanger sequencing, and in silico studies predicted functional effects on the protein. Also, short tandem repeat markers revealed the de novo nature of the mutation. The maternal mutation in the CFTR gene was c.1000C > T. The de novo mutation was c.178G > A, p.Glu60Lys. This mutation is located in the lasso motif of the CFTR protein and, according to in silico structural analysis, disrupts the interaction of the lasso motif and R-domain, thus influencing protein function. This first reported case of de novo mutation in Asia has notable implications for molecular diagnostics, genetic counseling, and understanding the genetic etiology of recessive disorders in the Iranian population.
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Affiliation(s)
- Amin Hosseini Nami
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
- Dr. Zeinali’s Medical Genetics Lab, Kawsar Human Genetics Research Center (KHGRC), Tehran, Iran
| | - Mahboubeh Kabiri
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | | | - Tina Shirzadeh
- Dr. Zeinali’s Medical Genetics Lab, Kawsar Human Genetics Research Center (KHGRC), Tehran, Iran
| | - Hamideh Bagherian
- Dr. Zeinali’s Medical Genetics Lab, Kawsar Human Genetics Research Center (KHGRC), Tehran, Iran
| | - Razie Zeinali
- Dr. Zeinali’s Medical Genetics Lab, Kawsar Human Genetics Research Center (KHGRC), Tehran, Iran
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Ali Karimi
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Sirous Zeinali
- Dr. Zeinali’s Medical Genetics Lab, Kawsar Human Genetics Research Center (KHGRC), No. 41, Irna St., Valiasr St., Tehran, Iran
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11
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Aitken RJ, Lewis SEM. DNA damage in testicular germ cells and spermatozoa. When and how is it induced? How should we measure it? What does it mean? Andrology 2023; 11:1545-1557. [PMID: 36604857 DOI: 10.1111/andr.13375] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/09/2022] [Accepted: 12/24/2022] [Indexed: 01/07/2023]
Abstract
This review surveys the causes and consequences of DNA damage in the male germ line from spermatogonial stem cells to fully differentiated spermatozoa. Within the stem cell population, DNA integrity is well maintained as a result of excellent DNA surveillance and repair; however, a progressive increase in background mutation rates does occur with paternal age possibly as a result of aberrant DNA repair as well as replication error. Once a germ cell has committed to spermatogenesis, it responds to genetic damage via a range of DNA repair pathways or, if this process fails, by the induction of apoptosis. When fully-differentiated spermatozoa are stressed, they also activate a truncated intrinsic apoptotic pathway which results in the activation of nucleases in the mitochondria and cytoplasm; however, the physical architecture of these cells prevents these enzymes from translocating to the nucleus to induce DNA fragmentation. Conversely, hydrogen peroxide released from the sperm midpiece during apoptosis is able to penetrate the nucleus and induce DNA damage. The base excision repair pathway responds to such damage by cleaving oxidized bases from the DNA, leaving abasic sites that are alkali-labile and readily detected with the comet assay. As levels of oxidative stress increase and these cells enter the perimortem, topoisomerase integrated into the sperm chromatin becomes activated by SUMOylation. Such activation may initially facilitate DNA repair by reannealing double strand breaks but ultimately prepares the DNA for destruction by nucleases released from the male reproductive tract. The abasic sites and oxidized base lesions found in live spermatozoa are mutagenic and may increase the mutational load carried by the offspring, particularly in the context of assisted conception. A variety of strategies are described for managing patients expressing high levels of DNA damage in their spermatozoa, to reduce the risks such lesions might pose to offspring health.
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Affiliation(s)
- Robert John Aitken
- Priority Research Centre for Reproductive, Science, College of Engineering, Science and Environment, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Medical Research Institute (HMRI), New Lambton, New South Wales, Australia
| | - Sheena E M Lewis
- Queens University Belfast, Belfast, UK
- Examen Ltd., Weavers Court, Belfast, UK
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12
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Aitken RJ. Male reproductive ageing: a radical road to ruin. Hum Reprod 2023; 38:1861-1871. [PMID: 37568254 PMCID: PMC10546083 DOI: 10.1093/humrep/dead157] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
In modern post-transition societies, we are reproducing later and living longer. While the impact of age on female reproductive function has been well studied, much less is known about the intersection of age and male reproduction. Our current understanding is that advancing age brings forth a progressive decline in male fertility accompanied by a reduction in circulating testosterone levels and the appearance of age-dependent reproductive pathologies including benign prostatic hypertrophy and erectile dysfunction. Paternal ageing is also associated with a profound increase in sperm DNA damage, the appearance of multiple epigenetic changes in the germ line and an elevated mutational load in the offspring. The net result of such changes is an increase in the disease burden carried by the progeny of ageing males, including dominant genetic diseases such as Apert syndrome and achondroplasia, as well as neuropsychiatric conditions including autism and spontaneous schizophrenia. The genetic basis of these age-related effects appears to involve two fundamental mechanisms. The first is a positive selection mechanism whereby stem cells containing mutations in a mitogen-activated protein kinase pathway gain a selective advantage over their non-mutant counterparts and exhibit significant clonal expansion with the passage of time. The second is dependent on an age-dependent increase in oxidative stress which impairs the steroidogenic capacity of the Leydig cells, disrupts the ability of Sertoli cells to support the normal differentiation of germ cells, and disrupts the functional and genetic integrity of spermatozoa. Given the central importance of oxidative stress in defining the impact of chronological age on male reproduction, there may be a role for antioxidants in the clinical management of this process. While animal studies are supportive of this strategy, carefully designed clinical trials are now needed if we are to realize the therapeutic potential of this approach in a clinical context.
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Affiliation(s)
- R John Aitken
- Priority Research Centre for Reproductive Science, Discipline of Biological Sciences, School of Environmental and Life Sciences, College of Engineering Science and Environment, University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
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13
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Xu N, Shi W, Cao X, Zhou X, Jin L, Huang HF, Chen S, Xu C. Parental mosaicism detection and preimplantation genetic testing in families with multiple transmissions of de novo mutations. J Med Genet 2023; 60:910-917. [PMID: 36707240 PMCID: PMC10447385 DOI: 10.1136/jmg-2022-108920] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 01/14/2023] [Indexed: 01/28/2023]
Abstract
BACKGROUND De novo mutations (DNMs) are linked with many severe early-onset disorders ranging from rare congenital malformation to intellectual disability. Conventionally, DNMs are considered to have an estimated recurrence rate of 1%. Recently, studies have revealed a higher prevalence of parental mosaicism, leading to a greater recurrence risk, resulting in a second child harbouring the same DNM as a previous child. METHODS In this study, we included 10 families with DNMs leading to adverse pregnancy outcomes. DNA was extracted from tissue samples, including parental peripheral blood, parental saliva and paternal sperm. High-throughput sequencing was used to screen for parental mosaicism with a depth of more than 5000× on average and a variant allele fraction (VAF) detection limit of 0.5%. RESULTS The presence of mosaicism was detected in sperms in two families, with VAFs of 2.8% and 2.5%, respectively. Both families have a history of multiple adverse pregnancies and DNMs shared by siblings. Preimplantation genetic testing (PGT) and prenatal diagnosis were performed in one family, thereby preventing the reoccurrence of DNMs. CONCLUSION This study is the first to report the successful implementation of PGT for monogenic/single gene defects in the parental mosaicism family. Our study suggests that mosaic detection of paternal sperm is warranted in families with recurrent DNMs leading to adverse pregnancy outcomes, and PGT can effectively block the transmission of the pathogenic mutation.
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Affiliation(s)
- Naixin Xu
- International Peace Maternity and Child Health Hospital, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
| | - Weihui Shi
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xianling Cao
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xuanyou Zhou
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Li Jin
- International Peace Maternity and Child Health Hospital, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - He-Feng Huang
- International Peace Maternity and Child Health Hospital, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China
| | - Songchang Chen
- International Peace Maternity and Child Health Hospital, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chenming Xu
- International Peace Maternity and Child Health Hospital, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
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14
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Cappola AR, Auchus RJ, El-Hajj Fuleihan G, Handelsman DJ, Kalyani RR, McClung M, Stuenkel CA, Thorner MO, Verbalis JG. Hormones and Aging: An Endocrine Society Scientific Statement. J Clin Endocrinol Metab 2023; 108:1835-1874. [PMID: 37326526 DOI: 10.1210/clinem/dgad225] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Indexed: 06/17/2023]
Abstract
Multiple changes occur across various endocrine systems as an individual ages. The understanding of the factors that cause age-related changes and how they should be managed clinically is evolving. This statement reviews the current state of research in the growth hormone, adrenal, ovarian, testicular, and thyroid axes, as well as in osteoporosis, vitamin D deficiency, type 2 diabetes, and water metabolism, with a specific focus on older individuals. Each section describes the natural history and observational data in older individuals, available therapies, clinical trial data on efficacy and safety in older individuals, key points, and scientific gaps. The goal of this statement is to inform future research that refines prevention and treatment strategies in age-associated endocrine conditions, with the goal of improving the health of older individuals.
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Affiliation(s)
- Anne R Cappola
- Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Richard J Auchus
- Departments of Pharmacology and Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI 48109, USA
- Endocrinology and Metabolism Section, Medical Service, LTC Charles S. Kettles Veteran Affairs Medical Center, Ann Arbor, MI 48015, USA
| | - Ghada El-Hajj Fuleihan
- Calcium Metabolism and Osteoporosis Program, WHO Collaborating Center for Metabolic Bone Disorders, Division of Endocrinology, Department of Internal Medicine, American University of Beirut, Beirut 1107-2020, Lebanon
| | - David J Handelsman
- ANZAC Research Institute, University of Sydney and Andrology Department, Concord Repatriation General Hospital, Sydney 2139, Australia
| | - Rita R Kalyani
- Division of Endocrinology, Diabetes, and Metabolism, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Michael McClung
- Oregon Osteoporosis Center, Portland, OR 97213, USA
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC 3000, Australia
| | - Cynthia A Stuenkel
- Department of Medicine, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Michael O Thorner
- Division of Endocrinology and Metabolism, University of Virginia, Charlottesville, VA 22903, USA
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Joseph G Verbalis
- Division of Endocrinology and Metabolism, Georgetown University Medical Center, Washington, DC 20057, USA
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15
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Rockweiler NB, Ramu A, Nagirnaja L, Wong WH, Noordam MJ, Drubin CW, Huang N, Miller B, Todres EZ, Vigh-Conrad KA, Zito A, Small KS, Ardlie KG, Cohen BA, Conrad DF. The origins and functional effects of postzygotic mutations throughout the human life span. Science 2023; 380:eabn7113. [PMID: 37053313 PMCID: PMC11246725 DOI: 10.1126/science.abn7113] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/17/2023] [Indexed: 04/15/2023]
Abstract
Postzygotic mutations (PZMs) begin to accrue in the human genome immediately after fertilization, but how and when PZMs affect development and lifetime health remain unclear. To study the origins and functional consequences of PZMs, we generated a multitissue atlas of PZMs spanning 54 tissue and cell types from 948 donors. Nearly half the variation in mutation burden among tissue samples can be explained by measured technical and biological effects, and 9% can be attributed to donor-specific effects. Through phylogenetic reconstruction of PZMs, we found that their type and predicted functional impact vary during prenatal development, across tissues, and through the germ cell life cycle. Thus, methods for interpreting effects across the body and the life span are needed to fully understand the consequences of genetic variants.
