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Effah W, Khalil M, Hwang DJ, Miller DD, Narayanan R. Advances in the understanding of androgen receptor structure and function and in the development of next-generation AR-targeted therapeutics. Steroids 2024; 210:109486. [PMID: 39111362 DOI: 10.1016/j.steroids.2024.109486] [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: 05/23/2024] [Revised: 07/29/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024]
Abstract
Androgen receptor (AR) and its ligand androgens are important for development and physiology of various tissues. AR and its ligands also play critical role in the development of various diseases, making it a valuable therapeutic target. AR ligands, both agonists and antagonists, are being widely used to treat pathological conditions, including prostate cancer and hypogonadism. Despite AR being studied widely over the last five decades, the last decade has seen striking advances in the knowledge on AR and discoveries that have the potential to translate to the clinic. This review provides an overview of the advances in AR biology, AR molecular mechanisms of action, and next generation molecules that are currently in development. Several of the areas described in the review are just unraveling and the next decade will bring more clarity on these developments that will put AR at the forefront of both basic biology and drug development.
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Affiliation(s)
- Wendy Effah
- Department of Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Marjana Khalil
- Department of Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Dong-Jin Hwang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Duane D Miller
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Ramesh Narayanan
- Department of Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States; UTHSC Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, United States.
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2
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Pozojevic J, Sivaprasad R, Laß J, Haarich F, Trinh J, Kakar N, Schulz K, Händler K, Verrijn Stuart AA, Giltay JC, van Gassen KL, Caliebe A, Holterhus PM, Spielmann M, Hornig NC. LINE1-mediated epigenetic repression of androgen receptor transcription causes androgen insensitivity syndrome. Sci Rep 2024; 14:16302. [PMID: 39009627 PMCID: PMC11251026 DOI: 10.1038/s41598-024-65439-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/20/2024] [Indexed: 07/17/2024] Open
Abstract
Androgen insensitivity syndrome (AIS) is a difference of sex development (DSD) characterized by different degrees of undervirilization in individuals with a 46,XY karyotype despite normal to high gonadal testosterone production. Classically, AIS is explained by hemizygous mutations in the X-chromosomal androgen receptor (AR) gene. Nevertheless, the majority of individuals with clinically diagnosed AIS do not carry an AR gene mutation. Here, we present a patient with a 46,XY karyotype, born with undervirilized genitalia, age-appropriate testosterone levels and no uterus, characteristic for AIS. Diagnostic whole exome sequencing (WES) showed a maternally inherited LINE1 (L1) retrotransposon insertion in the 5' untranslated region (5'UTR) of the AR gene. Long-read nanopore sequencing confirmed this as an insertion of a truncated L1 element of ≈ 2.7 kb and showed an increased DNA methylation at the L1 insertion site in patient-derived genital skin fibroblasts (GSFs) compared to healthy controls. The insertion coincided with reduced AR transcript and protein levels in patient-derived GSFs confirming the clinical diagnosis AIS. Our results underline the relevance of retrotransposons in human disease, and expand the growing list of human diseases associated with them.
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Affiliation(s)
- Jelena Pozojevic
- Institute of Human Genetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany.
| | - Radhika Sivaprasad
- Institute of Human Genetics, University of Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Joshua Laß
- Institute of Neurogenetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Franziska Haarich
- Institute of Cardiogenetics, University of Lübeck and German Centre for Cardiovascular Research (DZHK), Partner Site Hamburg/Lübeck/Kiel, Lübeck, Germany
| | - Joanne Trinh
- Institute of Neurogenetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Naseebullah Kakar
- Institute of Human Genetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
- Department of Biotechnology, FLS&I, BUITEMS, Quetta, Pakistan
| | - Kristin Schulz
- Institute of Human Genetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Kristian Händler
- Institute of Human Genetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Annemarie A Verrijn Stuart
- Department of Pediatric Endocrinology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jacques C Giltay
- Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Koen L van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Almuth Caliebe
- Institute of Human Genetics, University of Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Paul-Martin Holterhus
- Division of Paediatric Endocrinology and Diabetes, Department of Paediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Malte Spielmann
- Institute of Human Genetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
- Institute of Human Genetics, University of Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Hamburg/Lübeck/Kiel, Lübeck, Germany
| | - Nadine C Hornig
- Institute of Human Genetics, University of Kiel and University Hospital Schleswig-Holstein, Kiel, Germany.
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3
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Zimmer J, Mueller L, Frank-Herrmann P, Rehnitz J, Dietrich JE, Bettendorf M, Strowitzki T, Krivega M. Low androgen signaling rescues genome integrity with innate immune response by reducing fertility in humans. Cell Death Dis 2024; 15:30. [PMID: 38212646 PMCID: PMC10784536 DOI: 10.1038/s41419-023-06397-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/13/2024]
Abstract
Development of the gonads under complex androgen regulation is critical for germ cells specification. In this work we addressed the relationship between androgens and genomic integrity determining human fertility. We used different study groups: individuals with Differences of Sex Development (DSD), including Complete Androgen Insensitivity Syndrome (CAIS) due to mutated androgen receptor (AR), and men with idiopathic nonobstructive azoospermia. Both showed genome integrity status influenced by androgen signaling via innate immune response activation in blood and gonads. Whole proteome analysis connected low AR to interleukin-specific gene expression, while compromised genome stability and tumorigenesis were also supported by interferons. AR expression was associated with predominant DNA damage phenotype, that eliminated AR-positive Sertoli cells as the degeneration of gonads increased. Low AR contributed to resistance from the inhibition of DNA repair in primary leukocytes. Downregulation of androgen promoted apoptosis and specific innate immune response with higher susceptibility in cells carrying genomic instability.
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Affiliation(s)
- J Zimmer
- Research Group of Gonadal Differentiation and Embryonic Development, Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - L Mueller
- Research Group of Gonadal Differentiation and Embryonic Development, Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - P Frank-Herrmann
- Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - J Rehnitz
- Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - J E Dietrich
- Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - M Bettendorf
- Division of Pediatric Endocrinology, Children's Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - T Strowitzki
- Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - M Krivega
- Research Group of Gonadal Differentiation and Embryonic Development, Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany.
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4
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Zhang W, Mao J, Wang X, Zhao Z, Zhang X, Sun B, Cao Y, Nie M, Wu X. The genetic spectrum of a Chinese series of patients with 46, XY disorders of the sex development. Andrology 2024; 12:98-108. [PMID: 37147882 DOI: 10.1111/andr.13446] [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: 12/19/2022] [Revised: 04/10/2023] [Accepted: 04/28/2023] [Indexed: 05/07/2023]
Abstract
PURPOSE The etiology of 46, XY disorders of sex development (46, XY DSD) is complex, and studies have shown that different series of patients with 46, XY DSD has different genetic spectrum. In this study, we aimed to investigate the underlying genetic etiology in a Chinese series of patients with 46, XY DSD by whole exome sequencing (WES). METHODS Seventy patients with 46, XY DSD were enrolled from the Peking Union Medical College Hospital (Beijing, China). The detailed clinical characteristics were evaluated, and peripheral blood was collected for WES to find the patients' rare variants (RVs) of genes related to 46, XY DSD. The clinical significance of the RVs was annotated according to American College of Medical Genetics and Genomics (ACMG) guidelines. RESULTS A total of 57 RVs from nine genes were identified in 56 patients with 46, XY DSD, which include 21 novel RVs and 36 recurrent RVs. Based on the American ACMG guidelines, 43 variants were classified as pathogenic(P) or likely pathogenic (LP) variants and 14 variants were defined as variants of uncertain significance (VUS). P or LP variants were identified in 64.3% (45/70) patients of the series. Thirty-nine, 14, and 4 RVs were involved in the process of androgen synthesis and action, testicular determination and developmental process, and syndromic 46, XY DSD, respectively. The top three genes most frequently affected to cause 46, XY DSD were AR, SRD5A2, and NR5A1. Seven patients were found harboring RVs of the 46, XY DSD pathogenic genes identified in recent years, namely DHX37 in four patients, MYRF in two patients, and PPP2R3C in one patient. CONCLUSION We identified 21 novel RVs of nine genes, which extended the genetic spectrum of 46, XY DSD pathogenic variants. Our study showed that 60% of the patients were caused by AR, SRD5A2 or NR5A1 P/LP variants. Therefore, polymerase chain reaction (PCR) amplification and Sanger sequencing of these three genes could be performed first to identify the pathogeny of the patients. For those patients whose pathogenic variants had not been found, whole-exome sequencing could be helpful in determining the etiology.
