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DiAdamo A, Chai H, Chong ML, Wang G, Wen J, Jiang YH, Li P. Patterns of Cytogenomic Findings from a Case Series of Recurrent Pregnancy Loss Provide Insight into the Extent of Genetic Defects Causing Miscarriages. Glob Med Genet 2024; 11:123-131. [PMID: 38560483 PMCID: PMC10980555 DOI: 10.1055/s-0044-1785227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Background A retrospective study was performed to evaluate the patterns of cytogenomic findings detected from a case series of products of conception (POC) in recurrent pregnancy loss (RPL) over a 16-year period from 2007 to 2023. Results This case series of RPL was divided into a single analysis (SA) group of 266 women and a consecutive analysis (CA) group of 225 women with two to three miscarriages analyzed. Of the 269 POC from the SA group and the 469 POC from the CA group, a spectrum of cytogenomic abnormalities of simple aneuploidies, compound aneuploidies, polyploidies, and structural rearrangements/pathogenic copy number variants (pCNVs) were detected in 109 (41%) and 160 cases (34%), five (2%) and 11 cases (2%), 35 (13%) and 36 cases (8%), and 10 (4%) and 19 cases (4%), respectively. Patterns with recurrent normal karyotypes, alternating normal and abnormal karyotypes, and recurrent abnormal karyotypes were detected in 74 (33%), 71 (32%), and 80 (35%) of consecutive miscarriages, respectively. Repeat aneuploidies of monosomy X and trisomy 16, triploidy, and tetraploidy were detected in nine women. Conclusions A comparable spectrum of cytogenomic abnormalities was noted in the SA and CA groups of RPL. A skewed likelihood of 2/3 for recurrent normal and abnormal karyotypes and 1/3 for alternating normal and abnormal karyotypes in consecutive miscarriages was observed. Routine cytogenetic analysis should be performed for consecutive miscarriages. Further genomic sequencing to search for detrimental and embryonic lethal variants causing miscarriages and pathogenic variants inducing aneuploidies and polyploidies should be considered for RPL with recurrent normal and abnormal karyotypes.
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Affiliation(s)
- Autumn DiAdamo
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States
| | - Hongyan Chai
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States
| | - Mei Ling Chong
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States
| | - Guilin Wang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States
- Yale Center for Genome Analysis, New Haven, Connecticut, United States
| | - Jiadi Wen
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States
| | - Yong-Hui Jiang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States
- Yale Center for Genomic Health, Yale University School of Medicine, New Haven, Connecticut, United States
| | - Peining Li
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States
- Yale Center for Genomic Health, Yale University School of Medicine, New Haven, Connecticut, United States
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Turner N, Abeysinghe P, Flay H, Meier S, Sadowski P, Mitchell MD. SWATH-MS Analysis of Blood Plasma and Circulating Small Extracellular Vesicles Enables Detection of Putative Protein Biomarkers of Fertility in Young and Aged Dairy Cows. J Proteome Res 2023; 22:3580-3595. [PMID: 37830897 DOI: 10.1021/acs.jproteome.3c00406] [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] [Indexed: 10/14/2023]
Abstract
The development of biomarkers of fertility could provide benefits for the genetic improvement of dairy cows. Circulating small extracellular vesicles (sEVs) show promise as diagnostic or prognostic markers since their cargo reflects the metabolic state of the cell of origin; thus, they mirror the physiological status of the host. Here, we employed data-independent acquisition mass spectrometry to survey the plasma and plasma sEV proteomes of two different cohorts of Young (Peripubertal; n = 30) and Aged (Primiparous; n = 20) dairy cows (Bos taurus) of high- and low-genetic merit of fertility and known pregnancy outcomes (ProteomeXchange data set identifier PXD042891). We established predictive models of fertility status with an area under the curve of 0.97 (sEV; p value = 3.302e-07) and 0.95 (plasma; p value = 6.405e-08). Biomarker candidates unique to high-fertility Young cattle had a sensitivity of 0.77 and specificity of 0.67 (*p = 0.0287). Low-fertility biomarker candidates uniquely identified in sEVs from Young and Aged cattle had a sensitivity and specificity of 0.69 and 1.0, respectively (***p = 0.0005). Our bioinformatics pipeline enabled quantification of plasma and circulating sEV proteins associated with fertility phenotype. Further investigations are warranted to validate this research in a larger population, which may lead to improved classification of fertility status in cattle.