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Affiliation(s)
- Nicole B. Rockweiler
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Present address: Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Avinash Ramu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Liina Nagirnaja
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA
| | - Wing H. Wong
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Present Address: Departments of Genetics and Medicine, Stanford University, CA 94305, USA
| | - Michiel J. Noordam
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Casey W. Drubin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ni Huang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Present Address: T-Therapeutics Ltd., Cambridge CB21 6AD, UK
| | - Brian Miller
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA
| | - Ellen Z. Todres
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Katinka A. Vigh-Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA
| | - Antonino Zito
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
- Present Address: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA; Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Kerrin S. Small
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
| | | | - Barak A. Cohen
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Donald F. Conrad
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA
- Center for Embryonic Cell & Gene Therapy, Oregon Health & Science University, Portland, OR, 97239, USA
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16
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Marmion RA, Simpkins AG, Barrett LA, Denberg DW, Zusman S, Schottenfeld-Roames J, Schüpbach T, Shvartsman SY. Stochastic phenotypes in RAS-dependent developmental diseases. Curr Biol 2023; 33:807-816.e4. [PMID: 36706752 PMCID: PMC10026697 DOI: 10.1016/j.cub.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 12/02/2022] [Accepted: 01/05/2023] [Indexed: 01/27/2023]
Abstract
Germline mutations upregulating RAS signaling are associated with multiple developmental disorders. A hallmark of these conditions is that the same mutation may present vastly different phenotypes in different individuals, even in monozygotic twins. Here, we demonstrate how the origins of such largely unexplained phenotypic variations may be dissected using highly controlled studies in Drosophila that have been gene edited to carry activating variants of MEK, a core enzyme in the RAS pathway. This allowed us to measure the small but consistent increase in signaling output of such alleles in vivo. The fraction of mutation carriers reaching adulthood was strongly reduced, but most surviving animals had normal RAS-dependent structures. We rationalize these results using a stochastic signaling model and support it by quantifying cell fate specification errors in bilaterally symmetric larval trachea, a RAS-dependent structure that allows us to isolate the effects of mutations from potential contributions of genetic modifiers and environmental differences. We propose that the small increase in signaling output shifts the distribution of phenotypes into a regime, where stochastic variation causes defects in some individuals, but not in others. Our findings shed light on phenotypic heterogeneity of developmental disorders caused by deregulated RAS signaling and offer a framework for investigating causal effects of other pathogenic alleles and mild mutations in general.
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Affiliation(s)
- Robert A Marmion
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | - Alison G Simpkins
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | - Lena A Barrett
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.
| | - David W Denberg
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | - Susan Zusman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | | | - Trudi Schüpbach
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Stanislav Y Shvartsman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Flatiron Institute, Simons Foundation, New York, NY 10010, USA.
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17
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Eboreime J, Choi SK, Yoon SR, Sadybekov A, Katritch V, Calabrese P, Arnheim N. Germline selection of PTPN11 (HGNC:9644) variants make a major contribution to both Noonan syndrome's high birth rate and the transmission of sporadic cancer variants resulting in fetal abnormality. Hum Mutat 2022; 43:2205-2221. [PMID: 36349709 PMCID: PMC10099774 DOI: 10.1002/humu.24493] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 09/20/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022]
Abstract
Some spontaneous germline gain-of-function mutations promote spermatogonial stem cell clonal expansion and disproportionate variant sperm production leading to unexpectedly high transmission rates for some human genetic conditions. To measure the frequency and spatial distribution of de novo mutations we divided three testes into 192 pieces each and used error-corrected deep-sequencing on each piece. We focused on PTPN11 (HGNC:9644) Exon 3 that contains 30 different PTPN11 Noonan syndrome (NS) mutation sites. We found 14 of these variants formed clusters among the testes; one testis had 11 different variant clusters. The mutation frequencies of these different clusters were not correlated with their case-recurrence rates nor were case recurrence rates of PTPN11 variants correlated with their tyrosine phosphatase levels thereby confusing PTPN11's role in germline clonal expansion. Six of the PTPN11 exon 3 de novo variants associated with somatic mutation-induced sporadic cancers (but not NS) also formed testis clusters. Further, three of these six variants were observed among fetuses that underwent prenatal ultrasound screening for NS-like features. Mathematical modeling showed that germline selection can explain both the mutation clusters and the high incidence of NS (1/1000-1/2500).
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Affiliation(s)
- Jordan Eboreime
- Department of Biological Sciences, Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA
| | - Soo-Kyung Choi
- Department of Biological Sciences, Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA
| | - Song-Ro Yoon
- Department of Biological Sciences, Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA
| | - Anastasiia Sadybekov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California, USA
| | - Vsevolod Katritch
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California, USA
| | - Peter Calabrese
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Norman Arnheim
- Department of Biological Sciences, Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA
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18
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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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19
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Stella A, Lastella P, Viggiano L, Bagnulo R, Resta N. Clinical presentation and genetic analyses of neurofibromatosis type 1 in independent patients with monoallelic double de novo closely spaced mutations in the NF1 gene. Hum Mutat 2022; 43:1354-1360. [PMID: 35723633 PMCID: PMC9540858 DOI: 10.1002/humu.24423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 12/15/2022]
Abstract
Neurofibromatosis type 1 (NF1) belongs to RASopathies, a group of syndromes caused by germline mutations in Ras/MAPK pathway genes. Most NF1 patients exhibit single inactivating pathogenic variants within the NF1 gene. We performed extensive genetic analyses in two NF1 families disclosing the first two cases of double de novo monoallelic NF1 variants. Both index patients described in this study had classical NF1. Probands were born from fathers in their late 30s and presented closely spaced double mutations (<100 bp) in NF1 regions showing an excess of somatic mutations. Closely spaced multiple mutations have been reported in RAS/MAPK signaling genes but never in NF1. Mutagenesis is a quasi-random process in humans, therefore two causative variants in the same gene, moreover in the same allele are exceptional. Here, we discuss possible mechanisms for this ultrarare event. Our findings confirm the possibility of a higher risk of concurrent de novo variants in NF1.
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Affiliation(s)
- Alessandro Stella
- Department of Biomedical Sciences and Human OncologyLaboratory of Medical Genetics, Università di Bari Aldo MoroBariItaly
| | - Patrizia Lastella
- Rare Disease CenterInternal MedicineUnit ‘C. Frugoni’, AOU Policlinico di BariBariItaly
| | - Luigi Viggiano
- Department of BiologyUniversity of Bari Aldo MoroBariItaly
| | - Rosanna Bagnulo
- Department of Biomedical Sciences and Human OncologyLaboratory of Medical Genetics, Università di Bari Aldo MoroBariItaly
| | - Nicoletta Resta
- Department of Biomedical Sciences and Human OncologyLaboratory of Medical Genetics, Università di Bari Aldo MoroBariItaly
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20
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Malaspina D. Editorial for Special Issue: From cytokines to climate and C-sections and from micronutrients to the microbiome: Neurodevelopment and the risk for psychosis. Schizophr Res 2022; 247:1-6. [PMID: 35396142 DOI: 10.1016/j.schres.2022.02.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Dolores Malaspina
- Icahn School of Medicine at Mount Sinai, Departments of Psychiatry, Neuroscience, Genetic and Genomic Sciences, New York, N.Y. , U.S.A..
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21
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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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22
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Salazar R, Arbeithuber B, Ivankovic M, Heinzl M, Moura S, Hartl I, Mair T, Lahnsteiner A, Ebner T, Shebl O, Pröll J, Tiemann-Boege I. Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing. Genome Res 2022; 32:499-511. [PMID: 35210354 PMCID: PMC8896467 DOI: 10.1101/gr.275695.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 01/14/2022] [Indexed: 11/25/2022]
Abstract
De novo mutations (DNMs) are important players in heritable diseases and evolution. Of particular interest are highly recurrent DNMs associated with congenital disorders that have been described as selfish mutations expanding in the male germline, thus becoming more frequent with age. Here, we have adapted duplex sequencing (DS), an ultradeep sequencing method that renders sequence information on both DNA strands; thus, one mutation can be reliably called in millions of sequenced bases. With DS, we examined ∼4.5 kb of the FGFR3 coding region in sperm DNA from older and younger donors. We identified sites with variant allele frequencies (VAFs) of 10-4 to 10-5, with an overall mutation frequency of the region of ∼6 × 10-7 Some of the substitutions are recurrent and are found at a higher VAF in older donors than in younger ones or are found exclusively in older donors. Also, older donors harbor more mutations associated with congenital disorders. Other mutations are present in both age groups, suggesting that these might result from a different mechanism (e.g., postzygotic mosaicism). We also observe that independent of age, the frequency and deleteriousness of the mutational spectra are more similar to COSMIC than to gnomAD variants. Our approach is an important strategy to identify mutations that could be associated with a gain of function of the receptor tyrosine kinase activity, with unexplored consequences in a society with delayed fatherhood.