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Affiliation(s)
- Wei Zhang
- Department of Endocrinology, NHC Key laboratory of Endocrinology (Peking Union Medical College Hospital), Peking Union Medical College, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiangfeng Mao
- Department of Endocrinology, NHC Key laboratory of Endocrinology (Peking Union Medical College Hospital), Peking Union Medical College, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xi Wang
- Department of Endocrinology, NHC Key laboratory of Endocrinology (Peking Union Medical College Hospital), Peking Union Medical College, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhiyuan Zhao
- Department of Endocrinology, NHC Key laboratory of Endocrinology (Peking Union Medical College Hospital), Peking Union Medical College, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoxia Zhang
- Department of Endocrinology, NHC Key laboratory of Endocrinology (Peking Union Medical College Hospital), Peking Union Medical College, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Bang Sun
- Department of Endocrinology, NHC Key laboratory of Endocrinology (Peking Union Medical College Hospital), Peking Union Medical College, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yaqing Cao
- Department of Endocrinology, NHC Key laboratory of Endocrinology (Peking Union Medical College Hospital), Peking Union Medical College, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Min Nie
- Department of Endocrinology, NHC Key laboratory of Endocrinology (Peking Union Medical College Hospital), Peking Union Medical College, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xueyan Wu
- Department of Endocrinology, NHC Key laboratory of Endocrinology (Peking Union Medical College Hospital), Peking Union Medical College, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
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5
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Noveski P, Plaseski T, Dimitrovska M, Plaseska-Karanfilska D. Androgen Insensitivity Syndrome DUE to Non-Coding Variation in the Androgen Receptor Gene: Review of the Literature and Case Report of a Patient with Mosaic c.-547C>T Variant. Balkan J Med Genet 2023; 26:51-56. [PMID: 37576790 PMCID: PMC10413879 DOI: 10.2478/bjmg-2023-0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023] Open
Abstract
Sexual development (SD) is a complex process with strict spatiotemporal regulation of gene expression. Despite advancements in molecular diagnostics, disorders of sexual development (DSD) have a diagnostic rate of ~50%. Androgen insensitivity syndrome (AIS) represents the most common form of 46,XY DSD, with a spectrum of defects in androgen action. Considering the importance of very strict regulation of the SD, it is reasonable to assume that the genetic cause for proportion of the DSD lies in the non-coding part of the genome that regulates proper gene functioning. Here we present a patient with partial AIS (PAIS) due to a mosaic de novo c.-547C>T pathogenic variant in the 5'UTR of androgen receptor (AR) gene. The same mutation was previously described as inherited, in two unrelated patients with complete AIS (CAIS). Thus, our case further confirms the previous findings that variable gene expressivity could be attributed to mosaicism. Mutations in 5'UTR could create new upstream open reading frames (uORFs) or could disrupt the existing one. A recent systematic genome-wide study identified AR as a member of a subset of genes where modifications of uORFs represents an important disease mechanism. Only a small number of studies are reporting non-coding mutations in the AR gene and our case emphasizes the importance of molecular testing of the entire AR locus in AIS patients. The introduction of new methods for comprehensive molecular testing in routine genetic diagnosis, accompanied with new tools for in sillico analysis could improve the genetic diagnosis of AIS, and DSD in general.
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Affiliation(s)
- P Noveski
- Research Centre for Genetic Engineering and Biotechnology ‘Georgi D. Efremov’, Macedonian Academy of Sciences and Arts, 1000Skopje, Republic of North Macedonia
| | - T Plaseski
- University Clinic of Endocrinology, Diabetes and Metabolic Disorders, Clinical Centre “Mother Teresa“, 1000Skopje, Republic of North Macedonia
| | - M Dimitrovska
- University Clinic of Endocrinology, Diabetes and Metabolic Disorders, Clinical Centre “Mother Teresa“, 1000Skopje, Republic of North Macedonia
| | - D Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology ‘Georgi D. Efremov’, Macedonian Academy of Sciences and Arts, 1000Skopje, Republic of North Macedonia
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He X, Ma Q, Zhang Q, Hong X, Qi M, Li Y, Li X. Case report: Identification of a frameshift mutation in GC enrichment and the GCC repeat region of the androgen insensitivity receptor (AR) gene in a patient with complete androgen insensitivity syndrome by whole-exome sequencing (WES) combined with specific PCR and deep sequencing. Front Genet 2022; 13:1038997. [PMID: 36506311 PMCID: PMC9732716 DOI: 10.3389/fgene.2022.1038997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/07/2022] [Indexed: 11/26/2022] Open
Abstract
Background: Androgen insensitivity syndrome (AIS) is an X-linked recessive hereditary disease caused due to a reduced or absent function of the androgen receptor (AR) protein encoded by the AR gene (OMIM-Gene# 313,700). Genetic testing is important in the diagnosis, clinical management, and prevention of AIS (MIM# 300,068). The AR (HGNC: 644) pathogenic variant detection rate ranges from 65% to 95% for patients with complete AIS (CAIS) and 40%-45% for patients with partial androgen insensitivity syndrome (PAIS). Identification of a pathogenic mutation in the AR confirms the diagnosis of AIS, especially in the milder forms that may have a phenotypic overlap with other disorders of sex development. Improvement of the molecular diagnostic rate of AIS is urgently required in clinical practice. We reported the results of the molecular diagnosis of a patient with CAIS who failed previously in either the traditional Sanger sequencing or next-generation sequencing (NGS). Using whole-exome sequencing (WES) combined with a special polymerase chain reaction (PCR) and deep sequencing, we successfully identified a pathogenic variant, a hemizygous mutation (c.1395-1396insGA), in the GC-enriched and unstable GCC repeat regions of the AR gene of the proband. Conclusion: The results may be advantageous for the improvement of the detection rate of AIS, as well as other inherited disorders whose disease-causing genes contain GC-enriched and unstable GCC repeat regions.
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Affiliation(s)
- Xiaojing He
- Department of Obstetrics and Gynaecology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Qingya Ma
- Department of Gynecology, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Qiaoli Zhang
- Department of Human Reproductive Medicine, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China,Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Xutao Hong
- Zhejiang University Medical School Affiliated SRRS Hospital, Zhejiang, China,Dian Diagnostics GroupCo., Ltd., Zhejiang, China
| | - Ming Qi
- Zhejiang University Medical School Affiliated SRRS Hospital, Zhejiang, China,University of Rochester Medical Center, Rochester, NY, United States
| | - Yongkai Li
- Department of Gynecology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Xiaodong Li
- Department of Gynecology, The First Hospital of Hebei Medical University, Shijiazhuang, China,*Correspondence: Xiaodong Li,
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7
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Sergeeva OV, Shcherbinina EY, Shomron N, Zatsepin TS. Modulation of RNA Splicing by Oligonucleotides: Mechanisms of Action and Therapeutic Implications. Nucleic Acid Ther 2022; 32:123-138. [PMID: 35166605 DOI: 10.1089/nat.2021.0067] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Dysregulation of RNA splicing causes many diseases and disorders. Several therapeutic approaches have been developed to correct aberrant alternative splicing events for the treatment of cancers and hereditary diseases, including gene therapy and redirecting splicing, using small molecules or splice switching oligonucleotides (SSO). Significant advances in the chemistry and pharmacology of nucleic acid have led to the development of clinically approved SSO drugs for the treatment of spinal muscular dystrophy and Duchenne muscular dystrophy (DMD). In this review, we discuss the mechanisms of SSO action with emphasis on "less common" approaches to modulate alternative splicing, including bipartite and bifunctional SSO, oligonucleotide decoys for splice factors and SSO-mediated mRNA degradation via AS-NMD and NGD pathways. We briefly discuss the current progress and future perspectives of SSO therapy for rare and ultrarare diseases.
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Affiliation(s)
- Olga V Sergeeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Timofei S Zatsepin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Department of Chemistry, Moscow State University, Moscow, Russia
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8
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Keegan NP, Wilton SD, Fletcher S. Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. Front Genet 2022; 12:806946. [PMID: 35140743 PMCID: PMC8819188 DOI: 10.3389/fgene.2021.806946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding pre-mRNA splicing is crucial to accurately diagnosing and treating genetic diseases. However, mutations that alter splicing can exert highly diverse effects. Of all the known types of splicing mutations, perhaps the rarest and most difficult to predict are those that activate pseudoexons, sometimes also called cryptic exons. Unlike other splicing mutations that either destroy or redirect existing splice events, pseudoexon mutations appear to create entirely new exons within introns. Since exon definition in vertebrates requires coordinated arrangements of numerous RNA motifs, one might expect that pseudoexons would only arise when rearrangements of intronic DNA create novel exons by chance. Surprisingly, although such mutations do occur, a far more common cause of pseudoexons is deep-intronic single nucleotide variants, raising the question of why these latent exon-like tracts near the mutation sites have not already been purged from the genome by the evolutionary advantage of more efficient splicing. Possible answers may lie in deep intronic splicing processes such as recursive splicing or poison exon splicing. Because these processes utilize intronic motifs that benignly engage with the spliceosome, the regions involved may be more susceptible to exonization than other intronic regions would be. We speculated that a comprehensive study of reported pseudoexons might detect alignments with known deep intronic splice sites and could also permit the characterisation of novel pseudoexon categories. In this report, we present and analyse a catalogue of over 400 published pseudoexon splice events. In addition to confirming prior observations of the most common pseudoexon mutation types, the size of this catalogue also enabled us to suggest new categories for some of the rarer types of pseudoexon mutation. By comparing our catalogue against published datasets of non-canonical splice events, we also found that 15.7% of pseudoexons exhibit some splicing activity at one or both of their splice sites in non-mutant cells. Importantly, this included seven examples of experimentally confirmed recursive splice sites, confirming for the first time a long-suspected link between these two splicing phenomena. These findings have the potential to improve the fidelity of genetic diagnostics and reveal new targets for splice-modulating therapies.
