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Brakta S, Du Q, Chorich LP, Hawkins ZA, Sullivan ME, Ko EK, Kim HG, Knight J, Taylor HS, Friez M, Phillips JA, Layman LC. Heterozygous ZNHIT3 variants within the 17q12 recurrent deletion region are associated with Mayer-Rokitansky-Kuster Hauser (MRKH) syndrome. Mol Cell Endocrinol 2024; 589:112237. [PMID: 38599276 DOI: 10.1016/j.mce.2024.112237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024]
Abstract
The molecular basis of mullerian aplasia, also known as Mayer-Rokitansky-Kuster Hauser (MRKH) or congenital absence of the uterus and vagina, is largely unknown. We applied a multifaceted genetic approach to studying the pathogenesis of MRKH including exome sequencing of trios and duos, genome sequencing of families, qPCR, RT-PCR, and Sanger sequencing to detect intragenic deletions, insertions, splice variants, single nucleotide variants, and rearrangements in 132 persons with MRKH. We identified two heterozygous variants in ZNHIT3 localized to a commonly involved CNV region at chromosome 17q12 in two different families with MRKH. One is a frameshift, truncating variant that is predicted to interfere with steroid hormone binding of the LxxLL sequence of the C-terminal region. The second variant is a double missense/stopgain variant. Both variants impair protein expression in vitro. In addition, four more probands with MRKH harbored the stopgain variant without the nearby missense variant. In total, 6/132 (4.5%) of patients studied, including five with associated anomalies (type 2 MRKH), had ZNHIT3 variants that impair function in vitro. Our findings implicate ZNHIT3 as an important gene associated with MRKH within the 17q12 CNV region.
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Affiliation(s)
- Soumia Brakta
- Section of Reproductive Endocrine, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia at Augusta University, Augusta, GA, USA.
| | - Quansheng Du
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Lynn P Chorich
- Section of Reproductive Endocrine, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Zoe A Hawkins
- Section of Reproductive Endocrine, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | | | - Eun Kyung Ko
- University of Pennsylvania, Philadelphia, PA, USA
| | - Hyung-Goo Kim
- Department of Neurosurgery, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - James Knight
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
| | - Hugh S Taylor
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
| | | | - John A Phillips
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics, Vanderbilt University, Nashville, TN, USA
| | - Lawrence C Layman
- Section of Reproductive Endocrine, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia at Augusta University, Augusta, GA, USA; Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, GA, USA; Department of Physiology, Medical College of Georgia at Augusta University, Augusta, GA, USA
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Poch A, Dougherty MP, Roman RA, Chorich L, Hawkins Z, Kim SH, Kim HG, Layman LC. Prevalence of pathogenic variants and digenic disease in patients diagnosed with normosmic hypogonadotropic hypogonadism/Kallmann Syndrome. Mol Cell Endocrinol 2024; 589:112224. [PMID: 38593951 DOI: 10.1016/j.mce.2024.112224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/26/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Hypogonadotropic hypogonadism (HH) is due to impaired gonadotropin releasing hormone (GnRH) action resulting in absent puberty and infertility. At least 44 genes have been identified to possess genetic variants in 40-50% of nHH/KS, and 2-20% have presumed digenic disease, but not all variants have been characterized in vitro. HYPOTHESIS The prevalence of pathogenic (P)/likely pathogenic (LP) variants in monogenic and digenic nHH/KS is lower than reported. DESIGN Cross-sectional study. SETTING University Research Laboratory. SUBJECTS 158 patients with nHH/KS. METHODS Exome sequencing (ES) was performed and variants were filtered for 44 known genes using Varsome and confirmed by Sanger Sequencing. MAIN OUTCOME MEASURES P/LP variants in nHH/KS genes. RESULTS ES resulted in >370,000 variants, from which variants in 44 genes were filtered. Thirty-one confirmed P/LP variants in 10 genes (ANOS1, CHD7, DUSP6, FGFR1, HS6ST1, KISS1, PROKR2, SEMA3A, SEMA3E, TACR3), sufficient to cause disease, were identified in 30/158 (19%) patients. Only 2/158 (1.2%) patients had digenic variant combinations: a male with hemizygous ANOS1 and heterozygous TACR3 variants and a male with heterozygous SEMA3A and SEMA3E variants. Two patients (1.2%) had compound heterozygous GNRHR (autosomal recessive) variants-one P and one variant of uncertain significance (VUS). Five patients (3.2%) had heterozygous P/LP variants in either GNRHR or TACR3 (both autosomal recessive), but no second variant. CONCLUSION Our prevalence of P/LP variants in nHH/KS was 19%, and digenicity was observed in 1.2%. These findings are less than those previously reported, and probably represent a more accurate estimation since VUS are not included.