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Affiliation(s)
- Renato Salazar
- Institute of Biophysics, Johannes Kepler University, Linz, Austria 4020
| | | | - Maja Ivankovic
- Institute of Biophysics, Johannes Kepler University, Linz, Austria 4020
| | - Monika Heinzl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria 4020
| | - Sofia Moura
- Institute of Biophysics, Johannes Kepler University, Linz, Austria 4020
| | - Ingrid Hartl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria 4020
| | - Theresa Mair
- Institute of Biophysics, Johannes Kepler University, Linz, Austria 4020
| | | | - Thomas Ebner
- Department of Gynecology, Obstetrics and Gynecological Endocrinology, Kepler University Hospital, Linz, Austria 4020
| | - Omar Shebl
- Department of Gynecology, Obstetrics and Gynecological Endocrinology, Kepler University Hospital, Linz, Austria 4020
| | - Johannes Pröll
- Center for Medical Research, Faculty of Medicine, Johannes Kepler University, Linz, Austria 4020
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23
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Aitken RJ. Role of sperm DNA damage in creating de novo mutations in human offspring: the ‘post-meiotic oocyte collusion’ hypothesis. Reprod Biomed Online 2022; 45:109-124. [DOI: 10.1016/j.rbmo.2022.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 11/24/2022]
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24
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Motta M, Fasano G, Gredy S, Brinkmann J, Bonnard AA, Simsek-Kiper PO, Gulec EY, Essaddam L, Utine GE, Guarnetti Prandi I, Venditti M, Pantaleoni F, Radio FC, Ciolfi A, Petrini S, Consoli F, Vignal C, Hepbasli D, Ullrich M, de Boer E, Vissers LELM, Gritli S, Rossi C, De Luca A, Ben Becher S, Gelb BD, Dallapiccola B, Lauri A, Chillemi G, Schuh K, Cavé H, Zenker M, Tartaglia M. SPRED2 loss-of-function causes a recessive Noonan syndrome-like phenotype. Am J Hum Genet 2021; 108:2112-2129. [PMID: 34626534 DOI: 10.1016/j.ajhg.2021.09.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022] Open
Abstract
Upregulated signal flow through RAS and the mitogen-associated protein kinase (MAPK) cascade is the unifying mechanistic theme of the RASopathies, a family of disorders affecting development and growth. Pathogenic variants in more than 20 genes have been causally linked to RASopathies, the majority having a dominant role in promoting enhanced signaling. Here, we report that SPRED2 loss of function is causally linked to a recessive phenotype evocative of Noonan syndrome. Homozygosity for three different variants-c.187C>T (p.Arg63∗), c.299T>C (p.Leu100Pro), and c.1142_1143delTT (p.Leu381Hisfs∗95)-were identified in four subjects from three families. All variants severely affected protein stability, causing accelerated degradation, and variably perturbed SPRED2 functional behavior. When overexpressed in cells, all variants were unable to negatively modulate EGF-promoted RAF1, MEK, and ERK phosphorylation, and time-course experiments in primary fibroblasts (p.Leu100Pro and p.Leu381Hisfs∗95) documented an increased and prolonged activation of the MAPK cascade in response to EGF stimulation. Morpholino-mediated knockdown of spred2a and spred2b in zebrafish induced defects in convergence and extension cell movements indicating upregulated RAS-MAPK signaling, which were rescued by expressing wild-type SPRED2 but not the SPRED2Leu381Hisfs∗95 protein. The clinical phenotype of the four affected individuals included developmental delay, intellectual disability, cardiac defects, short stature, skeletal anomalies, and a typical facial gestalt as major features, without the occurrence of the distinctive skin signs characterizing Legius syndrome. These features, in part, characterize the phenotype of Spred2-/- mice. Our findings identify the second recessive form of Noonan syndrome and document pleiotropic consequences of SPRED2 loss of function in development.
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Affiliation(s)
- Marialetizia Motta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Giulia Fasano
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Sina Gredy
- Institute of Physiology, University of Wuerzburg, 97070 Wuerzburg, Germany
| | - Julia Brinkmann
- Institute of Human Genetics, University Hospital Magdeburg, 39120 Magdeburg, Germany
| | - Adeline Alice Bonnard
- Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Département de Génétique, 75019 Paris, France; INSERM UMR 1131, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Pelin Ozlem Simsek-Kiper
- Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Sihhiye, 06100 Ankara, Turkey
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, Health Sciences University, Istanbul Kanuni Sultan Suleyman Training and Research Hospital, 34303 Istanbul, Turkey
| | - Leila Essaddam
- Department of Pediatrics-PUC, Béchir Hamza Children's Hospital, Faculty of Medicine, University of Tunis El Manar, Jebbari 1007, Tunis, Tunisia
| | - Gulen Eda Utine
- Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Sihhiye, 06100 Ankara, Turkey
| | - Ingrid Guarnetti Prandi
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università Della Tuscia, 01100 Viterbo, Italy
| | - Martina Venditti
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Francesca Pantaleoni
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Stefania Petrini
- Confocal Microscopy Core Facility, Ospedale Pediatrico Bambino Gesù, 00146 Rome, Italy
| | - Federica Consoli
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy
| | - Cédric Vignal
- Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Département de Génétique, 75019 Paris, France
| | - Denis Hepbasli
- Institute of Physiology, University of Wuerzburg, 97070 Wuerzburg, Germany
| | - Melanie Ullrich
- Institute of Physiology, University of Wuerzburg, 97070 Wuerzburg, Germany
| | - Elke de Boer
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Sami Gritli
- Department of Immunology, Pasteur Institute of Tunis, 1002 Tunis-Belvédère, Tunisia
| | - Cesare Rossi
- Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Alessandro De Luca
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy
| | - Saayda Ben Becher
- Department of Pediatrics-PUC, Béchir Hamza Children's Hospital, Faculty of Medicine, University of Tunis El Manar, Jebbari 1007, Tunis, Tunisia
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Antonella Lauri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Giovanni Chillemi
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università Della Tuscia, 01100 Viterbo, Italy; Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Centro Nazionale Delle Ricerche, 70126 Bari, Italy
| | - Kai Schuh
- Institute of Physiology, University of Wuerzburg, 97070 Wuerzburg, Germany
| | - Hélène Cavé
- Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Département de Génétique, 75019 Paris, France; INSERM UMR 1131, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, 39120 Magdeburg, Germany
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy.
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25
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Abstract
[Figure: see text].
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Affiliation(s)
- Mitinori Saitou
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Katsuhiko Hayashi
- Department of Developmental Stem Cell Biology, Faculty of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan.,Department of Germline Genetics, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan
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26
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Breuss MW, Yang X, Gleeson JG. Sperm mosaicism: implications for genomic diversity and disease. Trends Genet 2021; 37:890-902. [PMID: 34158173 PMCID: PMC9484299 DOI: 10.1016/j.tig.2021.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 12/18/2022]
Abstract
While sperm mosaicism has few consequences for men, the offspring and future generations are unwitting recipients of gonadal cell mutations, often yielding severe disease. Recent studies, fueled by emergent technologies, show that sperm mosaicism is a common source of de novo mutations (DNMs) that underlie severe pediatric disease as well as human genetic diversity. Sperm mosaicism can be divided into three types: Type I arises during sperm meiosis and is non-age dependent; Type II arises in spermatogonia and increases as men age; and Type III arises during paternal embryogenesis, spreads throughout the body, and contributes stably to sperm throughout life. Where Types I and II confer little risk of recurrence, Type III may confer identifiable risk to future offspring. These mutations are likely to be the single largest contributor to human genetic diversity. New sequencing approaches may leverage this framework to evaluate and reduce disease risk for future generations.
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Affiliation(s)
- Martin W Breuss
- Department of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO, USA
| | - Xiaoxu Yang
- Rady Children's Institute for Genomic Medicine, Department of Neurosciences, University of California, San Diego, CA, USA
| | - Joseph G Gleeson
- Rady Children's Institute for Genomic Medicine, Department of Neurosciences, University of California, San Diego, CA, USA.
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27
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Riva M, Martorana D, Uliana V, Caleffi E, Boschi E, Garavelli L, Ponti G, Sangiorgi L, Graziano C, Bigoni S, Rocchetti LM, Madeo S, Soli F, Grosso E, Carli D, Goldoni M, Pisani F, Percesepe A. Recurrent NF1 gene variants and their genotype/phenotype correlations in patients with Neurofibromatosis type I. Genes Chromosomes Cancer 2021; 61:10-21. [PMID: 34427956 PMCID: PMC9291954 DOI: 10.1002/gcc.22997] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 11/08/2022] Open
Abstract
Neurofibromatosis type I, a genetic condition due to pathogenic variants in the NF1 gene, is burdened by a high rate of complications, including neoplasms, which increase morbidity and mortality for the disease. We retrospectively re-evaluated the NF1 gene variants found in the period 2000-2019 and we studied for genotype/phenotype correlations of disease complications and neoplasms 34 variants, which were shared by at least two unrelated families (range 2-11) for a total 141 of probands and 21 relatives affected by Neurofibromatosis type I. Recurrent variants could be ascribed to the most common mutational mechanisms (C to T transition, microsatellite slippage, non-homologous recombination). In genotype/phenotype correlations, the variants p.Arg440*, p.Tyr489Cys, and p.Arg1947*, together with the gross gene deletions, displayed the highest rates of complications. When considering neoplasms, carriers of variants falling in the extradomain region at the 5' end of NF1 had a lower age-related cancer frequency than the rest of the gene sequence, showing a borderline significance (p = 0.045), which was not conserved after correction with covariates. We conclude that (1) hotspots in NF1 occur via different mutational mechanisms, (2) several variants are associated with high rates of complications and cancers, and (3) there is an initial evidence toward a lower cancer risk for carriers of variants in the 5' end of the NF1 gene although not significant at the multivariate analysis.