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Affiliation(s)
- Niall P. Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
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9
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Durward-Akhurst SA, Schaefer RJ, Grantham B, Carey WK, Mickelson JR, McCue ME. Genetic Variation and the Distribution of Variant Types in the Horse. Front Genet 2021; 12:758366. [PMID: 34925451 PMCID: PMC8676274 DOI: 10.3389/fgene.2021.758366] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/10/2021] [Indexed: 11/13/2022] Open
Abstract
Genetic variation is a key contributor to health and disease. Understanding the link between an individual's genotype and the corresponding phenotype is a major goal of medical genetics. Whole genome sequencing (WGS) within and across populations enables highly efficient variant discovery and elucidation of the molecular nature of virtually all genetic variation. Here, we report the largest catalog of genetic variation for the horse, a species of importance as a model for human athletic and performance related traits, using WGS of 534 horses. We show the extent of agreement between two commonly used variant callers. In data from ten target breeds that represent major breed clusters in the domestic horse, we demonstrate the distribution of variants, their allele frequencies across breeds, and identify variants that are unique to a single breed. We investigate variants with no homozygotes that may be potential embryonic lethal variants, as well as variants present in all individuals that likely represent regions of the genome with errors, poor annotation or where the reference genome carries a variant. Finally, we show regions of the genome that have higher or lower levels of genetic variation compared to the genome average. This catalog can be used for variant prioritization for important equine diseases and traits, and to provide key information about regions of the genome where the assembly and/or annotation need to be improved.
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Affiliation(s)
- S. A. Durward-Akhurst
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, MN, United States
| | - R. J. Schaefer
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, MN, United States
| | - B. Grantham
- Interval Bio LLC, Mountain View, CA, United States
| | - W. K. Carey
- Interval Bio LLC, Mountain View, CA, United States
| | - J. R. Mickelson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Minneapolis, MN, United States
| | - M. E. McCue
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, MN, United States
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10
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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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11
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Kumar A, Sharma R, Faruq M, Kumar M, Sharma S, Werner R, Hiort O, Vandana J. Clinical, Biochemical, and Molecular Characterization of Indian Children with Clinically Suspected Androgen Insensitivity Syndrome. Sex Dev 2021; 16:34-45. [PMID: 34689141 DOI: 10.1159/000519047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 08/16/2021] [Indexed: 11/19/2022] Open
Abstract
This study describes the clinical, biochemical, and molecular characteristics of Indian children with 46,XY DSD and suspected androgen insensitivity syndrome (AIS). Fifty children (median age 3.0 years, range 0-16.5 years) with 46,XY DSD and a suspected diagnosis of AIS were enrolled. Sanger sequencing was performed to identify pathogenic variants in the androgen receptor (AR) gene and to study genotype-phenotype correlations. All 5 (100%) patients with CAIS and 14/45 (31%) patients with PAIS had pathogenic/likely pathogenic variants in the AR gene (overall, 14 different variants in 19 patients; 38.8%). There was no significant difference in clinical (cryptorchidism, hypospadias, or external masculinizing score) or biochemical parameters (gonadotropins and testosterone) between patients with or without pathogenic variants. However, patients with AIS were more likely to have a positive family history, be assigned female gender at birth, and present with gynaecomastia at puberty. Three novel pathogenic/likely pathogenic variants, including one splice donor site variant c.2318+1G>A, one frameshift variant p.H790Lfs*40, and one missense variant p.G821E, were identified in 3 patients with CAIS. The missense variant p.G821E was predicted as deleterious, damaging, disease-causing, and likely functionally inactive by in silico analysis and protein modelling study. Two previously not reported pathogenic/likely pathogenic variants, including p.R386H and p.G396R, were identified in patients with PAIS. This study contributes in expanding the spectrum of pathogenic variants in the AR gene in patients with AIS. Only 31% patients with a provisional diagnosis of PAIS had pathogenic variants in the AR gene, suggesting other possible mechanisms or candidate genes may be responsible for such a phenotypic presentation.
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Affiliation(s)
- Anil Kumar
- Division of Pediatric Endocrinology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India,
| | - Rajni Sharma
- Division of Pediatric Endocrinology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Manoj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Shilpa Sharma
- Department of Pediatric Surgery, All India Institute of Medical Sciences, New Delhi, India
| | - Ralf Werner
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, University of Lübeck, Lübeck, Germany.,Institute of Molecular Medicine, University of Lübeck, Lübeck, Germany
| | - Olaf Hiort
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, University of Lübeck, Lübeck, Germany
| | - Jain Vandana
- Division of Pediatric Endocrinology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
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12
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Atlas G, Sreenivasan R, Sinclair A. Targeting the Non-Coding Genome for the Diagnosis of Disorders of Sex Development. Sex Dev 2021; 15:392-410. [PMID: 34634785 DOI: 10.1159/000519238] [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: 06/18/2021] [Accepted: 08/12/2021] [Indexed: 11/19/2022] Open
Abstract
Disorders of sex development (DSD) are a complex group of conditions with highly variable clinical phenotypes, most often caused by failure of gonadal development. DSD are estimated to occur in around 1.7% of all live births. Whilst the understanding of genes involved in gonad development has increased exponentially, approximately 50% of patients with a DSD remain without a genetic diagnosis, possibly implicating non-coding genomic regions instead. Here, we review how variants in the non-coding genome of DSD patients can be identified using techniques such as array comparative genomic hybridization (CGH) to detect copy number variants (CNVs), and more recently, whole genome sequencing (WGS). Once a CNV in a patient's non-coding genome is identified, putative regulatory elements such as enhancers need to be determined within these vast genomic regions. We will review the available online tools and databases that can be used to refine regions with potential enhancer activity based on chromosomal accessibility, histone modifications, transcription factor binding site analysis, chromatin conformation, and disease association. We will also review the current in vitro and in vivo techniques available to demonstrate the functionality of the identified enhancers. The review concludes with a clinical update on the enhancers linked to DSD.
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Affiliation(s)
- Gabby Atlas
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia, .,Department of Endocrinology and Diabetes, Royal Children's Hospital, Melbourne, Victoria, Australia, .,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia,
| | - Rajini Sreenivasan
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew Sinclair
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
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13
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Kalinchenko NY, Petrov VM, Panova AV, Tiulpakov AN. [A deep intronic mutation in AR gene causing androgen insensitivity syndrome: difficulties of diagnostics]. PROBLEMY ĖNDOKRINOLOGII 2021; 67:48-52. [PMID: 34766490 DOI: 10.14341/probl12799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/09/2021] [Accepted: 09/19/2021] [Indexed: 11/06/2022]
Abstract
Partial androgen resistance syndrome (PAIS) is the most difficult form of disorders/differences of sex development 46,XY (DSD 46,XY) for choosing of patient management. To date, there are no clear biochemical criteria, especially before puberty, that allow differentiating PAIS from other PAIS-like forms of DSD 46, XY, and genetic verification of the partial form of AIS plays an important role. Meanwhile, according to the literature, mutations in the coding region of AR gene have not been identified in more than 50% of patients with suspected AIS. We performed an extensive analysis of the AR gene in a patient with clinical and laboratory signs of AIS and found a deep intron mutation in the AR gene (p. 2450-42G>A). This variant creates an alternative splice acceptor site resulted a disturbance of the AR function. These findings indicate the need for extensive genetic analysis in a cohort of patients with suspected CPA in the absence of mutations in the AR gene using standard methods of genetic diagnosis.
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Affiliation(s)
- N Y Kalinchenko
- Endocrinology Research Centre; Vavilov Institute of General Genetics
| | - V M Petrov
- Endocrinology Research Centre; Vavilov Institute of General Genetics
| | - A V Panova
- Endocrinology Research Centre; Vavilov Institute of General Genetics, Russian Academy of Sciences
| | - A N Tiulpakov
- Research Centre for Medical Genetics; Republican children's clinical hospital
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14
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A novel de novo androgen receptor nonsense mutation in a sex-reversed 46,XY infant. Hum Genome Var 2021; 8:35. [PMID: 34471093 PMCID: PMC8410801 DOI: 10.1038/s41439-021-00167-5] [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] [Received: 06/11/2021] [Revised: 07/11/2021] [Accepted: 07/28/2021] [Indexed: 11/25/2022] Open
Abstract
An infant with 46,XY karyotype, and unambiguous female phenotype was found to have testes in the inguinal regions. Capillary sequencing of the androgen receptor (AR) gene identified a hemizygous de novo mutation (NM_000044.6:c.1621G > T) in exon 2 resulting in a termination codon p.(Glu541*) at the DNA binding domain (DBD). This novel nonsense mutation adds to the compendium of AR mutations which result in complete androgen insensitivity syndrome (AIS).