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Affiliation(s)
- Alexandra Poch
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia at Augusta University, Augusta, GA, USA.
| | - Michael P Dougherty
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Robert A Roman
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Lynn Chorich
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Zoe Hawkins
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Soo-Hyun Kim
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, Cranmer Terrace, London, SW17 0RE, United Kingdom
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Center, Hamad Bin Khalifa University, Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Lawrence C Layman
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia at Augusta University, Augusta, GA, USA; Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, GA, USA; Department of Physiology, Medical College of Georgia at Augusta University, Augusta, GA, USA
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Yatsenko SA, Witchel SF, Gordon CM. Primary Amenorrhea and Premature Ovarian Insufficiency. Endocrinol Metab Clin North Am 2024; 53:293-305. [PMID: 38677871 PMCID: PMC11110077 DOI: 10.1016/j.ecl.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2024]
Abstract
This review focuses on primary amenorrhea and primary/premature ovarian insufficiency due to hypergonadotropic hypogonadism. Following a thoughtful, thorough evaluation, a diagnosis can usually be discerned. Pubertal induction and ongoing estrogen replacement therapy are often necessary. Shared decision-making involving the patient, family, and health-care team can empower the young person and family to successfully thrive with these chronic conditions.
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Affiliation(s)
- Svetlana A Yatsenko
- Department of Pathology, University of Pittsburgh, Magee-Womens Research Institute, Pittsburgh, PA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Magee-Womens Research Institute, Pittsburgh, PA, USA
| | - Selma F Witchel
- Division of Pediatric Endocrinology, Department of Pediatrics, UPMC Children's Hospital, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Catherine M Gordon
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
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Herlin MK. Genetics of Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome: advancements and implications. Front Endocrinol (Lausanne) 2024; 15:1368990. [PMID: 38699388 PMCID: PMC11063329 DOI: 10.3389/fendo.2024.1368990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/04/2024] [Indexed: 05/05/2024] Open
Abstract
Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is a congenital anomaly characterized by agenesis/aplasia of the uterus and upper part of the vagina in females with normal external genitalia and a normal female karyotype (46,XX). Patients typically present during adolescence with complaints of primary amenorrhea where the diagnosis is established with significant implications including absolute infertility. Most often cases appear isolated with no family history of MRKH syndrome or related anomalies. However, cumulative reports of familial recurrence suggest genetic factors to be involved. Early candidate gene studies had limited success in their search for genetic causes of MRKH syndrome. More recently, genomic investigations using chromosomal microarray and genome-wide sequencing have been successful in detecting promising genetic variants associated with MRKH syndrome, including 17q12 (LHX1, HNF1B) and 16p11.2 (TBX6) deletions and sequence variations in GREB1L and PAX8, pointing towards a heterogeneous etiology with various genes involved. With uterus transplantation as an emerging fertility treatment in MRKH syndrome and increasing evidence for genetic etiologies, the need for genetic counseling concerning the recurrence risk in offspring will likely increase. This review presents the advancements in MRKH syndrome genetics from early familial occurrences and candidate gene searches to current genomic studies. Moreover, the review provides suggestions for future genetic investigations and discusses potential implications for clinical practice.