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Affiliation(s)
- Matteo Riva
- Medical Genetics, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | | | | | - Elena Boschi
- Plastic Surgery, University Hospital of Parma, Parma, Italy
| | - Livia Garavelli
- Medical Genetics Unit, Azienda USL-IRCCS, Reggio Emilia, Italy
| | - Giovanni Ponti
- Division of Clinical Pathology, University of Modena and Reggio Emilia, Modena, Italy
| | - Luca Sangiorgi
- Medical Genetics and Skeletal Rare Diseases, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Claudio Graziano
- Medical Genetics, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Stefania Bigoni
- Medical Genetics, Ferrara University Hospital, Ferrara, Italy
| | | | - Simona Madeo
- Pediatrics, University Hospital of Modena, Italy
| | - Fiorenza Soli
- Medical Genetics, Santa Chiara Hospital, Trento, Italy
| | - Enrico Grosso
- Medical Genetics, Città della Salute e della Scienza University Hospital, Torino, Italy
| | - Diana Carli
- Department of Public Health and Pediatric Sciences, University of Torino, Torino, Italy
| | - Matteo Goldoni
- Statistics, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Francesco Pisani
- Children's Neuropsycological Services, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Antonio Percesepe
- Medical Genetics, Department of Medicine and Surgery, University of Parma, Parma, Italy.,University Hospital of Parma, Parma, Italy
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28
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Zhytnik L, Peters M, Tilk K, Simm K, Tõnisson N, Reimand T, Maasalu K, Acharya G, Krjutškov K, Salumets A. From late fatherhood to prenatal screening of monogenic disorders: evidence and ethical concerns. Hum Reprod Update 2021; 27:1056-1085. [PMID: 34329448 DOI: 10.1093/humupd/dmab023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/27/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND With the help of ART, an advanced parental age is not considered to be a serious obstacle for reproduction anymore. However, significant health risks for future offspring hide behind the success of reproductive medicine for the treatment of reduced fertility associated with late parenthood. Although an advanced maternal age is a well-known risk factor for poor reproductive outcomes, understanding the impact of an advanced paternal age on offspring is yet to be elucidated. De novo monogenic disorders (MDs) are highly associated with late fatherhood. MDs are one of the major sources of paediatric morbidity and mortality, causing significant socioeconomic and psychological burdens to society. Although individually rare, the combined prevalence of these disorders is as high as that of chromosomal aneuploidies, indicating the increasing need for prenatal screening. With the help of advanced reproductive technologies, families with late paternity have the option of non-invasive prenatal testing (NIPT) for multiple MDs (MD-NIPT), which has a sensitivity and specificity of almost 100%. OBJECTIVE AND RATIONALE The main aims of the current review were to examine the effect of late paternity on the origin and nature of MDs, to highlight the role of NIPT for the detection of a variety of paternal age-associated MDs, to describe clinical experiences and to reflect on the ethical concerns surrounding the topic of late paternity and MD-NIPT. SEARCH METHODS An extensive search of peer-reviewed publications (1980-2021) in English from the PubMed and Google Scholar databases was based on key words in different combinations: late paternity, paternal age, spermatogenesis, selfish spermatogonial selection, paternal age effect, de novo mutations (DNMs), MDs, NIPT, ethics of late fatherhood, prenatal testing and paternal rights. OUTCOMES An advanced paternal age provokes the accumulation of DNMs, which arise in continuously dividing germline cells. A subset of DNMs, owing to their effect on the rat sarcoma virus protein-mitogen-activated protein kinase signalling pathway, becomes beneficial for spermatogonia, causing selfish spermatogonial selection and outgrowth, and in some rare cases may lead to spermatocytic seminoma later in life. In the offspring, these selfish DNMs cause paternal age effect (PAE) disorders with a severe and even life-threatening phenotype. The increasing tendency for late paternity and the subsequent high risk of PAE disorders indicate an increased need for a safe and reliable detection procedure, such as MD-NIPT. The MD-NIPT approach has the capacity to provide safe screening for pregnancies at risk of PAE disorders and MDs, which constitute up to 20% of all pregnancies. The primary risks include pregnancies with a paternal age over 40 years, a previous history of an affected pregnancy/child, and/or congenital anomalies detected by routine ultrasonography. The implementation of NIPT-based screening would support the early diagnosis and management needed in cases of affected pregnancy. However, the benefits of MD-NIPT need to be balanced with the ethical challenges associated with the introduction of such an approach into routine clinical practice, namely concerns regarding reproductive autonomy, informed consent, potential disability discrimination, paternal rights and PAE-associated issues, equity and justice in accessing services, and counselling. WIDER IMPLICATIONS Considering the increasing parental age and risks of MDs, combined NIPT for chromosomal aneuploidies and microdeletion syndromes as well as tests for MDs might become a part of routine pregnancy management in the near future. Moreover, the ethical challenges associated with the introduction of MD-NIPT into routine clinical practice need to be carefully evaluated. Furthermore, more focus and attention should be directed towards the ethics of late paternity, paternal rights and paternal genetic guilt associated with pregnancies affected with PAE MDs.
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Affiliation(s)
- Lidiia Zhytnik
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Maire Peters
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Kadi Tilk
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Kadri Simm
- Institute of Philosophy and Semiotics, Faculty of Arts and Humanities, University of Tartu, Tartu, Estonia.,Centre of Ethics, University of Tartu, Tartu, Estonia
| | - Neeme Tõnisson
- Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.,Department of Reproductive Medicine, West Tallinn Central Hospital, Tallinn, Estonia
| | - Tiia Reimand
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Katre Maasalu
- Clinic of Traumatology and Orthopaedics, Tartu University Hospital, Tartu, Estonia.,Department of Traumatology and Orthopaedics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Ganesh Acharya
- Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Institute of Genomics, University of Tartu, Tartu, Estonia.,Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
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Chico-Sordo L, Córdova-Oriz I, Polonio AM, S-Mellado LS, Medrano M, García-Velasco JA, Varela E. Reproductive aging and telomeres: Are women and men equally affected? Mech Ageing Dev 2021; 198:111541. [PMID: 34245740 DOI: 10.1016/j.mad.2021.111541] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 02/06/2023]
Abstract
Successful reproduction is very important for individuals and for society. Currently, the human health span and lifespan are the object of intense and productive investigation with great achievements, compared to the last century. However, reproduction span does not progress concomitantly with lifespan. Reproductive organs age, decreasing the levels of sexual hormones, which are protectors of health through their action on several organs of the body. Thus, this is the starting point of the organismal decay and infertility. This starting point is easily detected in women. In men, it goes under the surface, undetected, but it goes, nevertheless. Regarding fertility, aging alters the hormonal equilibrium, decreases the potential of reproductive organs, diminishes the quality of the gametes and worsen the reproductive outcomes. All these events happen at a different pace and affecting different organs in women and men. The question is what molecular pathways are involved in reproductive aging and if there is a possible halting or even reversion of the aging events. Answers to all these points will be explained in the present review.
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Affiliation(s)
- Lucía Chico-Sordo
- IVI Foundation, Instituto de Investigación Sanitaria La Fe (IISLAFE), Valencia, Spain; Instituto de Investigación Sanitaria La Fe, Valencia, Spain.
| | - Isabel Córdova-Oriz
- IVI Foundation, Instituto de Investigación Sanitaria La Fe (IISLAFE), Valencia, Spain; Instituto de Investigación Sanitaria La Fe, Valencia, Spain.
| | - Alba María Polonio
- IVI Foundation, Instituto de Investigación Sanitaria La Fe (IISLAFE), Valencia, Spain; Instituto de Investigación Sanitaria La Fe, Valencia, Spain.
| | - Lucía Sánchez S-Mellado
- IVI Foundation, Instituto de Investigación Sanitaria La Fe (IISLAFE), Valencia, Spain; Instituto de Investigación Sanitaria La Fe, Valencia, Spain.
| | - Marta Medrano
- IVI Foundation, Instituto de Investigación Sanitaria La Fe (IISLAFE), Valencia, Spain; IVIRMA Madrid, Spain.
| | - Juan Antonio García-Velasco
- IVI Foundation, Instituto de Investigación Sanitaria La Fe (IISLAFE), Valencia, Spain; Instituto de Investigación Sanitaria La Fe, Valencia, Spain; IVIRMA Madrid, Spain; Rey Juan Carlos University, Madrid, Spain.
| | - Elisa Varela
- IVI Foundation, Instituto de Investigación Sanitaria La Fe (IISLAFE), Valencia, Spain; Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Rey Juan Carlos University, Madrid, Spain.
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30
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Tiemann‐Boege I, Mair T, Yasari A, Zurovec M. Pathogenic postzygotic mosaicism in the tyrosine receptor kinase pathway: potential unidentified human disease hidden away in a few cells. FEBS J 2021; 288:3108-3119. [PMID: 32810928 PMCID: PMC8247027 DOI: 10.1111/febs.15528] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 07/17/2020] [Accepted: 08/14/2020] [Indexed: 01/19/2023]
Abstract
Mutations occurring during embryonic development affect only a subset of cells resulting in two or more distinct cell populations that are present at different levels, also known as postzygotic mosaicism (PZM). Although PZM is a common biological phenomenon, it is often overlooked as a source of disease due to the challenges associated with its detection and characterization, especially for very low-frequency variants. Moreover, PZM can cause a different phenotype compared to constitutional mutations. Especially, lethal mutations in receptor tyrosine kinase (RTK) pathway genes, which exist only in a mosaic state, can have completely new clinical manifestations and can look very different from the associated monogenic disorder. However, some key questions are still not addressed, such as the level of mosaicism resulting in a pathogenic phenotype and how the clinical outcome changes with the development and age. Addressing these questions is not trivial as we require methods with the sensitivity to capture some of these variants hidden away in very few cells. Recent ultra-accurate deep-sequencing approaches can now identify these low-level mosaics and will be central to understand systemic and local effects of mosaicism in the RTK pathway. The main focus of this review is to highlight the importance of low-level mosaics and the need to include their detection in studies of genomic variation associated with disease.
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Affiliation(s)
| | - Theresa Mair
- Institute of BiophysicsJohannes Kepler UniversityLinzAustria
| | - Atena Yasari
- Institute of BiophysicsJohannes Kepler UniversityLinzAustria
| | - Michal Zurovec
- Biology Centre of the Czech Academy of SciencesInstitute of EntomologyCeske BudejoviceCzech Republic
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31
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Laan M, Kasak L, Timinskas K, Grigorova M, Venclovas Č, Renaux A, Lenaerts T, Punab M. NR5A1 c.991-1G > C splice-site variant causes familial 46,XY partial gonadal dysgenesis with incomplete penetrance. Clin Endocrinol (Oxf) 2021; 94:656-666. [PMID: 33296094 DOI: 10.1111/cen.14381] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/22/2020] [Accepted: 11/24/2020] [Indexed: 12/19/2022]
Abstract
OBJECTIVE The study aimed to identify the genetic basis of partial gonadal dysgenesis (PGD) in a non-consanguineous family from Estonia. PATIENTS Cousins P (proband) 1 (12 years; 46,XY) and P2 (18 years; 46,XY) presented bilateral cryptorchidism, severe penoscrotal hypospadias, low bitesticular volume and azoospermia in P2. Their distant relative, P3 (30 years; 46,XY), presented bilateral cryptorchidism and cryptozoospermia. DESIGN Exome sequencing was targeted to P1-P3 and five unaffected family members. RESULTS P1-P2 were identified as heterozygous carriers of NR5A1 c.991-1G > C. NR5A1 encodes the steroidogenic factor-1 essential in gonadal development and specifically expressed in adrenal, spleen, pituitary and testes. Together with a previous PGD case from Belgium (Robevska et al 2018), c.991-1G > C represents the first recurrent NR5A1 splice-site mutation identified in patients. The majority of previous reports on NR5A1 mutation carriers have not included phenotype-genotype data of the family members. Segregation analysis across three generations showed incomplete penetrance (<50%) and phenotypic variability among the carriers of NR5A1 c.991-1G > C. The variant pathogenicity was possibly modulated by rare heterozygous variants inherited from the other parent, OTX2 p.P134R (P1) or PROP1 c.301_302delAG (P2). For P3, the pedigree structure supported a distinct genetic cause. He carries a previously undescribed likely pathogenic variant SOS1 p.Y136H. SOS1, critical in Ras/MAPK signalling and foetal development, is a strong novel candidate gene for cryptorchidism. CONCLUSIONS Detailed genetic profiling facilitates counselling and clinical management of the probands, and supports unaffected mutation carriers in the family for their reproductive decision making.