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15
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Arya S, Barnabas R, Lila AR, Sarathi V, Memon SS, Bhandare VV, Thakkar K, Patil V, Shah NS, Kunwar A, Bandgar T. Clinical, Hormonal, Genetic, and Molecular Characteristics in Androgen Insensitivity Syndrome in an Asian Indian Cohort from a Single Centre in Western India. Sex Dev 2021; 15:253-261. [PMID: 34333495 DOI: 10.1159/000517763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/09/2021] [Indexed: 11/19/2022] Open
Abstract
The study aimed to analyze clinical and hormonal phenotype,and genotype in patients with genetically proven androgen insensitivity syndrome (AIS) from Western India. Index patients with pathogenic variants in the androgen receptor (AR) gene were identified from a consecutive 46,XY DSD cohort (n = 150) evaluated with clinical exome sequencing, and their genetically-proven affected relatives were also included. In sum, 15 index cases (9 complete AIS [CAIS] and 6 partial AIS [PAIS]) were identified making AIS the second most common (10%) cause of 46,XY DSD, next to 5α-reductase 2 deficiency (n = 26; 17.3%). Most patients presented late in the postpubertal period with primary amenorrhoea in CAIS (89%) and atypical genitalia with gynecomastia in PAIS (71.4%). All CAIS were reared as females and 83.3% of PAIS as males with no gender dysphoria. Four of 6 patients with available testosterone to dihydrotestosterone ratio had a false elevation (>10). Metastatic dysgerminoma was seen in 1 patient in CAIS, while none in the PAIS group had malignancy. Fifteen different (including 6 novel) pathogenic/likely pathogenic variants in AR were found. Nonsense and frameshift variants exclusively led to CAIS phenotype, whereas missense variants led to variable phenotypes. In this largest, monocentric study from the Asian Indian subcontinent, AIS was the second most common cause of 46,XY DSD with similar phenotype but later presentation when compared to cases in the rest of the world. The study reports 6 novel pathogenic variants in AR.
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Affiliation(s)
- Sneha Arya
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Rohit Barnabas
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Anurag Ranjan Lila
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Vijaya Sarathi
- Department of Endocrinology, Vydehi Institute of Medical Sciences and Research Centre, Bangalore, India
| | - Saba Samad Memon
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | | | - Kunal Thakkar
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Virendra Patil
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Nalini Samir Shah
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Ambarish Kunwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Tushar Bandgar
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
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16
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Sakaguchi N, Suyama M. In silico identification of pseudo-exon activation events in personal genome and transcriptome data. RNA Biol 2021; 18:382-390. [PMID: 32865117 PMCID: PMC7951959 DOI: 10.1080/15476286.2020.1809195] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/03/2020] [Accepted: 08/08/2020] [Indexed: 12/25/2022] Open
Abstract
Causative mutations for human genetic disorders have mainly been identified in exonic regions that code for amino acid sequences. Recently, however, it has been reported that mutations in deep intronic regions can also cause certain human genetic disorders by creating novel splice sites, leading to pseudo-exon activation. To investigate how frequently pseudo-exon activation events occur in normal individuals, we conducted in silico identification of such events using personal genome data and corresponding high-quality transcriptome data. With rather stringent conditions, on average, 2.6 pseudo-exon activation events per individual were identified. More pseudo-exon activation events were found in 5' donor splice sites than in 3' acceptor splice sites. Although pseudo-exon activation events have sporadically been reported as causative mutations in genetic disorders, it is revealed in this study that such events can be observed in normal individuals at a certain frequency. We estimate that human genomes typically contain on average at least 10 pseudo-exon activation events. The actual number should be higher than this, because we used stringent criteria to identify pseudo-exon activation events. This suggests that it is worth considering the possibility of pseudo-exon activation when searching for causative mutations of genetic disorders if candidate mutations are not identified in coding regions or RNA splice sites.
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Affiliation(s)
- Narumi Sakaguchi
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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17
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Bianchi P, Fermo E, Lezon‐Geyda K, Beers EJ, Morton HD, Barcellini W, Glader B, Chonat S, Ravindranath Y, Newburger PE, Kollmar N, Despotovic JM, Verhovsek M, Sharma M, Kwiatkowski JL, Kuo KHM, Wlodarski MW, Yaish HM, Holzhauer S, Wang H, Kunz J, Addonizio K, Al‐Sayegh H, London WB, Andres O, Wijk R, Gallagher PG, Grace RFF. Genotype-phenotype correlation and molecular heterogeneity in pyruvate kinase deficiency. Am J Hematol 2020; 95:472-482. [PMID: 32043619 DOI: 10.1002/ajh.25753] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 01/15/2020] [Accepted: 01/21/2020] [Indexed: 01/19/2023]
Abstract
Pyruvate kinase (PK) deficiency is a rare recessive congenital hemolytic anemia caused by mutations in the PKLR gene. This study reports the molecular features of 257 patients enrolled in the PKD Natural History Study. Of the 127 different pathogenic variants detected, 84 were missense and 43 non-missense, including 20 stop-gain, 11 affecting splicing, five large deletions, four in-frame indels, and three promoter variants. Within the 177 unrelated patients, 35 were homozygous and 142 compound heterozygous (77 for two missense, 48 for one missense and one non-missense, and 17 for two non-missense variants); the two most frequent mutations were p.R510Q in 23% and p.R486W in 9% of mutated alleles. Fifty-five (21%) patients were found to have at least one previously unreported variant with 45 newly described mutations. Patients with two non-missense mutations had lower hemoglobin levels, higher numbers of lifetime transfusions, and higher rates of complications including iron overload, extramedullary hematopoiesis, and pulmonary hypertension. Rare severe complications, including lower extremity ulcerations and hepatic failure, were seen more frequently in patients with non-missense mutations or with missense mutations characterized by severe protein instability. The PKLR genotype did not correlate with the frequency of complications in utero or in the newborn period. With ICCs ranging from 0.4 to 0.61, about the same degree of clinical similarity exists within siblings as it does between siblings, in terms of hemoglobin, total bilirubin, splenectomy status, and cholecystectomy status. Pregnancy outcomes were similar across genotypes in PK deficient women. This report confirms the wide genetic heterogeneity of PK deficiency.
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Affiliation(s)
- Paola Bianchi
- U.O.C. EmatologiaU.O.S. Fisiopatologia delle Anemie, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico Milan Italy
| | - Elisa Fermo
- U.O.C. EmatologiaU.O.S. Fisiopatologia delle Anemie, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico Milan Italy
| | | | - Eduard J. Beers
- Division Internal Medicine and DermatologyVan Creveldkliniek, University Medical Center Utrecht Utrecht The Netherlands
| | - Holmes D. Morton
- Central Pennsylvania Clinic for Special Children & AdultsBelleville, PA; Lancaster General Hospital Lancaster PA
| | - Wilma Barcellini
- U.O.C. EmatologiaU.O.S. Fisiopatologia delle Anemie, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico Milan Italy
| | - Bertil Glader
- Lucile Packard Children's HospitalStanford University Palo Alto CA
| | - Satheesh Chonat
- Department of PediatricsEmory University School of Medicine, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta Atlanta GA
| | - Yaddanapudi Ravindranath
- School of MedicinePediatrics, Children's Hospital of Michigan, Wayne State University School of Medicine Detroit MI
| | - Peter E. Newburger
- Department of PediatricsUniversity of Massachusetts Medical School Worcester MA
| | - Nina Kollmar
- Department of Pediatric Hematology/OncologyKlinikum Kassel GmbH Kassel Germany
| | | | | | - Mukta Sharma
- Department of PediatricsChildren's Mercy, School of Medicine University of Missouri Kansas City MO
| | - Janet L. Kwiatkowski
- Division of HematologyChildren's Hospital of Philadelphia, and Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania Philadelphia PA
| | - Kevin H. M. Kuo
- Division of Hematology, Department of MedicineUniversity Health Network, University of Toronto Toronto Ontario Canada
| | | | - Hassan M. Yaish
- Primary Children's HospitalUniversity of Utah Salt Lake City UT
| | - Susanne Holzhauer
- CharitéUniversity Medicine, Pediatric Hematology and Oncology Berlin Germany
| | - Heng Wang
- DDC Clinic for Special Needs Children Middlefield OH
| | - Joachim Kunz
- Zentrumfür Kinder‐und Jugendmedizin Heidelberg Germany
| | - Kathryn Addonizio
- Dana‐Farber/Boston Children's Cancer and Blood Disorder Center Boston MA
| | - Hasan Al‐Sayegh
- Dana‐Farber/Boston Children's Cancer and Blood Disorder Center Boston MA
| | - Wendy B. London
- Dana‐Farber/Boston Children's Cancer and Blood Disorder Center Boston MA
| | - Oliver Andres
- Department of PediatricsUniversity of Würzburg Würzburg Germany
| | - Richard Wijk
- Central Diagnostic LaboratoryUniversity Medical Center Utrecht Utrecht The Netherlands
| | - Patrick G. Gallagher
- Department of Pediatrics, Department of Genetics, Department of PathologyYale University School of Medicine New Haven CT
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18
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Hujová P, Souček P, Grodecká L, Grombiříková H, Ravčuková B, Kuklínek P, Hakl R, Litzman J, Freiberger T. Deep Intronic Mutation in SERPING1 Caused Hereditary Angioedema Through Pseudoexon Activation. J Clin Immunol 2020; 40:435-446. [PMID: 31982983 DOI: 10.1007/s10875-020-00753-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/17/2020] [Indexed: 01/26/2023]
Abstract
PURPOSE Hereditary angioedema (HAE) is a rare autosomal dominant life-threatening disease characterized by low levels of C1 inhibitor (type I HAE) or normal levels of ineffective C1 inhibitor (type II HAE), typically occurring as a consequence of a SERPING1 mutation. In some cases, a causal mutation remains undetected after using a standard molecular genetic analysis. RESULTS Here we show a long methodological way to the final discovery of c.1029 + 384A > G, a novel deep intronic mutation in intron 6 which is responsible for HAE type I in a large family and has not been identified by a conventional diagnostic approach. This mutation results in de novo donor splice site creation and subsequent pseudoexon inclusion, the mechanism firstly described to occur in SERPING1 in this study. We additionally discovered that the proximal part of intron 6 is a region potentially prone to pseudoexon-activating mutations, since natural alternative exons and additional cryptic sites occur therein. Indeed, we confirmed the existence of at least two different alternative exons in this region not described previously. CONCLUSIONS In conclusion, our results suggest that detecting aberrant transcripts, which are often low abundant because of nonsense-mediated decay, requires a modified methodological approach. We suggest SERPING1 intron 6 sequencing and/or tailored mRNA analysis to be routinely used in HAE patients with no mutation identified in the coding sequence.