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Affiliation(s)
- Morten Krogh Herlin
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus N, Denmark
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Roth LP, Yu LX, Johnson J, Qu'd D, McCracken K, Simpson BN, Pennesi CM. Müllerian Agenesis in a patient with Rubinstein-Taybi Syndrome: A Case Series and Review of the Overlapping Developmental Biologic Pathways. J Pediatr Adolesc Gynecol 2024; 37:67-71. [PMID: 37704034 DOI: 10.1016/j.jpag.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023]
Abstract
BACKGROUND Rubinstein-Taybi syndrome (RSTS) is a multi-system neurodevelopmental condition caused by deficiency of CREBBP (16p13.3) or EP300 (22q13.2). Müllerian agenesis, or Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome, is defined as congenital agenesis of the uterus, cervix, and upper vagina without a definite genetic cause. INDEX CASE AND CASE SERIES We present a 14-year-old female with RSTS type 1 (CREBBP, c.4395-2A>C) and MRKH, the first documented in the literature. Following presentation to Gynecology for anticipatory guidance regarding future menstrual suppression and follow-up of previously diagnosed labial adhesions, exam under anesthesia revealed a single urogenital opening with cystoscopy demonstrating a normal urethra and bladder. Laboratory evaluation was consistent with peripubertal female gonadotropins and estradiol, 46,XX karyotype, and normal microarray, and a pelvic MRI confirmed Müllerian agenesis. Given this case, we assessed our cohort of females with RSTS and found that 4 of 12 individuals also had Müllerian anomalies. CONCLUSION Gynecologic evaluation should be a part of medical care for females with RSTS, particularly in individuals with delayed menarche or abnormal menstrual history, on the basis of the observed association between RSTS and Müllerian anomalies in this case series. Although several candidate genes and copy number variants are associated with MRKH, no candidate genes in close proximity to the 16p13.3 region have been identified to explain both RSTS and MRKH in the index patient. Due to the regulatory nature of CREBBP during embryonic development, we theorize that CREBBP may play a role in the migration of Müllerian structures during embryogenesis.
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Affiliation(s)
- Lauryn P Roth
- Cincinnati Children's Hospital Medical Center, Division of Pediatric and Adolescent Gynecology, Cincinnati, Ohio.
| | - Lissa X Yu
- Cincinnati Children's Hospital Medical Center, Division of Pediatric and Adolescent Gynecology, Cincinnati, Ohio; University of Washington, Division of Pediatric and Adolescent Gynecology, Seattle, Washington
| | - Jodie Johnson
- Cincinnati Children's Hospital Medical Center, Division of Human Genetics, Cincinnati, Ohio
| | - Dima Qu'd
- Cincinnati Children's Hospital Medical Center, Division of Human Genetics, Cincinnati, Ohio
| | - Kyle McCracken
- Cincinnati Children's Hospital Medical Center, Division of Nephrology, Cincinnati, Ohio
| | - Brittany N Simpson
- Cincinnati Children's Hospital Medical Center, Division of Human Genetics, Cincinnati, Ohio
| | - Christine M Pennesi
- Cincinnati Children's Hospital Medical Center, Division of Pediatric and Adolescent Gynecology, Cincinnati, Ohio
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Thomson E, Tran M, Robevska G, Ayers K, van der Bergen J, Gopalakrishnan Bhaskaran P, Haan E, Cereghini S, Vash-Margita A, Margetts M, Hensley A, Nguyen Q, Sinclair A, Koopman P, Pelosi E. Functional genomics analysis identifies loss of HNF1B function as a cause of Mayer-Rokitansky-Küster-Hauser syndrome. Hum Mol Genet 2023; 32:1032-1047. [PMID: 36282544 PMCID: PMC9990990 DOI: 10.1093/hmg/ddac262] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/04/2022] [Accepted: 10/17/2022] [Indexed: 11/12/2022] Open
Abstract
Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is a congenital condition characterized by aplasia or hypoplasia of the uterus and vagina in women with a 46,XX karyotype. This condition can occur as type I when isolated or as type II when associated with extragenital anomalies including kidney and skeletal abnormalities. The genetic basis of MRKH syndrome remains unexplained and several candidate genes have been proposed to play a role in its etiology, including HNF1B, LHX1 and WNT4. Here, we conducted a microarray analysis of 13 women affected by MRKH syndrome, resulting in the identification of chromosomal changes, including the deletion at 17q12, which contains both HNF1B and LHX1. We focused on HNF1B for further investigation due to its known association with, but unknown etiological role in, MRKH syndrome. We ablated Hnf1b specifically in the epithelium of the Müllerian ducts in mice and found that this caused hypoplastic development of the uterus, as well as kidney anomalies, closely mirroring the MRKH type II phenotype. Using single-cell RNA sequencing of uterine tissue in the Hnf1b-ablated embryos, we analyzed the molecules and pathways downstream of Hnf1b, revealing a dysregulation of processes associated with cell proliferation, migration and differentiation. Thus, we establish that loss of Hnf1b function leads to an MRKH phenotype and generate the first mouse model of MRKH syndrome type II. Our results support the investigation of HNF1B in clinical genetic settings of MRKH syndrome and shed new light on the molecular mechanisms underlying this poorly understood condition in women's reproductive health.