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Affiliation(s)
- Maris Laan
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Laura Kasak
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Kęstutis Timinskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Marina Grigorova
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Alexandre Renaux
- Interuniversity Institute of Bioinformatics in Brussels, Université libre de Bruxelles, Vrije Universiteit Brussel, Brussels, Belgium
- Machine Learning Group, Université libre de Bruxelles, Brussels, Belgium
- Artificial Intelligence lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels, Université libre de Bruxelles, Vrije Universiteit Brussel, Brussels, Belgium
- Machine Learning Group, Université libre de Bruxelles, Brussels, Belgium
- Artificial Intelligence lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Margus Punab
- Andrology Center, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
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Marmion RA, Yang L, Goyal Y, Jindal GA, Wetzel JL, Singh M, Schüpbach T, Shvartsman SY. Molecular mechanisms underlying cellular effects of human MEK1 mutations. Mol Biol Cell 2021; 32:974-983. [PMID: 33476180 PMCID: PMC8108529 DOI: 10.1091/mbc.e20-10-0625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Terminal regions of Drosophila embryos are patterned by signaling through ERK, which is genetically deregulated in multiple human diseases. Quantitative studies of terminal patterning have been recently used to investigate gain-of-function variants of human MEK1, encoding the MEK kinase that directly activates ERK by dual phosphorylation. Unexpectedly, several mutations reduced ERK activation by extracellular signals, possibly through a negative feedback triggered by signal-independent activity of the mutant variants. Here we present experimental evidence supporting this model. Using a MEK variant that combines a mutation within the negative regulatory region with alanine substitutions in the activation loop, we prove that pathogenic variants indeed acquire signal-independent kinase activity. We also demonstrate that signal-dependent activation of these variants is independent of kinase suppressor of Ras, a conserved adaptor that is indispensable for activation of normal MEK. Finally, we show that attenuation of ERK activation by extracellular signals stems from transcriptional induction of Mkp3, a dual specificity phosphatase that deactivates ERK by dephosphorylation. These findings in the Drosophila embryo highlight its power for investigating diverse effects of human disease mutations.
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Affiliation(s)
- Robert A Marmion
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Liu Yang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Yogesh Goyal
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544.,Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Granton A Jindal
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544.,Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Joshua L Wetzel
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Computer Science, Princeton University, Princeton, NJ 08540
| | - Mona Singh
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Computer Science, Princeton University, Princeton, NJ 08540
| | - Trudi Schüpbach
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Stanislav Y Shvartsman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544.,Flatiron Institute, Simons Foundation, New York, NY 10010
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33
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Dviri M, Madjunkova S, Koziarz A, Madjunkov M, Mashiach J, Nekolaichuk E, Trivodaliev K, Al-Asmar N, Moskovtsev SI, Librach C. Is there an association between paternal age and aneuploidy? Evidence from young donor oocyte-derived embryos: a systematic review and individual patient data meta-analysis. Hum Reprod Update 2020; 27:486-500. [PMID: 33355342 DOI: 10.1093/humupd/dmaa052] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/15/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Delayed parenthood, by both women and men, has become more common in developed countries. The adverse effect of advanced maternal age on embryo aneuploidy and reproductive outcomes is well known. However, whether there is an association between paternal age (PA) and embryonic chromosomal aberrations remains controversial. Oocyte donation (OD) is often utilized to minimize maternal age effects on oocyte and embryo aneuploidy, thus providing an optimal model to assess the effect of PA. Several studies have revealed a higher than expected rate of aneuploidy in embryos derived from young oocyte donors, which warrants examination as to whether this may be attributed to advanced PA (APA). OBJECTIVE AND RATIONALE The objective of this systematic review and individual patient data (IPD) meta-analysis is to evaluate existing evidence regarding an association between PA and chromosomal aberrations in an OD model. SEARCH METHODS This review was conducted according to PRISMA guidelines for systematic reviews and meta-analyses. Medline, Embase and Cochrane databases were searched from inception through March 2020 using the (MeSH) terms: chromosome aberrations, preimplantation genetic screening and IVF. Original research articles, reporting on the types and/or frequency of chromosomal aberrations in embryos derived from donor oocytes, including data regarding PA, were included. Studies reporting results of IVF cycles using only autologous oocytes were excluded. Quality appraisal of included studies was conducted independently by two reviewers using a modified Newcastle-Ottawa Assessment Scale. A one-stage IPD meta-analysis was performed to evaluate whether an association exists between PA and aneuploidy. Meta-analysis was performed using a generalized linear mixed model to account for clustering of embryos within patients and clustering of patients within studies. OUTCOMES The search identified 13 032 references, independently screened by 2 reviewers, yielding 6 studies encompassing a total of 2637 IVF-OD cycles (n = 20 024 embryos). Two 'low' quality studies using FISH to screen 12 chromosomes on Day 3 embryos (n = 649) reported higher total aneuploidy rates and specifically higher rates of trisomy 21, 18 and 13 in men ≥50 years. One 'moderate' and three 'high' quality studies, which used 24-chromosome screening, found no association between PA and aneuploidy in Day 5/6 embryos (n = 12 559). The IPD meta-analysis, which included three 'high' quality studies (n = 10 830 Day 5/6 embryos), found no significant effect of PA on the rate of aneuploidy (odds ratio (OR) 0.97 per decade of age, 95% CI 0.91-1.03), which was robust to sensitivity analyses. There was no association between PA and individual chromosome aneuploidy or segmental aberrations, including for chromosomes X and Y (OR 1.06 per decade of age, 95% CI 0.92-1.21). Monosomy was most frequent for chromosome 16 (217/10802, 2.01%, 95% CI 1.76-2.29%) and trisomy was also most frequent for chromosome 16 (194/10802, 1.80%, 95% CI 1.56-2.06%). WIDER IMPLICATIONS We conclude, based on the available evidence, that APA is not associated with higher rates of aneuploidy in embryos derived from OD. These results will help fertility practitioners when providing preconception counselling, particularly to older men who desire to have a child.
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Affiliation(s)
- Michal Dviri
- CReATe Fertility Centre, Reproductive Genetics, Toronto, Canada.,Department of Obstetrics and Gynecology, University of Toronto, Toronto, Canada
| | | | - Alex Koziarz
- Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Mitko Madjunkov
- CReATe Fertility Centre, Reproductive Genetics, Toronto, Canada
| | - Jordana Mashiach
- CReATe Fertility Centre, Reproductive Genetics, Toronto, Canada.,Department of Obstetrics and Gynecology, University of Toronto, Toronto, Canada
| | - Erica Nekolaichuk
- Gerstein Science Information Centre, University of Toronto, Toronto, Canada
| | - Kire Trivodaliev
- Faculty of Computer Science and Engineering, Ss Cyril and Methodius University, Skopje, Macedonia
| | - Nasser Al-Asmar
- Igenomix, Narcís Monturiol Estarriol n°11, Paterna, Valencia, Spain
| | - Sergey Ivanovovich Moskovtsev
- CReATe Fertility Centre, Reproductive Genetics, Toronto, Canada.,Department of Obstetrics and Gynecology, University of Toronto, Toronto, Canada
| | - Clifford Librach
- CReATe Fertility Centre, Reproductive Genetics, Toronto, Canada.,Department of Obstetrics and Gynecology, University of Toronto, Toronto, Canada.,Institute of Medical Sciences, University of Toronto, Toronto, Canada.,Department of Physiology, University of Toronto, Toronto, Canada
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Rauen KA, Maeda Y, Egense A, Tidyman WE. Familial cardio-facio-cutaneous syndrome: Vertical transmission of the BRAF p.G464R pathogenic variant and review of the literature. Am J Med Genet A 2020; 185:469-475. [PMID: 33274568 DOI: 10.1002/ajmg.a.61995] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/26/2020] [Accepted: 11/07/2020] [Indexed: 12/25/2022]
Abstract
Cardio-facio-cutaneous syndrome (CFC) is one of the RASopathies and is caused by germline mutations that activate the Ras/mitogen-activated protein kinase (MAPK) pathway. CFC is due to heterozygous germline mutations in protein kinases BRAF, MEK1, or MEK2 and rarely in KRAS, a small GTPase. CFC is a multiple congenital anomaly disorder in which individuals may have craniofacial dysmorphia, heart issues, skin and hair anomalies, and delayed development. Pathogenic variants for CFC syndrome are usually considered de novo because vertical transmission has only been reported with MEK2 and KRAS. The index case was a 3-year-old male with features consistent with the clinical diagnosis of CFC. Sequencing revealed a previously reported heterozygous likely pathogenic variant BRAF p.G464R. Upon detailed family history, the index case's pregnant mother was noted to have similar features to her son. Targeted familial testing of the BRAF pathogenic variant was performed on the mother, confirming her diagnosis. Prenatal genetic testing for the fetus was declined, but postnatal molecular testing of the index case's sister was positive for the familial BRAF p.G464R variant. Functional analysis of the variant demonstrated increased kinase activity. We report the first identified vertically transmitted functional BRAF pathogenic variant. Our findings emphasize the importance of obtaining a comprehensive evaluation of family members and that activating pathogenic variants within the canonical MAPK cascade mediated by BRAF are compatible with human reproduction.