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Affiliation(s)
- Pavla Hujová
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic.,Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Přemysl Souček
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Lucie Grodecká
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
| | - Hana Grombiříková
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic.,Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Barbora Ravčuková
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
| | - Pavel Kuklínek
- Department of Allergology and Clinical Immunology, St. Anne's University Hospital in Brno, Brno, Czech Republic
| | - Roman Hakl
- Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Department of Allergology and Clinical Immunology, St. Anne's University Hospital in Brno, Brno, Czech Republic
| | - Jiří Litzman
- Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Department of Allergology and Clinical Immunology, St. Anne's University Hospital in Brno, Brno, Czech Republic
| | - Tomáš Freiberger
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic. .,Faculty of Medicine, Masaryk University, Brno, Czech Republic. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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19
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Jarzabek K, Koda M, Chrusciel M, Kanczuga-Koda L, Sobczynska-Tomaszewska A, Rahman NA, Wolczynski S. Features of the fetal gonad in androgen synthesis in the postpubertal testis are preserved in complete androgen insensitivity syndrome due to a novel genetic splice site donor variant in androgen receptor gene intron 1. J Steroid Biochem Mol Biol 2019; 193:105420. [PMID: 31283987 DOI: 10.1016/j.jsbmb.2019.105420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/19/2019] [Accepted: 06/26/2019] [Indexed: 12/14/2022]
Abstract
Mutations in the X-linked androgen receptor (AR) gene cause complete androgen insensitivity syndrome (CAIS). CAIS may cause congenital sexual development disorder, which frequently develops into testicular tumors. Here, we describe a novel splice-site intron 1 mutation in AR leading to improper splicing and AR protein absence in CAIS gonads. We characterized a patient's postpubertal gonadal steroidogenic enzyme expression profile. Localization of both CYP11A1 and CYP17A1 enzymes was restricted to both Leydig tumor cells and adjacent to tumor gonadal tissues. Sertoli cells of the CAIS gonad showed abundant HSD17B3 protein, which is an adult Leydig cell marker that enables the conversion of androstenedione to testosterone. Such HSD17B3 expression is typical for fetal-type Sertoli cells in rodents. The postpubertal CAIS gonad of our patient was completely devoid of androgen signaling pathway activity. Plausibly, the postpubertal Leydig cells consisted of two distinct cell populations: postpubertal fetal-type Leydig cells that persisted as androgen-independent cells and immature adult Leydig cells that failed to differentiate. Taken together, in this CAIS postpubertal testis, both Leydig and fetal-type Sertoli cells participated in testosterone production. Our results indicate the importance of molecular analysis as well as the characterization of steroidogenic enzyme profiling in the CAIS patient's gonad.
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Affiliation(s)
- Katarzyna Jarzabek
- Department of Reproduction and Gynaecological Endocrinology, Medical University of Bialystok, Poland.
| | - Mariusz Koda
- Department of General Pathomorphology, Medical University of Bialystok, Poland
| | | | - Luiza Kanczuga-Koda
- Department of Pathology, Maria Curie-Sklodowska Bialystok Oncology Center, Bialystok, Poland
| | | | - Nafis A Rahman
- Department of Reproduction and Gynaecological Endocrinology, Medical University of Bialystok, Poland; Institute of Biomedicine, University of Turku, Turku, Finland
| | - Slawomir Wolczynski
- Department of Reproduction and Gynaecological Endocrinology, Medical University of Bialystok, Poland
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20
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Mäkelä JA, Koskenniemi JJ, Virtanen HE, Toppari J. Testis Development. Endocr Rev 2019; 40:857-905. [PMID: 30590466 DOI: 10.1210/er.2018-00140] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/17/2018] [Indexed: 12/28/2022]
Abstract
Production of sperm and androgens is the main function of the testis. This depends on normal development of both testicular somatic cells and germ cells. A genetic program initiated from the Y chromosome gene sex-determining region Y (SRY) directs somatic cell specification to Sertoli cells that orchestrate further development. They first guide fetal germ cell differentiation toward spermatogenic destiny and then take care of the full service to spermatogenic cells during spermatogenesis. The number of Sertoli cells sets the limits of sperm production. Leydig cells secrete androgens that determine masculine development. Testis development does not depend on germ cells; that is, testicular somatic cells also develop in the absence of germ cells, and the testis can produce testosterone normally to induce full masculinization in these men. In contrast, spermatogenic cell development is totally dependent on somatic cells. We herein review germ cell differentiation from primordial germ cells to spermatogonia and development of the supporting somatic cells. Testicular descent to scrota is necessary for normal spermatogenesis, and cryptorchidism is the most common male birth defect. This is a mild form of a disorder of sex differentiation. Multiple genetic reasons for more severe forms of disorders of sex differentiation have been revealed during the last decades, and these are described along with the description of molecular regulation of testis development.
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Affiliation(s)
- Juho-Antti Mäkelä
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Jaakko J Koskenniemi
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland.,Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Helena E Virtanen
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Jorma Toppari
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland.,Department of Pediatrics, Turku University Hospital, Turku, Finland
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21
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Ebbert MTW, Jensen TD, Jansen-West K, Sens JP, Reddy JS, Ridge PG, Kauwe JSK, Belzil V, Pregent L, Carrasquillo MM, Keene D, Larson E, Crane P, Asmann YW, Ertekin-Taner N, Younkin SG, Ross OA, Rademakers R, Petrucelli L, Fryer JD. Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight. Genome Biol 2019; 20:97. [PMID: 31104630 PMCID: PMC6526621 DOI: 10.1186/s13059-019-1707-2] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/06/2019] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The human genome contains "dark" gene regions that cannot be adequately assembled or aligned using standard short-read sequencing technologies, preventing researchers from identifying mutations within these gene regions that may be relevant to human disease. Here, we identify regions with few mappable reads that we call dark by depth, and others that have ambiguous alignment, called camouflaged. We assess how well long-read or linked-read technologies resolve these regions. RESULTS Based on standard whole-genome Illumina sequencing data, we identify 36,794 dark regions in 6054 gene bodies from pathways important to human health, development, and reproduction. Of these gene bodies, 8.7% are completely dark and 35.2% are ≥ 5% dark. We identify dark regions that are present in protein-coding exons across 748 genes. Linked-read or long-read sequencing technologies from 10x Genomics, PacBio, and Oxford Nanopore Technologies reduce dark protein-coding regions to approximately 50.5%, 35.6%, and 9.6%, respectively. We present an algorithm to resolve most camouflaged regions and apply it to the Alzheimer's Disease Sequencing Project. We rescue a rare ten-nucleotide frameshift deletion in CR1, a top Alzheimer's disease gene, found in disease cases but not in controls. CONCLUSIONS While we could not formally assess the association of the CR1 frameshift mutation with Alzheimer's disease due to insufficient sample-size, we believe it merits investigating in a larger cohort. There remain thousands of potentially important genomic regions overlooked by short-read sequencing that are largely resolved by long-read technologies.