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Affiliation(s)
- Ella Thomson
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Minh Tran
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Gorjana Robevska
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Katie Ayers
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
| | - Jocelyn van der Bergen
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | | | - Eric Haan
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Silvia Cereghini
- Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Alla Vash-Margita
- Division of Pediatric and Adolescent Gynecology, Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
| | - Miranda Margetts
- Center for American Indian and Rural Health Equity, Montana State University, Bozeman, MT, USA
| | | | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Andrew Sinclair
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
| | | | - Emanuele Pelosi
- To whom correspondence should be addressed. Tel: +61 7 3346 6073;
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Brakta S, Hawkins ZA, Sahajpal N, Seman N, Kira D, Chorich LP, Kim HG, Xu H, Phillips JA, Kolhe R, Layman LC. Rare structural variants, aneuploidies, and mosaicism in individuals with Mullerian aplasia detected by optical genome mapping. Hum Genet 2023; 142:483-494. [PMID: 36797380 DOI: 10.1007/s00439-023-02522-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/06/2023] [Indexed: 02/18/2023]
Abstract
The molecular basis of Mayer-Rokitansky-Kuster-Hauser (MRKH) syndrome remains largely unknown. Pathogenic variants in WNT4 and HNF1B have been confirmed in a small percent of individuals. A variety of copy number variants have been reported, but causal gene(s) remain to be identified. We hypothesized that rare structural variants (SVs) would be present in some individuals with MRKH, which could explain the genetic basis of the syndrome. Large molecular weight DNA was extracted from lymphoblastoid cells from 87 individuals with MRKH and available parents. Optical genome mapping (OGM) was performed to identify SVs, which were confirmed by another method (quantitative PCR, chromosomal microarray, karyotype, or fluorescent in situ hybridization) when possible. Thirty-four SVs that overlapped coding regions of genes with potential involvement in MRKH were identified, 14 of which were confirmed by a second method. These 14 SVs were present in 17/87 (19.5%) of probands with MRKH and included seven deletions, three duplications, one new translocation in 5/50 cells-t(7;14)(q32;q32), confirmation of a previously identified translocation-t(3;16)(p22.3;p13.3), and two aneuploidies. Of interest, three cases of mosaicism (3.4% of probands) were identified-25% mosaicism for trisomy 12, 45,X(75%)/46,XX (25%), and 10% mosaicism for a 7;14 translocation. Our study constitutes the first systematic investigation of SVs by OGM in individuals with MRKH. We propose that OGM is a promising method that enables a comprehensive investigation of a variety of SVs in a single assay including cryptic translocations and mosaic aneuploidies. These observations suggest that mosaicism could play a role in the genesis of MRKH.