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Affiliation(s)
- Katherine A Rauen
- Department of Pediatrics, Division of Genomic Medicine, University of California Davis, Sacramento, California, USA.,MIND Institute, University of California Davis, Sacramento, California, USA
| | - Yoshiko Maeda
- Department of Pediatrics, Division of Genomic Medicine, University of California Davis, Sacramento, California, USA.,MIND Institute, University of California Davis, Sacramento, California, USA
| | - Alena Egense
- Department of Pediatrics, Division of Genomic Medicine, University of California Davis, Sacramento, California, USA.,MIND Institute, University of California Davis, Sacramento, California, USA
| | - William E Tidyman
- MIND Institute, University of California Davis, Sacramento, California, USA.,Department of Pediatrics, Division of Behavioral and Developmental Pediatrics, University of California Davis, Sacramento, California, USA
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He J, Xu S, Ji Z, Sun Y, Cai B, Zhang S, Wang P. The role of miR-7 as a potential switch in the mouse hypothalamus-pituitary-ovary axis through regulation of gonadotropins. Mol Cell Endocrinol 2020; 518:110969. [PMID: 32781248 DOI: 10.1016/j.mce.2020.110969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/06/2020] [Accepted: 07/27/2020] [Indexed: 12/11/2022]
Abstract
The hypothalamus-pituitary-ovary (HPO) axis plays fundamental roles in female neuroendocrinology and reproduction. Pituitary gonadotropins are located in the center of this axis. Previous investigation suggested that miR-7 is closely linked with gonadotropins. However, the interaction between miR-7 and the HPO axis remains unclear. This study aims to determine whether and how miR-7 functions in this axis. A mouse ovariectomy model and mouse primary pituitary cells were used in this study. The results showed that miR-7 is localized to gonadotrophs and somatotrophs. miR-7 can inhibit the expression, synthesis and secretion of gonadotropins, but not growth hormones. Gonadotropin-releasing hormone (GnRH) has inhibitory effects on miR-7, while estrogen enhances miR-7 expression. miR-7 is vital for the pathway by which GnRH and estrogen regulate gonadotropins by targeting v-raf-leukemia viral oncogene 1 (Raf1). Together, these results indicate that miR-7 acts as a potential switch in the feedback loop of the HPO axis by regulating gonadotropins.
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Affiliation(s)
- Jing He
- Department of Clinical Laboratory, Taizhou Second People's Hospital, Taizhou, Jiangsu, People's Republic of China
| | - Shirong Xu
- Department of Clinical Laboratory, Taizhou Second People's Hospital, Taizhou, Jiangsu, People's Republic of China
| | - Zengjun Ji
- Department of Clinical Laboratory, Taizhou Second People's Hospital, Taizhou, Jiangsu, People's Republic of China
| | - Youhong Sun
- Department of Gynecology, Taizhou Second People's Hospital, Taizhou, Jiangsu, People's Republic of China
| | - Bingyan Cai
- School of Veterinary Medicine, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, People's Republic of China
| | - Shanhui Zhang
- Department of Clinical Laboratory, Taizhou Second People's Hospital, Taizhou, Jiangsu, People's Republic of China.
| | - Pingping Wang
- Department of Clinical Laboratory, Taizhou Second People's Hospital, Taizhou, Jiangsu, People's Republic of China.
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36
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Kaplanis J, Samocha KE, Wiel L, Zhang Z, Arvai KJ, Eberhardt RY, Gallone G, Lelieveld SH, Martin HC, McRae JF, Short PJ, Torene RI, de Boer E, Danecek P, Gardner EJ, Huang N, Lord J, Martincorena I, Pfundt R, Reijnders MRF, Yeung A, Yntema HG, Vissers LELM, Juusola J, Wright CF, Brunner HG, Firth HV, FitzPatrick DR, Barrett JC, Hurles ME, Gilissen C, Retterer K. Evidence for 28 genetic disorders discovered by combining healthcare and research data. Nature 2020; 586:757-762. [PMID: 33057194 PMCID: PMC7116826 DOI: 10.1038/s41586-020-2832-5] [Citation(s) in RCA: 288] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 07/17/2020] [Indexed: 01/28/2023]
Abstract
De novo mutations in protein-coding genes are a well-established cause of developmental disorders1. However, genes known to be associated with developmental disorders account for only a minority of the observed excess of such de novo mutations1,2. Here, to identify previously undescribed genes associated with developmental disorders, we integrate healthcare and research exome-sequence data from 31,058 parent-offspring trios of individuals with developmental disorders, and develop a simulation-based statistical test to identify gene-specific enrichment of de novo mutations. We identified 285 genes that were significantly associated with developmental disorders, including 28 that had not previously been robustly associated with developmental disorders. Although we detected more genes associated with developmental disorders, much of the excess of de novo mutations in protein-coding genes remains unaccounted for. Modelling suggests that more than 1,000 genes associated with developmental disorders have not yet been described, many of which are likely to be less penetrant than the currently known genes. Research access to clinical diagnostic datasets will be critical for completing the map of genes associated with developmental disorders.
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Affiliation(s)
- Joanna Kaplanis
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kaitlin E Samocha
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Laurens Wiel
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | - Ruth Y Eberhardt
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Giuseppe Gallone
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Stefan H Lelieveld
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hilary C Martin
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Jeremy F McRae
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Patrick J Short
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Elke de Boer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Petr Danecek
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Eugene J Gardner
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ni Huang
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Jenny Lord
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Iñigo Martincorena
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Margot R F Reijnders
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Alison Yeung
- Victorian Clinical Genetics Services, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Helger G Yntema
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Han G Brunner
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
- GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands
- MHENS School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Helen V Firth
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jeffrey C Barrett
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Matthew E Hurles
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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Maher GJ, Bernkopf M, Koelling N, Wilkie AOM, Meistrich ML, Goriely A. The impact of chemo- and radiotherapy treatments on selfish de novo FGFR2 mutations in sperm of cancer survivors. Hum Reprod 2020; 34:1404-1415. [PMID: 31348830 PMCID: PMC6688873 DOI: 10.1093/humrep/dez090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/15/2019] [Indexed: 01/06/2023] Open
Abstract
STUDY QUESTION What effect does cancer treatment have on levels of spontaneous selfish fibroblast growth factor receptor 2 (FGFR2) point mutations in human sperm? SUMMARY ANSWER Chemotherapy and radiotherapy do not increase levels of spontaneous FGFR2 mutations in sperm but, unexpectedly, highly-sterilizing treatments dramatically reduce the levels of the disease-associated c.755C > G (Apert syndrome) mutation in sperm. WHAT IS KNOWN ALREADY Cancer treatments lead to short-term increases in gross DNA damage (chromosomal abnormalities and DNA fragmentation) but the long-term effects, particularly at the single nucleotide resolution level, are poorly understood. We have exploited an ultra-sensitive assay to directly quantify point mutation levels at the FGFR2 locus. STUDY DESIGN, SIZE, DURATION ‘Selfish’ mutations are disease-associated mutations that occur spontaneously in the sperm of most men and their levels typically increase with age. Levels of mutations at c.752–755 of FGFR2 (including c.755C > G and c.755C > T associated with Apert and Crouzon syndromes, respectively) in semen post-cancer treatment from 18 men were compared to levels in pre-treatment samples from the same individuals (n = 4) or levels in previously screened population controls (n = 99). PARTICIPANTS/MATERIALS, SETTING, METHODS Cancer patients were stratified into four different groups based on the treatments they received and the length of time for spermatogenesis recovery. DNA extracted from semen samples was analysed using a previously established highly sensitive assay to identify mutations at positions c.752–755 of FGFR2. Five to ten micrograms of semen genomic DNA was spiked with internal controls for quantification purposes, digested with MboI restriction enzyme and gel extracted. Following PCR amplification, further MboI digestion and a nested PCR with barcoding primers, samples were sequenced on Illumina MiSeq. Mutation levels were determined relative to the spiked internal control; in individuals heterozygous for a nearby common single nucleotide polymorphism (SNP), mutations were phased to their respective alleles. MAIN RESULTS AND THE ROLE OF CHANCE Patients treated with moderately-sterilizing alkylating regimens and who recovered spermatogenesis within <3 years after therapy (Group 3, n = 4) or non − alkylating chemotherapy and/or low gonadal radiation doses (Group 1, n = 4) had mutation levels similar to untreated controls. However, patients who had highly-sterilizing alkylating treatments (i.e. >5 years to spermatogenesis recovery) (Group 2, n = 7) or pelvic radiotherapy (Group 4, n = 3) exhibited c.755C > G mutation levels at or below background. Two patients (A and B) treated with highly-sterilizing alkylating agents demonstrated a clear reduction from pre-treatment levels; however pre-treatment samples were not available for the other patients with low mutation levels. Therefore, although based on their age we would expect detectable levels of mutations, we cannot exclude the possibility that these patients also had low mutation levels pre-treatment. In three patients with low c.755C > G levels at the first timepoint post-treatment, we observed increasing mutation levels over time. For two such patients we could phase the mutation to a nearby polymorphism (SNP) and determine that the mutation counts likely originated from a single or a small number of mutational events. LIMITATIONS, REASONS FOR CAUTION This study was limited to 18 patients with different treatment regimens; for nine of the 18 patients, samples from only one timepoint were available. Only 12 different de novo substitutions at the FGFR2 c.752–755 locus were assessed, two of which are known to be disease associated. WIDER IMPLICATIONS OF THE FINDINGS Our data add to the body of evidence from epidemiological studies and experimental data in humans suggesting that male germline stem cells are resilient to the accumulation of spontaneous mutations. Collectively, these data should provide physicians and health-care professionals with reassuring experimental-based evidence for counselling of male cancer patients contemplating their reproductive options several years after treatment. STUDY FUNDING/COMPETING INTEREST(S) This work was primarily supported by grants from the Wellcome (grant 091182 to AG and AOMW; grant 102 731 to AOMW), the University of Oxford Medical Sciences Division Internal Fund (grant 0005128 to GJM and AG), the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre Programme (to AG) and the US National Institutes of Health (to MLM). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. None of the authors has any conflicts of interest to declare. TRIAL REGISTRATION NUMBER NA
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Affiliation(s)
- Geoffrey J Maher
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Marie Bernkopf
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Nils Koelling
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Marvin L Meistrich
- Department of Experimental Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, USA
| | - Anne Goriely
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
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Martínez-Glez V, Tenorio J, Nevado J, Gordo G, Rodríguez-Laguna L, Feito M, de Lucas R, Pérez-Jurado LA, Ruiz Pérez VL, Torrelo A, Spinner NB, Happle R, Biesecker LG, Lapunzina P. A six-attribute classification of genetic mosaicism. Genet Med 2020; 22:1743-1757. [PMID: 32661356 PMCID: PMC8581815 DOI: 10.1038/s41436-020-0877-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 01/23/2023] Open
Abstract
Mosaicism denotes an individual who has at least two populations of cells with distinct genotypes that are derived from a single fertilized egg. Genetic variation among the cell lines can involve whole chromosomes, structural or copy number variants, small or single nucleotide variants, or epigenetic variants. The mutational events that underlie mosaic variants occur during mitotic cell divisions after fertilization and zygote formation. The initiating mutational event can occur in any types of cell at any time in development, leading to enormous variation in the distribution and phenotypic effect of mosaicism. A number of classification proposals have been put forward to classify genetic mosaicism into categories based on the location, pattern, and mechanisms of the disease. We here propose a new classification of genetic mosaicism that considers the affected tissue, the pattern and distribution of the mosaicism, the pathogenicity of the variant, the direction of the change (benign to pathogenic vs. pathogenic to benign), and the postzygotic mutational mechanism. The accurate and comprehensive categorization and subtyping of mosaicisms is important and has potential clinical utility to define the natural history of these disorders, tailor follow-up frequency and interventions, estimate recurrence risks, and guide therapeutic decisions.