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Affiliation(s)
- Mark T. W. Ebbert
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224 USA
| | - Tanner D. Jensen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | | | - Jonathon P. Sens
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Joseph S. Reddy
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Perry G. Ridge
- Department of Biology, Brigham Young University, Provo, UT 84602 USA
| | - John S. K. Kauwe
- Department of Biology, Brigham Young University, Provo, UT 84602 USA
| | - Veronique Belzil
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Luc Pregent
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | | | - Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA 98195 USA
| | - Eric Larson
- Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Paul Crane
- Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Yan W. Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Nilufer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
- Department of Neurology, Mayo Clinic, Jacksonville, FL 32224 USA
| | | | - Owen A. Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224 USA
| | - John D. Fryer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224 USA
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22
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Touzon MS, Garrido NP, Marino R, Ramirez P, Costanzo M, Guercio G, Berensztein E, Rivarola MA, Belgorosky A. Androgen Insensitivity Syndrome: Clinical Phenotype and Molecular Analysis in a Single Tertiary Center Cohort. J Clin Res Pediatr Endocrinol 2019; 11:24-33. [PMID: 30251955 PMCID: PMC6398199 DOI: 10.4274/jcrpe.galenos.2018.2018.0185] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
OBJECTIVE The aim of this study was the molecular characterization of the AR gene as the cause of 46,XY disorder in our population. METHODS We studied 41, non related, 46,XY disorder of sexual differentiation index cases, having characteristics consistent with androgen insensivity syndrome (AIS). Genomic DNA was isolated from peripheral blood leukocytes of all patients and 25 family members from 17 non-related families. RESULTS The AR gene analysis revealed an abnormal sequence in 58.5% of the index patients. All of the complete AIS (CAIS) cases were genetically confirmed, while in the partial form (PAIS) a mutation in AR was detected in only 13 (43.3%). Molecular studies revealed other affected or carrier relatives in 87% of the index cases. The AR mutations were found spread along the whole coding sequence, with a higher prevalence in the ligand binding domain. Nine out of 23 (39%) AR mutations were novel. In 17% of patients with detected AR mutations, somatic mosaicism was detected in leucocyte DNA. In our cohort, long-term follow up gender dysphoria, raised as male or female, was not found. Finally, in suspected PAIS, the identification of AR mutation occurred significantly less than in CAIS patients. CONCLUSION Improved knowledge of the components of the AR complex and signaling network might contribute to long term outcome and genetic counseling in AIS patients.
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Affiliation(s)
- Maria Sol Touzon
- Hospital de Pediatria Garrahan, Endocrinology Service, Buenos Aires, Argentina,National Scientific and Technical Research Council (CONICET), Endocrinology Service, Buenos Aires, Argentina
| | | | - Roxana Marino
- Hospital de Pediatria Garrahan, Endocrinology Service, Buenos Aires, Argentina
| | - Pablo Ramirez
- Hospital de Pediatria Garrahan, Endocrinology Service, Buenos Aires, Argentina
| | - Mariana Costanzo
- Hospital de Pediatria Garrahan, Endocrinology Service, Buenos Aires, Argentina
| | - Gabriela Guercio
- Hospital de Pediatria Garrahan, Endocrinology Service, Buenos Aires, Argentina,National Scientific and Technical Research Council (CONICET), Endocrinology Service, Buenos Aires, Argentina
| | | | - Marco A. Rivarola
- Hospital de Pediatria Garrahan, Endocrinology Service, Buenos Aires, Argentina,National Scientific and Technical Research Council (CONICET), Endocrinology Service, Buenos Aires, Argentina
| | - Alicia Belgorosky
- Hospital de Pediatria Garrahan, Endocrinology Service, Buenos Aires, Argentina,National Scientific and Technical Research Council (CONICET), Endocrinology Service, Buenos Aires, Argentina,* Address for Correspondence: Hospital de Pediatria Garrahan, Endocrinology Service, Buenos Aires, Argentina Phone: +541143080034 E-mail:
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23
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Helle E, Córdova-Palomera A, Ojala T, Saha P, Potiny P, Gustafsson S, Ingelsson E, Bamshad M, Nickerson D, Chong JX, Ashley E, Priest JR. Loss of function, missense, and intronic variants in NOTCH1 confer different risks for left ventricular outflow tract obstructive heart defects in two European cohorts. Genet Epidemiol 2019; 43:215-226. [PMID: 30511478 PMCID: PMC6375786 DOI: 10.1002/gepi.22176] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 10/03/2018] [Accepted: 10/17/2018] [Indexed: 01/08/2023]
Abstract
Loss of function variants in NOTCH1 cause left ventricular outflow tract obstructive defects (LVOTO). However, the risk conferred by rare and noncoding variants in NOTCH1 for LVOTO remains largely uncharacterized. In a cohort of 49 families affected by hypoplastic left heart syndrome, a severe form of LVOTO, we discovered predicted loss of function NOTCH1 variants in 6% of individuals. Rare or low-frequency missense variants were found in 16% of families. To make a quantitative estimate of the genetic risk posed by variants in NOTCH1 for LVOTO, we studied associations of 400 coding and noncoding variants in NOTCH1 in 1,085 cases and 332,788 controls from the UK Biobank. Two rare intronic variants in strong linkage disequilibrium displayed significant association with risk for LVOTO amongst European-ancestry individuals. This result was replicated in an independent analysis of 210 cases and 68,762 controls of non-European and mixed ancestry. In conclusion, carrying rare predicted loss of function variants in NOTCH1 confer significant risk for LVOTO. In addition, the two intronic variants seem to be associated with an increased risk for these defects. Our approach demonstrates the utility of population-based data sets in quantifying the specific risk of individual variants for disease-related phenotypes.
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Affiliation(s)
- Emmi Helle
- Pediatric Research Center, Children's Hospital, University of Helsinki, Helsinki, Finland
- Division of Cardiovascular Medicine, Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Aldo Córdova-Palomera
- Department of Pediatrics, Division of Pediatric Cardiology, Stanford University School of Medicine, Stanford, CA
| | - Tiina Ojala
- Pediatric Research Center, Children's Hospital, University of Helsinki, Helsinki, Finland
| | - Priyanka Saha
- Department of Pediatrics, Division of Pediatric Cardiology, Stanford University School of Medicine, Stanford, CA
| | - Praneetha Potiny
- Department of Pediatrics, Division of Pediatric Cardiology, Stanford University School of Medicine, Stanford, CA
| | - Stefan Gustafsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Erik Ingelsson
- Division of Cardiovascular Medicine, Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Michael Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA
- Department of Genome Sciences, University of Washington, Seattle, WA
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, Washington
| | - Deborah Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, WA
| | - Euan Ashley
- Division of Cardiovascular Medicine, Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - James R Priest
- Division of Cardiovascular Medicine, Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
- Department of Pediatrics, Division of Pediatric Cardiology, Stanford University School of Medicine, Stanford, CA
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24
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Understanding human DNA variants affecting pre-mRNA splicing in the NGS era. ADVANCES IN GENETICS 2019; 103:39-90. [PMID: 30904096 DOI: 10.1016/bs.adgen.2018.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pre-mRNA splicing, an essential step in eukaryotic gene expression, relies on recognition of short sequences on the primary transcript intron ends and takes place along transcription by RNA polymerase II. Exonic and intronic auxiliary elements may modify the strength of exon definition and intron recognition. Splicing DNA variants (SV) have been associated with human genetic diseases at canonical intron sites, as well as exonic substitutions putatively classified as nonsense, missense or synonymous variants. Their effects on mRNA may be modulated by cryptic splice sites associated to the SV allele, comprehending exon skipping or shortening, and partial or complete intron retention. As splicing mRNA outputs result from combinatorial effects of both intrinsic and extrinsic factors, in vitro functional assays supported by computational analyses are recommended to assist SV pathogenicity assessment for human Mendelian inheritance diseases. The increasing use of next-generating sequencing (NGS) targeting full genomic gene sequence has raised awareness of the relevance of deep intronic SV in genetic diseases and inclusion of pseudo-exons into mRNA. Finally, we take advantage of recent advances in sequencing and computational technologies to analyze alternative splicing in cancer. We explore the Catalog of Somatic Mutations in Cancer (COSMIC) to describe the proportion of splice-site mutations in cis and trans regulatory elements. Genomic data from large cohorts of different cancer types are increasingly available, in addition to repositories of normal and somatic genetic variations. These are likely to bring new insights to understanding the genetic control of alternative splicing by mapping splicing quantitative trait loci in tumors.
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25
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Wai H, Douglas AGL, Baralle D. RNA splicing analysis in genomic medicine. Int J Biochem Cell Biol 2018; 108:61-71. [PMID: 30594648 DOI: 10.1016/j.biocel.2018.12.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 12/03/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022]
Abstract
High-throughput next-generation sequencing technologies have led to a rapid increase in the number of sequence variants identified in clinical practice via diagnostic genetic tests. Current bioinformatic analysis pipelines fail to take adequate account of the possible splicing effects of such variants, particularly where variants fall outwith canonical splice site sequences, and consequently the pathogenicity of such variants may often be missed. The regulation of splicing is highly complex and as a result, in silico prediction tools lack sufficient sensitivity and specificity for reliable use. Variants of all kinds can be linked to aberrant splicing in disease and the need for correct identification and diagnosis grows ever more crucial as novel splice-switching antisense oligonucleotide therapies start to enter clinical usage. RT-PCR provides a useful targeted assay of the splicing effects of identified variants, while minigene assays, massive parallel reporter assays and animal models can also be used for more detailed study of a particular splicing system, given enough time and resources. However, RNA-sequencing (RNA-seq) has the potential to be used as a rapid diagnostic tool in genomic medicine. By utilising data science approaches and machine learning, it may prove possible to finally understand and interpret the 'splicing code' and apply this knowledge in human disease diagnostics.
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Affiliation(s)
- Htoo Wai
- Human Development and Health, Faculty of Medicine, University of Southampton, UK
| | - Andrew G L Douglas
- Human Development and Health, Faculty of Medicine, University of Southampton, UK; Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, UK; Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK.