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Affiliation(s)
- Soumia Brakta
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia.
| | - Zoe A Hawkins
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Nikhil Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia.,Department of Genetics, Greenwood Genetics Center, Greenwood, SC, USA
| | - Natalie Seman
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Dina Kira
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Lynn P Chorich
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Hongyan Xu
- Department of Population Health Sciences, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - John A Phillips
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Lawrence C Layman
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia. .,Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia. .,Department of Physiology, Medical College of Georgia, Augusta University, Augusta, Georgia.
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Liang Z, Duan J, Zhang D, You Y, Zhu L. Assessing the morphology and ovarian reserve of the ovaries from Mayer-Rokitansky-Küster-Hauser syndrome patients. SCIENCE CHINA. LIFE SCIENCES 2022; 66:1204-1207. [PMID: 36580162 DOI: 10.1007/s11427-022-2211-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/24/2022] [Indexed: 12/30/2022]
Affiliation(s)
- Ze Liang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Jiali Duan
- 4+4 Medical Doctor Program, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Duoduo Zhang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Yan You
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
| | - Lan Zhu
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
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Buchert R, Schenk E, Hentrich T, Weber N, Rall K, Sturm M, Kohlbacher O, Koch A, Riess O, Brucker SY, Schulze-Hentrich JM. Genome Sequencing and Transcriptome Profiling in Twins Discordant for Mayer-Rokitansky-Küster-Hauser Syndrome. J Clin Med 2022; 11:jcm11195598. [PMID: 36233463 PMCID: PMC9573672 DOI: 10.3390/jcm11195598] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/23/2022] Open
Abstract
To identify potential genetic causes for Mayer-Rokitansky-Küster-Hauser syndrome (MRKH), we analyzed blood and rudimentary uterine tissue of 5 MRKH discordant monozygotic twin pairs. Assuming that a variant solely identified in the affected twin or affected tissue could cause the phenotype, we identified a mosaic variant in ACTR3B with high allele frequency in the affected tissue, low allele frequency in the blood of the affected twin, and almost absent in blood of the unaffected twin. Focusing on MRKH candidate genes, we detected a pathogenic variant in GREB1L in one twin pair and their unaffected mother showing a reduced phenotypic penetrance. Furthermore, two variants of unknown clinical significance in PAX8 and WNT9B were identified. In addition, we conducted transcriptome analysis of affected tissue and observed perturbations largely similar to those in sporadic cases. These shared transcriptional changes were enriched for terms associated with estrogen and its receptors pointing at a role of estrogen in MRKH pathology. Our genome sequencing approach of blood and uterine tissue of discordant twins is the most extensive study performed on twins discordant for MRKH so far. As no clear pathogenic differences were detected, research to evaluate other regulatory layers are required to better understand the complex etiology of MRKH.
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Affiliation(s)
- Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Elisabeth Schenk
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Thomas Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Nico Weber
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
| | - Katharina Rall
- Department of Women’s Health, University of Tübingen, 72076 Tübingen, Germany
- Rare Disease Center Tübingen, University of Tübingen, 72076 Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Germany
- Institute for Translational Bioinformatics, University Hospital Tübingen, 72076 Tübingen, Germany
| | - André Koch
- Research Institute for Women’s Health, University of Tübingen, 72076 Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- Rare Disease Center Tübingen, University of Tübingen, 72076 Tübingen, Germany
| | - Sara Y. Brucker
- Department of Women’s Health, University of Tübingen, 72076 Tübingen, Germany
- Rare Disease Center Tübingen, University of Tübingen, 72076 Tübingen, Germany
| | - Julia M. Schulze-Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Germany
- Correspondence: ; Tel.: +49-7071-29-72276
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Yuan Y, Zhang L, Long Q, Jiang H, Li M. An accurate prediction model of digenic interaction for estimating pathogenic gene pairs of human diseases. Comput Struct Biotechnol J 2022; 20:3639-3652. [PMID: 35891796 PMCID: PMC9289819 DOI: 10.1016/j.csbj.2022.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 12/04/2022] Open
Abstract
Numerous pathogenic interactions are yet to be revealed efficiently due to dimension burden. Existing methods are underpowered and inaccurate to estimate pathogenic interactions. We developed an accurate bioinformatic method to predict digenic interaction effects based on gene-level features. The new method created a valuable resource of genome-wide pathogenic digenic interactions. We found that known causal genes in Mendelian and Oligogenic diseases may be enriched with interactive effects for the first time.