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Affiliation(s)
- Víctor Martínez-Glez
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain. .,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain. .,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.
| | - Jair Tenorio
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium
| | - Julián Nevado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium
| | - Gema Gordo
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Lara Rodríguez-Laguna
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Marta Feito
- Department of Pediatric Dermatology, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Raúl de Lucas
- Department of Pediatric Dermatology, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Luis A Pérez-Jurado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Genetics Unit, Universitat Pompeu Fabra and Hospital del Mar Research Institute (IMIM), Barcelona, Spain.,Women's and Children's Hospital, South Australia Medical and Health Research Institute (SAHMRI) and University of Adelaide, Adelaide, SA, Australia
| | - Víctor L Ruiz Pérez
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.,Instituto de Investigaciones Biomédicas de Madrid (CSIC-UAM), Madrid, Spain
| | - Antonio Torrelo
- Department of Pediatrics, Hospital Universitario Niño Jesús, Madrid, Spain
| | - Nancy B Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicines at The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rudolf Happle
- Department of Dermatology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, MD, USA
| | - Pablo Lapunzina
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain. .,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain. .,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.
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Castel P, Rauen KA, McCormick F. The duality of human oncoproteins: drivers of cancer and congenital disorders. Nat Rev Cancer 2020; 20:383-397. [PMID: 32341551 PMCID: PMC7787056 DOI: 10.1038/s41568-020-0256-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/20/2020] [Indexed: 01/29/2023]
Abstract
Human oncoproteins promote transformation of cells into tumours by dysregulating the signalling pathways that are involved in cell growth, proliferation and death. Although oncoproteins were discovered many years ago and have been widely studied in the context of cancer, the recent use of high-throughput sequencing techniques has led to the identification of cancer-associated mutations in other conditions, including many congenital disorders. These syndromes offer an opportunity to study oncoprotein signalling and its biology in the absence of additional driver or passenger mutations, as a result of their monogenic nature. Moreover, their expression in multiple tissue lineages provides insight into the biology of the proto-oncoprotein at the physiological level, in both transformed and unaffected tissues. Given the recent paradigm shift in regard to how oncoproteins promote transformation, we review the fundamentals of genetics, signalling and pathogenesis underlying oncoprotein duality.
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Affiliation(s)
- Pau Castel
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
| | - Katherine A Rauen
- MIND Institute, Department of Pediatrics, University of California, Davis, Sacramento, CA, USA
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
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40
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Looijenga LH, Van der Kwast TH, Grignon D, Egevad L, Kristiansen G, Kao CS, Idrees MT. Report From the International Society of Urological Pathology (ISUP) Consultation Conference on Molecular Pathology of Urogenital Cancers: IV: Current and Future Utilization of Molecular-Genetic Tests for Testicular Germ Cell Tumors. Am J Surg Pathol 2020; 44:e66-e79. [PMID: 32205480 PMCID: PMC7289140 DOI: 10.1097/pas.0000000000001465] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The International Society of Urological Pathology (ISUP) organized a Consultation Conference in March 2019 dealing with applications of molecular pathology in Urogenital Pathology, including testicular tumors (with a focus on germ cell tumors [GCTs]), preceded by a survey among its members to get insight into current practices in testicular germ cell tumor (TGCT) diagnostics and adoption of the ISUP immunohistochemical guidelines published in 2014. On the basis of the premeeting survey, the most commonly used immunomarker panel includes OCT3/4, placental alkaline phosphate, D2-40, SALL4, CD117, and CD30 for GCTs and the documentation of germ cell neoplasia in situ (GCNIS). Molecular testing, specifically 12p copy gain, is informative to distinguish non-GCNIS versus GCNIS related GCTs, and establishing germ cell origin of tumors both in the context of primary and metastatic lesions. Other molecular methodologies currently available but not widely utilized for TGCTs include genome-wide and targeted approaches for specific genetic anomalies, P53 mutations, genomic MDM2 amplification, and detection of the p53 inactivating miR-371a-3p. The latter also holds promise as a serum marker for malignant TGCTs. This manuscript provides an update on the classification of TGCTs, and describes the current and future role of molecular-genetic testing. The following recommendations are made: (1) Presence of GCNIS should be documented in all cases along with extent of spermatogenesis; (2) Immunohistochemical staining is optional in the following scenarios: identification of GCNIS, distinguishing embryonal carcinoma from seminoma, confirming presence of yolk sac tumor and/or choriocarcinoma, and differentiating spermatocytic tumor from potential mimics; (3) Detection of gain of the short arm of chromosome 12 is diagnostic to differentiate between non-GCNIS versus GCNIS related GCTs and supportive to the germ cell origin of both primary and metastatic tumors.
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Affiliation(s)
| | | | | | - Lars Egevad
- Department of Oncology and Pathology, Karolinska Institutet Sweden, Solna, Sweden
| | - Glen Kristiansen
- Department of Pathology, University Hospital Bonn, Bonn, Germany
| | - Chia-Sui Kao
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
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41
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Koelling N, Bernkopf M, Calpena E, Maher GJ, Miller KA, Ralph HK, Goriely A, Wilkie AOM. amplimap: a versatile tool to process and analyze targeted NGS data. Bioinformatics 2020; 35:5349-5350. [PMID: 31350555 PMCID: PMC6954648 DOI: 10.1093/bioinformatics/btz582] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 06/01/2019] [Accepted: 07/22/2019] [Indexed: 11/12/2022] Open
Abstract
SUMMARY amplimap is a command-line tool to automate the processing and analysis of data from targeted next-generation sequencing experiments with PCR-based amplicons or capture-based enrichment systems. From raw sequencing reads, amplimap generates output such as read alignments, annotated variant calls, target coverage statistics and variant allele counts and frequencies for each target base pair. In addition to its focus on user-friendliness and reproducibility, amplimap supports advanced features such as consensus base calling for read families based on unique molecular identifiers and filtering false positive variant calls caused by amplification of off-target loci. AVAILABILITY AND IMPLEMENTATION amplimap is available as a free Python package under the open-source Apache 2.0 License. Documentation, source code and installation instructions are available at https://github.com/koelling/amplimap.
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Affiliation(s)
- Nils Koelling
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Marie Bernkopf
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Geoffrey J Maher
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Kerry A Miller
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Hannah K Ralph
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Anne Goriely
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
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42
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FitzPatrick DR, Firth HV. Genomically Aided Diagnosis of Severe Developmental Disorders. Annu Rev Genomics Hum Genet 2020; 21:327-349. [PMID: 32421356 DOI: 10.1146/annurev-genom-120919-082329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Our ability to make accurate and specific genetic diagnoses in individuals with severe developmental disorders has been transformed by data derived from genomic sequencing technologies. These data reveal both the patterns and rates of different mutational mechanisms and identify regions of the human genome with fewer mutations than would be expected. In outbred populations, the most common identifiable cause of severe developmental disorders is de novo mutation affecting the coding region in one of approximately 500 different genes, almost universally showing constraint. Simply combining the location of a de novo genomic event with its predicted consequence on the gene product gives significant diagnostic power. Our knowledge of the diversity of phenotypic consequences associated with comparable diagnostic genotypes at each locus is improving. Computationally useful phenotype data will improve diagnostic interpretation of ultrarare genetic variants and, in the long run, indicate which specific embryonic processes have been perturbed.
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Affiliation(s)
- David R FitzPatrick
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom; .,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH8 9XD, United Kingdom.,Royal Hospital for Children and Young People, Edinburgh EH16 4SF, United Kingdom
| | - Helen V Firth
- Department of Clinical Genetics, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; .,Wellcome Sanger Institute, Hinxton CB10 1SA, United Kingdom
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43
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Ferreira LC, Dantas Junior JH. Report of a Father With Congenital Bilateral Absence of the Vas Deferens Fathering a Child With Beare–Stevenson Syndrome. Front Genet 2020; 11:104. [PMID: 32158469 PMCID: PMC7052335 DOI: 10.3389/fgene.2020.00104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/29/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Leonardo C. Ferreira
- Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, Brazil
- Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, Brazil
- *Correspondence: Leonardo C. Ferreira,
| | - José H. Dantas Junior
- University Hospital Onofre Lopes, Urologic Unit, Federal University of Rio Grande do Norte, Natal, Brazil
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44
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Huang G, Liu L, Wang H, Gou M, Gong P, Tian C, Deng W, Yang J, Zhou TT, Xu GL, Liu L. Tet1 Deficiency Leads to Premature Reproductive Aging by Reducing Spermatogonia Stem Cells and Germ Cell Differentiation. iScience 2020; 23:100908. [PMID: 32114381 PMCID: PMC7049665 DOI: 10.1016/j.isci.2020.100908] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/08/2019] [Accepted: 02/07/2020] [Indexed: 12/17/2022] Open
Abstract
Ten-eleven translocation (Tet) enzymes are involved in DNA demethylation, important in regulating embryo development, stem cell pluripotency and tumorigenesis. Alterations of DNA methylation with age have been shown in various somatic cell types. We investigated whether Tet1 and Tet2 regulate aging. We showed that Tet1-deficient mice undergo a progressive reduction of spermatogonia stem cells and spermatogenesis and thus accelerated infertility with age. Tet1 deficiency decreases 5hmC levels in spermatogonia and downregulates a subset of genes important for cell cycle, germ cell differentiation, meiosis and reproduction, such as Ccna1 and Spo11, resulting in premature reproductive aging. Moreover, Tet1 and 5hmC both regulate signaling pathways key for stem cell development, including Wnt and PI3K-Akt, autophagy and stress response genes. In contrast, effect of Tet2 deficiency on male reproductive aging is minor. Hence, Tet1 maintains spermatogonia stem cells with age, revealing an important role of Tet1 in regulating stem cell aging. Tet1 regulates stem cell aging and differentiation Tet1 plays an important role in maintaining spermatogonial stem cells Loss of Tet1 results in exhaustion of spermatogonia and premature reproductive aging Effect of Tet2 deficiency on reproductive aging in males is minor
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Affiliation(s)
- Guian Huang
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Linlin Liu
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Huasong Wang
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Mo Gou
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Peng Gong
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Chenglei Tian
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Wei Deng
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Jiao Yang
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Tian-Tian Zhou
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guo-Liang Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Lin Liu
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China.