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Affiliation(s)
- Natalie Turner
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, Queensland 4101, Australia
| | - Pevindu Abeysinghe
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, Queensland 4101, Australia
| | - Holly Flay
- DairyNZ Limited, Private Bag 3221, Hamilton 3240, New Zealand
| | - Susanne Meier
- DairyNZ Limited, Private Bag 3221, Hamilton 3240, New Zealand
| | - Pawel Sadowski
- Central Analytical Research Facility (CARF), QUT, Gardens Point Campus, 2 George Street, Brisbane City, Queensland 4000, Australia
| | - Murray D Mitchell
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, Queensland 4101, Australia
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Workalemahu T, Avery C, Lopez S, Blue NR, Wallace A, Quinlan AR, Coon H, Warner D, Varner MW, Branch DW, Jorde LB, Silver RM. Whole-genome sequencing analysis in families with recurrent pregnancy loss: A pilot study. PLoS One 2023; 18:e0281934. [PMID: 36800380 PMCID: PMC9937472 DOI: 10.1371/journal.pone.0281934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/03/2023] [Indexed: 02/18/2023] Open
Abstract
One to two percent of couples suffer recurrent pregnancy loss and over 50% of the cases are unexplained. Whole genome sequencing (WGS) analysis has the potential to identify previously unrecognized causes of pregnancy loss, but few studies have been performed, and none have included DNA from families including parents, losses, and live births. We conducted a pilot WGS study in three families with unexplained recurrent pregnancy loss, including parents, healthy live births, and losses, which included an embryonic loss (<10 weeks' gestation), fetal deaths (10-20 weeks' gestation) and stillbirths (≥ 20 weeks' gestation). We used the Illumina platform for WGS and state-of-the-art protocols to identify single nucleotide variants (SNVs) following various modes of inheritance. We identified 87 SNVs involving 75 genes in embryonic loss (n = 1), 370 SNVs involving 228 genes in fetal death (n = 3), and 122 SNVs involving 122 genes in stillbirth (n = 2). Of these, 22 de novo, 6 inherited autosomal dominant and an X-linked recessive SNVs were pathogenic (probability of being loss-of-function intolerant >0.9), impacting known genes (e.g., DICER1, FBN2, FLT4, HERC1, and TAOK1) involved in embryonic/fetal development and congenital abnormalities. Further, we identified inherited missense compound heterozygous SNVs impacting genes (e.g., VWA5B2) in two fetal death samples. The variants were not identified as compound heterozygous SNVs in live births and population controls, providing evidence for haplosufficient genes relevant to pregnancy loss. In this pilot study, we provide evidence for de novo and inherited SNVs relevant to pregnancy loss. Our findings provide justification for conducting WGS using larger numbers of families and warrant validation by targeted sequencing to ascertain causal variants. Elucidating genes causing pregnancy loss may facilitate the development of risk stratification strategies and novel therapeutics.
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Affiliation(s)
- Tsegaselassie Workalemahu
- Department of Obstetrics and Gynecology, University of Utah Health, Salt Lake City, Utah, United States of America
| | - Cecile Avery
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Sarah Lopez
- Department of Obstetrics and Gynecology, University of Utah Health, Salt Lake City, Utah, United States of America
| | - Nathan R. Blue
- Department of Obstetrics and Gynecology, University of Utah Health, Salt Lake City, Utah, United States of America
- Intermountain Healthcare, Maternal-Fetal Medicine, Salt Lake City, Utah, United States of America
| | - Amelia Wallace
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Aaron R. Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah, United States of America
| | - Hilary Coon
- Department of Psychiatry, University of Utah, Salt Lake City, Utah, United States of America
| | - Derek Warner
- DNA Sequencing Core, University of Utah, Salt Lake City, Utah, United States of America
| | - Michael W. Varner
- Department of Obstetrics and Gynecology, University of Utah Health, Salt Lake City, Utah, United States of America
- Intermountain Healthcare, Maternal-Fetal Medicine, Salt Lake City, Utah, United States of America
| | - D. Ware Branch
- Department of Obstetrics and Gynecology, University of Utah Health, Salt Lake City, Utah, United States of America
- Intermountain Healthcare, Maternal-Fetal Medicine, Salt Lake City, Utah, United States of America
| | - Lynn B. Jorde
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Robert M. Silver
- Department of Obstetrics and Gynecology, University of Utah Health, Salt Lake City, Utah, United States of America
- Intermountain Healthcare, Maternal-Fetal Medicine, Salt Lake City, Utah, United States of America
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Nikitina TV, Lebedev IN. Stem Cell-Based Trophoblast Models to Unravel the Genetic Causes of Human Miscarriages. Cells 2022; 11:1923. [PMID: 35741051 PMCID: PMC9221414 DOI: 10.3390/cells11121923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 02/01/2023] Open
Abstract
Miscarriage affects approximately 15% of clinically recognized pregnancies, and 1-3% of couples experience pregnancy loss recurrently. Approximately 50-60% of miscarriages result from chromosomal abnormalities, whereas up to 60% of euploid recurrent abortions harbor variants in candidate genes. The growing number of detected genetic variants requires an investigation into their role in adverse pregnancy outcomes. Since placental defects are the main cause of first-trimester miscarriages, the purpose of this review is to provide a survey of state-of-the-art human in vitro trophoblast models that can be used for the functional assessment of specific abnormalities/variants implicated in pregnancy loss. Since 2018, when primary human trophoblast stem cells were first derived, there has been rapid growth in models of trophoblast lineage. It has been found that a proper balance between self-renewal and differentiation in trophoblast progenitors is crucial for the maintenance of pregnancy. Different responses to aneuploidy have been shown in human embryonic and extra-embryonic lineages. Stem cell-based models provide a powerful tool to explore the effect of a specific aneuploidy/variant on the fetus through placental development, which is important, from a clinical point of view, for deciding on the suitability of embryos for transfer after preimplantation genetic testing for aneuploidy.
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Affiliation(s)
- Tatiana V. Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, 634050 Tomsk, Russia;
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Karipcin S, Wei S, Williams Z. Getting to the point (mutation). Fertil Steril 2021; 116:1359. [PMID: 34602259 DOI: 10.1016/j.fertnstert.2021.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 11/15/2022]
Affiliation(s)
- Sinem Karipcin
- Columbia University Fertility Center, New York, New York
| | - Shan Wei
- Columbia University Fertility Center, New York, New York
| | - Zev Williams
- Columbia University Fertility Center, New York, New York
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