Increasing evidence shows that genetic interaction across the entire genome may explain a non-trivial fraction of genetic diseases. Digenic interaction is the simplest manifestation of genetic interaction among genes. However, systematic exploration of digenic interactive effects on the whole genome is often discouraged by the high dimension burden. Thus, numerous digenic interactions are yet to be identified for many diseases. Here, we propose a Digenic Interaction Effect Predictor (DIEP), an accurate machine-learning approach to identify the genome-wide pathogenic coding gene pairs with digenic interaction effects. This approach achieved high accuracy and sensitivity in independent testing datasets, outperforming another gene-level digenic predictor (DiGePred). DIEP was also able to discriminate digenic interaction effect from bi-locus effects dual molecular diagnosis (pseudo-digenic). Using DIEP, we provided a valuable resource of genome-wide digenic interactions and demonstrated the enrichment of the digenic interaction effect in Mendelian and Oligogenic diseases. Therefore, DIEP will play a useful role in facilitating the genomic mapping of interactive causal genes for human diseases.
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Affiliation(s)
- Yangyang Yuan
- Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Center for Disease Genome Research, Sun Yat-sen University, Guangzhou 510080, China
| | - Liubin Zhang
- Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Center for Disease Genome Research, Sun Yat-sen University, Guangzhou 510080, China
| | - Qihan Long
- Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Center for Disease Genome Research, Sun Yat-sen University, Guangzhou 510080, China
| | - Hui Jiang
- Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Center for Disease Genome Research, Sun Yat-sen University, Guangzhou 510080, China
| | - Miaoxin Li
- Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Center for Disease Genome Research, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Disease Control (SYSU), Ministry of Education, Guangzhou 510080, China
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
- Corresponding author at: Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.
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11
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Identification of Genetic Causes in Mayer-Rokitansky-Küster-Hauser (MRKH) Syndrome: A Systematic Review of the Literature. CHILDREN 2022; 9:children9070961. [PMID: 35883945 PMCID: PMC9322756 DOI: 10.3390/children9070961] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 06/19/2022] [Accepted: 06/22/2022] [Indexed: 01/17/2023]
Abstract
Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is a congenital condition characterizing females with absence of the uterus and part of the vagina. Several genetic defects have been correlated with the presence of MRKH; however, the exact etiology is still unknown due to the complexity of the genetic pathways implicated during the embryogenetic development of the Müllerian ducts. A systematic review (SR) of the literature was conducted to investigate the genetic causes associated with MRKH syndrome and Congenital Uterine Anomalies (CUAs). This study aimed to identify the most affected chromosomal areas and genes along with their associated clinical features in order to aid clinicians in distinguishing and identifying the possible genetic cause in each patient offering better genetic counseling. We identified 76 studies describing multiple genetic defects potentially contributing to the pathogenetic mechanism of MRKH syndrome. The most reported chromosomal regions and the possible genes implicated were: 1q21.1 (RBM8A gene), 1p31-1p35 (WNT4 gene), 7p15.3 (HOXA gene), 16p11 (TBX6 gene), 17q12 (LHX1 and HNF1B genes), 22q11.21, and Xp22. Although the etiology of MRKH syndrome is complex, associated clinical features can aid in the identification of a specific genetic defect.