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26
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Clark MM, Stark Z, Farnaes L, Tan TY, White SM, Dimmock D, Kingsmore SF. Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases. NPJ Genom Med 2018; 3:16. [PMID: 30002876 PMCID: PMC6037748 DOI: 10.1038/s41525-018-0053-8] [Citation(s) in RCA: 360] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/30/2018] [Accepted: 05/10/2018] [Indexed: 12/14/2022] Open
Abstract
Genetic diseases are leading causes of childhood mortality. Whole-genome sequencing (WGS) and whole-exome sequencing (WES) are relatively new methods for diagnosing genetic diseases, whereas chromosomal microarray (CMA) is well established. Here we compared the diagnostic utility (rate of causative, pathogenic, or likely pathogenic genotypes in known disease genes) and clinical utility (proportion in whom medical or surgical management was changed by diagnosis) of WGS, WES, and CMA in children with suspected genetic diseases by systematic review of the literature (January 2011–August 2017) and meta-analysis, following MOOSE/PRISMA guidelines. In 37 studies, comprising 20,068 children, diagnostic utility of WGS (0.41, 95% CI 0.34–0.48, I2 = 44%) and WES (0.36, 95% CI 0.33–0.40, I2 = 83%) were qualitatively greater than CMA (0.10, 95% CI 0.08–0.12, I2 = 81%). Among studies published in 2017, the diagnostic utility of WGS was significantly greater than CMA (P < 0.0001, I2 = 13% and I2 = 40%, respectively). Among studies featuring within-cohort comparisons, the diagnostic utility of WES was significantly greater than CMA (P < 0.001, I2 = 36%). The diagnostic utility of WGS and WES were not significantly different. In studies featuring within-cohort comparisons of WGS/WES, the likelihood of diagnosis was significantly greater for trios than singletons (odds ratio 2.04, 95% CI 1.62–2.56, I2 = 12%; P < 0.0001). Diagnostic utility of WGS/WES with hospital-based interpretation (0.42, 95% CI 0.38–0.45, I2 = 48%) was qualitatively higher than that of reference laboratories (0.29, 95% CI 0.27–0.31, I2 = 49%); this difference was significant among studies published in 2017 (P < .0001, I2 = 22% and I2 = 26%, respectively). The clinical utility of WGS (0.27, 95% CI 0.17–0.40, I2 = 54%) and WES (0.17, 95% CI 0.12–0.24, I2 = 76%) were higher than CMA (0.06, 95% CI 0.05–0.07, I2 = 42%); this difference was significant for WGS vs CMA (P < 0.0001). In conclusion, in children with suspected genetic diseases, the diagnostic and clinical utility of WGS/WES were greater than CMA. Subgroups with higher WGS/WES diagnostic utility were trios and those receiving hospital-based interpretation. WGS/WES should be considered a first-line genomic test for children with suspected genetic diseases. Children with suspected genetic disease are more likely to receive a diagnosis when gene sequencing technologies are employed. At present, a microarray test for short pieces of missing or extra chromosomes (chromosomal microarray, CMA) is the recommended test for diagnosing genetic disease in children. The recent use of whole-genome sequencing (WGS) and whole-exome sequencing (WES) for diagnosing genetic disease prompted Stephen Kingsmore at Rady Children’s Institute for Genomic Medicine in San Diego, California, USA, and colleagues to examine the effectiveness of these methods compared with CMA. Analyses of studies comprising over 20,000 children showed that using WGS and WES increased the likelihood of diagnosis and led to a change in inpatient management to prevent or ameliorate adverse health outcomes. The authors advocate the use of WGS or WES as a first-line genomic test for genetic disease in children.
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Affiliation(s)
- Michelle M Clark
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
| | - Zornitza Stark
- 2Murdoch Children's Research Institute, Melbourne, Australia
| | - Lauge Farnaes
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA.,3Department of Pediatrics, University of California San Diego, San Diego, CA USA
| | - Tiong Y Tan
- 2Murdoch Children's Research Institute, Melbourne, Australia.,4Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Susan M White
- 2Murdoch Children's Research Institute, Melbourne, Australia.,4Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
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27
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Anna A, Monika G. Splicing mutations in human genetic disorders: examples, detection, and confirmation. J Appl Genet 2018; 59:253-268. [PMID: 29680930 PMCID: PMC6060985 DOI: 10.1007/s13353-018-0444-7] [Citation(s) in RCA: 381] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 04/08/2018] [Accepted: 04/10/2018] [Indexed: 01/02/2023]
Abstract
Precise pre-mRNA splicing, essential for appropriate protein translation, depends on the presence of consensus "cis" sequences that define exon-intron boundaries and regulatory sequences recognized by splicing machinery. Point mutations at these consensus sequences can cause improper exon and intron recognition and may result in the formation of an aberrant transcript of the mutated gene. The splicing mutation may occur in both introns and exons and disrupt existing splice sites or splicing regulatory sequences (intronic and exonic splicing silencers and enhancers), create new ones, or activate the cryptic ones. Usually such mutations result in errors during the splicing process and may lead to improper intron removal and thus cause alterations of the open reading frame. Recent research has underlined the abundance and importance of splicing mutations in the etiology of inherited diseases. The application of modern techniques allowed to identify synonymous and nonsynonymous variants as well as deep intronic mutations that affected pre-mRNA splicing. The bioinformatic algorithms can be applied as a tool to assess the possible effect of the identified changes. However, it should be underlined that the results of such tests are only predictive, and the exact effect of the specific mutation should be verified in functional studies. This article summarizes the current knowledge about the "splicing mutations" and methods that help to identify such changes in clinical diagnosis.
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Affiliation(s)
- Abramowicz Anna
- Department of Medical Genetics, Institute of Mother and Child, Kasprzaka 17a, 01-211, Warsaw, Poland
| | - Gos Monika
- Department of Medical Genetics, Institute of Mother and Child, Kasprzaka 17a, 01-211, Warsaw, Poland.
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28
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Witchel SF. Disorders of sex development. Best Pract Res Clin Obstet Gynaecol 2018; 48:90-102. [PMID: 29503125 PMCID: PMC5866176 DOI: 10.1016/j.bpobgyn.2017.11.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 12/14/2022]
Abstract
Normal sex development depends on the precise spatio-temporal sequence and coordination of mutually antagonistic activating and repressing factors. These factors regulate the commitment of the unipotential gonad into the binary pathways governing normal sex development. Typically, the presence of the SRY gene on the Y chromosome triggers the cascade of molecular events that lead to male sex development. Disorders of sex development comprise a heterogeneous group of congenital conditions associated with atypical development of internal and external genitalia. These disorders are generally attributed to deviations from the typical progression of sex development. Disorders of sex development can be classified into several categories including chromosomal, gonadal, and anatomic abnormalities. Genetic tools such as microarray analyses and next-generation sequencing techniques have identified novel genetic variants among patients with disorders of sexual development. Most importantly, patient management needs to be individualized, especially for decisions related to sex of rearing, surgical interventions, hormone treatment, and potential for fertility preservation.
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Affiliation(s)
- Selma Feldman Witchel
- Division of Pediatric Endocrinology, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA 15224, USA.
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29
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Petrikin JE, Cakici JA, Clark MM, Willig LK, Sweeney NM, Farrow EG, Saunders CJ, Thiffault I, Miller NA, Zellmer L, Herd SM, Holmes AM, Batalov S, Veeraraghavan N, Smith LD, Dimmock DP, Leeder JS, Kingsmore SF. The NSIGHT1-randomized controlled trial: rapid whole-genome sequencing for accelerated etiologic diagnosis in critically ill infants. NPJ Genom Med 2018; 3:6. [PMID: 29449963 PMCID: PMC5807510 DOI: 10.1038/s41525-018-0045-8] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 01/02/2018] [Accepted: 01/12/2018] [Indexed: 12/31/2022] Open
Abstract
Genetic disorders are a leading cause of morbidity and mortality in infants in neonatal and pediatric intensive care units (NICU/PICU). While genomic sequencing is useful for genetic disease diagnosis, results are usually reported too late to guide inpatient management. We performed an investigator-initiated, partially blinded, pragmatic, randomized, controlled trial to test the hypothesis that rapid whole-genome sequencing (rWGS) increased the proportion of NICU/PICU infants receiving a genetic diagnosis within 28 days. The participants were families with infants aged <4 months in a regional NICU and PICU, with illnesses of unknown etiology. The intervention was trio rWGS. Enrollment from October 2014 to June 2016, and follow-up until November 2016. Of all, 26 female infants, 37 male infants, and 2 infants of undetermined sex were randomized to receive rWGS plus standard genetic tests (n = 32, cases) or standard genetic tests alone (n = 33, controls). The study was terminated early due to loss of equipoise: 73% (24) controls received genomic sequencing as standard tests, and 15% (five) controls underwent compassionate cross-over to receive rWGS. Nevertheless, intention to treat analysis showed the rate of genetic diagnosis within 28 days of enrollment (the primary end-point) to be higher in cases (31%, 10 of 32) than controls (3%, 1 of 33; difference, 28% [95% CI, 10-46%]; p = 0.003). Among infants enrolled in the first 25 days of life, the rate of neonatal diagnosis was higher in cases (32%, 7 of 22) than controls (0%, 0 of 23; difference, 32% [95% CI, 11-53%];p = 0.004). Median age at diagnosis (25 days [range 14-90] in cases vs. 130 days [range 37-451] in controls) and median time to diagnosis (13 days [range 1-84] in cases, vs. 107 days [range 21-429] in controls) were significantly less in cases than controls (p = 0.04). In conclusion, rWGS increased the proportion of NICU/PICU infants who received timely diagnoses of genetic diseases.