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45
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Abstract
DNA repair pathways permit some damage, leading to mutagenesis but not always cancer
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Affiliation(s)
- Serena Nik-Zainal
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK.
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
| | - Benjamin A Hall
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
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Goldmann JM, Veltman JA, Gilissen C. De Novo Mutations Reflect Development and Aging of the Human Germline. Trends Genet 2019; 35:828-839. [PMID: 31610893 DOI: 10.1016/j.tig.2019.08.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/15/2019] [Accepted: 08/28/2019] [Indexed: 01/19/2023]
Abstract
Human germline de novo mutations (DNMs) are both a driver of evolution and an important cause of genetic diseases. In the past few years, whole-genome sequencing (WGS) of parent-offspring trios has facilitated the large-scale detection and study of human DNMs, which has led to exciting discoveries. The overarching theme of all of these studies is that the DNMs of an individual are a complex mixture of mutations that arise through different biological processes acting at different times during human development and life.
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Affiliation(s)
- J M Goldmann
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands
| | - J A Veltman
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, UK; Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands
| | - C Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands.
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47
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Predicting Gonadal Germ Cell Cancer in People with Disorders of Sex Development; Insights from Developmental Biology. Int J Mol Sci 2019; 20:ijms20205017. [PMID: 31658757 PMCID: PMC6834166 DOI: 10.3390/ijms20205017] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/03/2019] [Accepted: 10/05/2019] [Indexed: 01/03/2023] Open
Abstract
The risk of gonadal germ cell cancer (GGCC) is increased in selective subgroups, amongst others, defined patients with disorders of sex development (DSD). The increased risk is due to the presence of part of the Y chromosome, i.e., GonadoBlastoma on Y chromosome GBY region, as well as anatomical localization and degree of testicularization and maturation of the gonad. The latter specifically relates to the germ cells present being at risk when blocked in an embryonic stage of development. GGCC originates from either germ cell neoplasia in situ (testicular environment) or gonadoblastoma (ovarian-like environment). These precursors are characterized by presence of the markers OCT3/4 (POU5F1), SOX17, NANOG, as well as TSPY, and cKIT and its ligand KITLG. One of the aims is to stratify individuals with an increased risk based on other parameters than histological investigation of a gonadal biopsy. These might include evaluation of defined susceptibility alleles, as identified by Genome Wide Association Studies, and detailed evaluation of the molecular mechanism underlying the DSD in the individual patient, combined with DNA, mRNA, and microRNA profiling of liquid biopsies. This review will discuss the current opportunities as well as limitations of available knowledge in the context of predicting the risk of GGCC in individual patients.
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Pacot L, Burin des Roziers C, Laurendeau I, Briand-Suleau A, Coustier A, Mayard T, Tlemsani C, Faivre L, Thomas Q, Rodriguez D, Blesson S, Dollfus H, Muller YG, Parfait B, Vidaud M, Gilbert-Dussardier B, Yardin C, Dauriat B, Derancourt C, Vidaud D, Pasmant E. One NF1 Mutation may Conceal Another. Genes (Basel) 2019; 10:genes10090633. [PMID: 31443423 PMCID: PMC6769760 DOI: 10.3390/genes10090633] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/10/2019] [Accepted: 08/20/2019] [Indexed: 01/01/2023] Open
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant disease with complete penetrance but high variable expressivity. NF1 is caused by loss-of-function mutations in the NF1 gene, a negative regulator of the RAS-MAPK pathway. The NF1 gene has one of the highest mutation rates in human disorders, which may explain the outbreak of independent de novo variants in the same family. Here, we report the co-occurrence of pathogenic variants in the NF1 and SPRED1 genes in six families with NF1 and Legius syndrome, using next-generation sequencing. In five of these families, we observed the co-occurrence of two independent NF1 variants. All NF1 variants were classified as pathogenic, according to the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG-AMP) guidelines. In the sixth family, one sibling inherited a complete deletion of the NF1 gene from her mother and carried a variant of unknown significance in the SPRED1 gene. This variant was also present in her brother, who was diagnosed with Legius syndrome, a differential diagnosis of NF1. This work illustrates the complexity of molecular diagnosis in a not-so-rare genetic disease.
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Affiliation(s)
- Laurence Pacot
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Cyril Burin des Roziers
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Ingrid Laurendeau
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Audrey Briand-Suleau
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Audrey Coustier
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
| | - Théodora Mayard
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
| | - Camille Tlemsani
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Laurence Faivre
- Inserm, UMR 1231, Génétique des Anomalies du Développement, Université de Bourgogne, 21079 Dijon, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d'Enfants, 21079 Dijon, France
| | - Quentin Thomas
- Inserm, UMR 1231, Génétique des Anomalies du Développement, Université de Bourgogne, 21079 Dijon, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d'Enfants, 21079 Dijon, France
| | - Diana Rodriguez
- Department of Child Neurology and National Reference Center for Neurogenetic Disorders, Armand Trousseau Hospital, GHUEP, AP-HP, INSERM U1141, 75012 Paris, France
- GRC n°19 ConCer-LD, Sorbonne Université, 75012 Paris, France
| | - Sophie Blesson
- Service de Génétique, CHRU de Tours, 37044 Tours, France
| | - Hélène Dollfus
- Centre de référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), Hôpital Civil, 67091 Strasbourg, France
- Service de Génétique Médicale, Hôpital de Hautepierre, 67200 Strasbourg, France
- Laboratoire de Génétique Médicale, INSERM U1112, 67000 Strasbourg, France
| | | | - Béatrice Parfait
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Michel Vidaud
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | | | - Catherine Yardin
- Department of Cytogenetics and clinical genetics, Limoges University Hospital, 87042 Limoges, France
- UMR 7252, Limoges University, CNRS, XLIM, 87000 Limoges, France
| | - Benjamin Dauriat
- Department of Cytogenetics and clinical genetics, Limoges University Hospital, 87042 Limoges, France
| | - Christian Derancourt
- EA 4537, Antilles University, 97261 Fort-de-France, Martinique, France
- DRCI, Martinique University Hospital, 97261 Fort-de-France, Martinique, France
| | - Dominique Vidaud
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Eric Pasmant
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France.
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France.
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49
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Xavier MJ, Roman SD, Aitken RJ, Nixon B. Transgenerational inheritance: how impacts to the epigenetic and genetic information of parents affect offspring health. Hum Reprod Update 2019; 25:518-540. [DOI: 10.1093/humupd/dmz017] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 03/19/2019] [Accepted: 04/04/2019] [Indexed: 12/18/2022] Open
Abstract
Abstract
BACKGROUND
A defining feature of sexual reproduction is the transmission of genomic information from both parents to the offspring. There is now compelling evidence that the inheritance of such genetic information is accompanied by additional epigenetic marks, or stable heritable information that is not accounted for by variations in DNA sequence. The reversible nature of epigenetic marks coupled with multiple rounds of epigenetic reprogramming that erase the majority of existing patterns have made the investigation of this phenomenon challenging. However, continual advances in molecular methods are allowing closer examination of the dynamic alterations to histone composition and DNA methylation patterns that accompany development and, in particular, how these modifications can occur in an individual’s germline and be transmitted to the following generation. While the underlying mechanisms that permit this form of transgenerational inheritance remain unclear, it is increasingly apparent that a combination of genetic and epigenetic modifications plays major roles in determining the phenotypes of individuals and their offspring.
OBJECTIVE AND RATIONALE
Information pertaining to transgenerational inheritance was systematically reviewed focusing primarily on mammalian cells to the exclusion of inheritance in plants, due to inherent differences in the means by which information is transmitted between generations. The effects of environmental factors and biological processes on both epigenetic and genetic information were reviewed to determine their contribution to modulating inheritable phenotypes.
SEARCH METHODS
Articles indexed in PubMed were searched using keywords related to transgenerational inheritance, epigenetic modifications, paternal and maternal inheritable traits and environmental and biological factors influencing transgenerational modifications. We sought to clarify the role of epigenetic reprogramming events during the life cycle of mammals and provide a comprehensive review of how the genomic and epigenomic make-up of progenitors may determine the phenotype of its descendants.
OUTCOMES
We found strong evidence supporting the role of DNA methylation patterns, histone modifications and even non-protein-coding RNA in altering the epigenetic composition of individuals and producing stable epigenetic effects that were transmitted from parents to offspring, in both humans and rodent species. Multiple genomic domains and several histone modification sites were found to resist demethylation and endure genome-wide reprogramming events. Epigenetic modifications integrated into the genome of individuals were shown to modulate gene expression and activity at enhancer and promoter domains, while genetic mutations were shown to alter sequence availability for methylation and histone binding. Fundamentally, alterations to the nuclear composition of the germline in response to environmental factors, ageing, diet and toxicant exposure have the potential to become hereditably transmitted.
WIDER IMPLICATIONS
The environment influences the health and well-being of progeny by working through the germline to introduce spontaneous genetic mutations as well as a variety of epigenetic changes, including alterations in DNA methylation status and the post-translational modification of histones. In evolutionary terms, these changes create the phenotypic diversity that fuels the fires of natural selection. However, rather than being adaptive, such variation may also generate a plethora of pathological disease states ranging from dominant genetic disorders to neurological conditions, including spontaneous schizophrenia and autism.
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Affiliation(s)
- Miguel João Xavier
- Reproductive Science Group, Faculty of Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Shaun D Roman
- Reproductive Science Group, Faculty of Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Chemical Biology and Clinical Pharmacology, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - R John Aitken
- Reproductive Science Group, Faculty of Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Brett Nixon
- Reproductive Science Group, Faculty of Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW 2308, Australia
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50
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Taylor J, Baumgartner A, Schmid T, Brinkworth M. Responses to genotoxicity in mouse testicular germ cells and epididymal spermatozoa are affected by increased age. Toxicol Lett 2019; 310:1-6. [DOI: 10.1016/j.toxlet.2019.04.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/06/2019] [Accepted: 04/08/2019] [Indexed: 12/25/2022]
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