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Chu C, Li L, Li S, Zhou Q, Zheng P, Zhang YD, Duan AH, Lu D, Wu YM. Variants in genes related to development of the urinary system are associated with Mayer-Rokitansky-Küster-Hauser syndrome. Hum Genomics 2022; 16:10. [PMID: 35361250 PMCID: PMC8969342 DOI: 10.1186/s40246-022-00385-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/18/2022] [Indexed: 11/12/2022] Open
Abstract
Mayer–Rokitansky–Küster–Hauser (MRKH) syndrome, also known as Müllerian agenesis, is characterized by uterovaginal aplasia in an otherwise phenotypically normal female with a normal 46,XX karyotype. Previous studies have associated sequence variants of PAX8, TBX6, GEN1, WNT4, WNT9B, BMP4, BMP7, HOXA10, EMX2, LHX1, GREB1L, LAMC1, and other genes with MRKH syndrome. The purpose of this study was to identify the novel genetic causes of MRKH syndrome. Ten patients with MRKH syndrome were recruited at Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China. Whole-exome sequencing was performed for each patient. Sanger sequencing confirmed the potential causative genetic variants in each patient. In silico analysis and American College of Medical Genetics and Genomics (ACMG) guidelines helped to classify the pathogenicity of each variant. The Robetta online protein structure prediction tool determined whether the variants affected protein structures. Eleven variants were identified in 90% (9/10) of the patients and were considered a molecular genetic diagnosis of MRKH syndrome. These 11 variants were related to nine genes: TBC1D1, KMT2D, HOXD3, DLG5, GLI3, HIRA, GATA3, LIFR, and CLIP1. Sequence variants of TBC1D1 were found in two unrelated patients. All variants were heterozygous. These changes included one frameshift variant, one stop-codon variant, and nine missense variants. All identified variants were absent or rare in gnomAD East Asian populations. Two of the 11 variants (18.2%) were classified as pathogenic according to the ACMG guidelines, and the remaining nine (81.8%) were classified as variants of uncertain significance. Robetta online protein structure prediction analysis suggested that missense variants in TBC1D1 (p.E357Q), HOXD3 (p.P192R), and GLI3 (p.L299V) proteins caused significant structural changes compared to those in wild-type proteins, which in turn may lead to changes in protein function. This study identified many novel genes, especially TBC1D1, related to the pathogenesis of MRKH syndrome. The identification of these variants provides new insights into the etiology of MRKH syndrome and a new molecular genetic reference for the development of the reproductive tract.
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Affiliation(s)
- Chunfang Chu
- Department of Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Chaoyang, Beijing, 100026, China
| | - Lin Li
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Dongcheng, Beijing, 100006, China
| | - Shenghui Li
- Department of Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Chaoyang, Beijing, 100026, China
| | - Qi Zhou
- Department of Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Chaoyang, Beijing, 100026, China
| | - Ping Zheng
- Department of Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Chaoyang, Beijing, 100026, China
| | - Yu-Di Zhang
- Department of Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Chaoyang, Beijing, 100026, China
| | - Ai-Hong Duan
- Department of Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Chaoyang, Beijing, 100026, China
| | - Dan Lu
- Department of Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Chaoyang, Beijing, 100026, China
| | - Yu-Mei Wu
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Dongcheng, Beijing, 100006, China.
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13
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Machado DA, Ontiveros AE, Behringer RR. Mammalian uterine morphogenesis and variations. Curr Top Dev Biol 2022; 148:51-77. [DOI: 10.1016/bs.ctdb.2021.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Kapczuk K, Kędzia W. Primary Amenorrhea Due to Anatomical Abnormalities of the Reproductive Tract: Molecular Insight. Int J Mol Sci 2021; 22:ijms222111495. [PMID: 34768925 PMCID: PMC8584168 DOI: 10.3390/ijms222111495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 10/17/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022] Open
Abstract
Congenital anomalies of the female reproductive tract that present with primary amenorrhea involve Müllerian aplasia, also known as Mayer-Rokitansky-Küster-Hauser syndrome (MRKHS), and cervical and vaginal anomalies that completely obstruct the reproductive tract. Karyotype abnormalities do not exclude the diagnosis of MRKHS. Familial cases of Müllerian anomalies and associated malformations of the urinary and skeletal systems strongly suggest a complex genetic etiology, but so far, the molecular mechanism in the vast majority of cases remains unknown. Primary amenorrhea may also be the first presentation of complete androgen insensitivity syndrome, steroid 5α-reductase type 2 deficiency, 17β-hydroxysteroid dehydrogenase type 3 deficiency, and Leydig cells hypoplasia type 1; therefore, these disorders should be considered in the differential diagnosis of the congenital absence of the uterus and vagina. The molecular diagnosis in the majority of these cases can be established.
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15
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Mukherjee S, Cogan JD, Newman JH, Phillips JA, Hamid R, Meiler J, Capra JA. Identifying digenic disease genes via machine learning in the Undiagnosed Diseases Network. Am J Hum Genet 2021; 108:1946-1963. [PMID: 34529933 PMCID: PMC8546038 DOI: 10.1016/j.ajhg.2021.08.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 08/25/2021] [Indexed: 12/20/2022] Open
Abstract
Rare diseases affect millions of people worldwide, and discovering their genetic causes is challenging. More than half of the individuals analyzed by the Undiagnosed Diseases Network (UDN) remain undiagnosed. The central hypothesis of this work is that many of these rare genetic disorders are caused by multiple variants in more than one gene. However, given the large number of variants in each individual genome, experimentally evaluating combinations of variants for potential to cause disease is currently infeasible. To address this challenge, we developed the digenic predictor (DiGePred), a random forest classifier for identifying candidate digenic disease gene pairs by features derived from biological networks, genomics, evolutionary history, and functional annotations. We trained the DiGePred classifier by using DIDA, the largest available database of known digenic-disease-causing gene pairs, and several sets of non-digenic gene pairs, including variant pairs derived from unaffected relatives of UDN individuals. DiGePred achieved high precision and recall in cross-validation and on a held-out test set (PR area under the curve > 77%), and we further demonstrate its utility by using digenic pairs from the recent literature. In contrast to other approaches, DiGePred also appropriately controls the number of false positives when applied in realistic clinical settings. Finally, to enable the rapid screening of variant gene pairs for digenic disease potential, we freely provide the predictions of DiGePred on all human gene pairs. Our work enables the discovery of genetic causes for rare non-monogenic diseases by providing a means to rapidly evaluate variant gene pairs for the potential to cause digenic disease.
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Affiliation(s)
- Souhrid Mukherjee
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Joy D Cogan
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - John H Newman
- Pulmonary Hypertension Center, Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - John A Phillips
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Rizwan Hamid
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN 37235, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Institute for Drug Discovery, Leipzig University Medical School, Leipzig 04103, Germany; Department of Chemistry, Leipzig University, Leipzig 04109, Germany; Department of Computer Science, Leipzig University, Leipzig 04109, Germany.
| | - John A Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA.
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16
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Abstract
Puberty is the process through which reproductive competence is achieved and comprises gonadarche and adrenarche. Breast development is the initial physical finding of pubertal onset in girls and typically occurs between 8 and 13 years. Menarche normally occurs 2 to 3 years after the onset of breast development. Pubertal onset is controlled by the gonadotropin-releasing hormone pulse generator in the hypothalamus; however, environmental factors such as alterations in energy balance and exposure to endocrine-disrupting chemicals can alter the timing of pubertal onset. Improvement in nutritional and socioeconomic conditions over the past two centuries has been associated with a secular trend in earlier pubertal onset. Precocious puberty is defined as onset of breast development prior to 8 years and can be central or peripheral. Delayed puberty can be hypogonadotropic or hypergonadotropic and is defined as lack of breast development by 13 years or lack of menarche by 16 years. Both precocious and delayed puberty may have negative effects on self-esteem, potentially leading to psychosocial stress. Patients who present with pubertal differences require a comprehensive assessment to determine the underlying etiology and to devise an effective treatment plan.
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Affiliation(s)
- Aviva B Sopher
- Division of Endocrinology, Diabetes and Metabolism, Department of Pediatrics, Columbia University Irving Medical Center, New York, New York
| | - Sharon E Oberfield
- Division of Endocrinology, Diabetes and Metabolism, Department of Pediatrics, Columbia University Irving Medical Center, New York, New York
| | - Selma F Witchel
- Division of Endocrinology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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