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Affiliation(s)
- Josh E. Petrikin
- Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO 64108 USA
- Department of Pediatrics, Children’s Mercy, Kansas City, MO 64108 USA
- School of Medicine, University of Missouri, Kansas City, MO 64108 USA
| | - Julie A. Cakici
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Michelle M. Clark
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Laurel K. Willig
- Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO 64108 USA
- Department of Pediatrics, Children’s Mercy, Kansas City, MO 64108 USA
- School of Medicine, University of Missouri, Kansas City, MO 64108 USA
| | - Nathaly M. Sweeney
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
- Department of Pediatrics, University of California, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Emily G. Farrow
- Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO 64108 USA
- Department of Pediatrics, Children’s Mercy, Kansas City, MO 64108 USA
- School of Medicine, University of Missouri, Kansas City, MO 64108 USA
| | - Carol J. Saunders
- Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO 64108 USA
- School of Medicine, University of Missouri, Kansas City, MO 64108 USA
- Department of Pathology, Children’s Mercy, Kansas City, MO 64108 USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO 64108 USA
- School of Medicine, University of Missouri, Kansas City, MO 64108 USA
- Department of Pathology, Children’s Mercy, Kansas City, MO 64108 USA
| | - Neil A. Miller
- Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO 64108 USA
| | - Lee Zellmer
- Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO 64108 USA
| | - Suzanne M. Herd
- Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO 64108 USA
| | - Anne M. Holmes
- Department of Pediatrics, Children’s Mercy, Kansas City, MO 64108 USA
| | - Serge Batalov
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | | | - Laurie D. Smith
- Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO 64108 USA
- School of Medicine, University of Missouri, Kansas City, MO 64108 USA
- Department of Pediatrics, University of North Carolina, Chapel Hill, NC 27599 USA
| | - David P. Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - J. Steven Leeder
- Department of Pediatrics, Children’s Mercy, Kansas City, MO 64108 USA
- School of Medicine, University of Missouri, Kansas City, MO 64108 USA
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30
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Ono H, Saitsu H, Horikawa R, Nakashima S, Ohkubo Y, Yanagi K, Nakabayashi K, Fukami M, Fujisawa Y, Ogata T. Partial androgen insensitivity syndrome caused by a deep intronic mutation creating an alternative splice acceptor site of the AR gene. Sci Rep 2018; 8:2287. [PMID: 29396419 PMCID: PMC5797100 DOI: 10.1038/s41598-018-20691-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 01/23/2018] [Indexed: 11/16/2022] Open
Abstract
Although partial androgen insensitivity syndrome (PAIS) is caused by attenuated responsiveness to androgens, androgen receptor gene (AR) mutations on the coding regions and their splice sites have been identified only in <25% of patients with a diagnosis of PAIS. We performed extensive molecular studies including whole exome sequencing in a Japanese family with PAIS, identifying a deep intronic variant beyond the branch site at intron 6 of AR (NM_000044.4:c.2450−42 G > A). This variant created the splice acceptor motif that was accompanied by pyrimidine-rich sequence and two candidate branch sites. Consistent with this, reverse transcriptase (RT)-PCR experiments for cycloheximide-treated lymphoblastoid cell lines revealed a relatively large amount of aberrant mRNA produced by the newly created splice acceptor site and a relatively small amount of wildtype mRNA produced by the normal splice acceptor site. Furthermore, most of the aberrant mRNA was shown to undergo nonsense mediated decay (NMD) and, if a small amount of aberrant mRNA may have escaped NMD, such mRNA was predicted to generate a truncated AR protein missing some functional domains. These findings imply that the deep intronic mutation creating an alternative splice acceptor site resulted in the production of a relatively small amount of wildtype AR mRNA, leading to PAIS.
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Affiliation(s)
- Hiroyuki Ono
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Reiko Horikawa
- Division of Endocrinology and Metabolism, National Medical Center for Children and Mother, Tokyo, Japan
| | - Shinichi Nakashima
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yumiko Ohkubo
- Department of Pediatrics, Shizuoka Saiseikai Hospital, Shizuoka, Japan
| | - Kumiko Yanagi
- Department of Genome Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yasuko Fujisawa
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan. .,Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.
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Konrade I, Zavorikina J, Fridvalde A, Rots D, Kalere I, Strumfa I, Dambrova M, Gailite L. Novel Variant of the Androgen Receptor Gene in a Patient With Complete Androgen Insensitivity Syndrome and Polyorchidism. Front Endocrinol (Lausanne) 2018; 9:795. [PMID: 30705665 PMCID: PMC6345100 DOI: 10.3389/fendo.2018.00795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/18/2018] [Indexed: 11/13/2022] Open
Abstract
Introduction: Complete androgen insensitivity (CAIS) in 65-95% cases is caused by pathogenic allelic variants (mutations) in the gene encoding androgen receptor (AR gene) and is characterized by female phenotype development with a male karyotype (46, XY). Patients are usually diagnosed during puberty and undergo gonadectomy due to increased testicular germ cell tumor risk. Only a few outcomes have been reported in older individuals with postponed gonadectomy. Case presentation: A 48-year-old CAIS patient presented with polyorchidism (four testes) without gonadal malignancies. Genetic testing identified a novel allelic variant in the AR gene [c.2141T>G (p.Phe805Cys)] causing the clinical symptoms. Conclusion: We have described a unique patient with CAIS and polyorchidism without malignancies in her late 40's bearing a novel likely pathogenic variant in the AR gene.
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Affiliation(s)
- Ilze Konrade
- Department of Internal Medicine, Riga Stradins University, Riga, Latvia
- Department of Endocrinology, Riga East University Hospital, Riga, Latvia
| | - Julija Zavorikina
- Department of Internal Medicine, Riga Stradins University, Riga, Latvia
| | - Aija Fridvalde
- Department of Internal Medicine, Riga Stradins University, Riga, Latvia
| | - Dmitrijs Rots
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Riga, Latvia
| | - Ieva Kalere
- Department of Pharmacy, Riga Stradins University, Riga, Latvia
| | - Ilze Strumfa
- Department of Pathology, Riga Stradins University, Riga, Latvia
| | - Maija Dambrova
- Department of Human Physiology and Biochemistry, Riga Stradins University, Riga, Latvia
| | - Linda Gailite
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Riga, Latvia
- *Correspondence: Linda Gailite
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Clark MM, Stark Z, Farnaes L, Tan TY, White SM, Dimmock D, Kingsmore SF. Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases. NPJ Genom Med 2018; 3:16. [PMID: 30002876 DOI: 10.1101/255299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/30/2018] [Accepted: 05/10/2018] [Indexed: 05/22/2023] Open
Abstract
Genetic diseases are leading causes of childhood mortality. Whole-genome sequencing (WGS) and whole-exome sequencing (WES) are relatively new methods for diagnosing genetic diseases, whereas chromosomal microarray (CMA) is well established. Here we compared the diagnostic utility (rate of causative, pathogenic, or likely pathogenic genotypes in known disease genes) and clinical utility (proportion in whom medical or surgical management was changed by diagnosis) of WGS, WES, and CMA in children with suspected genetic diseases by systematic review of the literature (January 2011-August 2017) and meta-analysis, following MOOSE/PRISMA guidelines. In 37 studies, comprising 20,068 children, diagnostic utility of WGS (0.41, 95% CI 0.34-0.48, I2 = 44%) and WES (0.36, 95% CI 0.33-0.40, I2 = 83%) were qualitatively greater than CMA (0.10, 95% CI 0.08-0.12, I2 = 81%). Among studies published in 2017, the diagnostic utility of WGS was significantly greater than CMA (P < 0.0001, I2 = 13% and I2 = 40%, respectively). Among studies featuring within-cohort comparisons, the diagnostic utility of WES was significantly greater than CMA (P < 0.001, I2 = 36%). The diagnostic utility of WGS and WES were not significantly different. In studies featuring within-cohort comparisons of WGS/WES, the likelihood of diagnosis was significantly greater for trios than singletons (odds ratio 2.04, 95% CI 1.62-2.56, I2 = 12%; P < 0.0001). Diagnostic utility of WGS/WES with hospital-based interpretation (0.42, 95% CI 0.38-0.45, I2 = 48%) was qualitatively higher than that of reference laboratories (0.29, 95% CI 0.27-0.31, I2 = 49%); this difference was significant among studies published in 2017 (P < .0001, I2 = 22% and I2 = 26%, respectively). The clinical utility of WGS (0.27, 95% CI 0.17-0.40, I2 = 54%) and WES (0.17, 95% CI 0.12-0.24, I2 = 76%) were higher than CMA (0.06, 95% CI 0.05-0.07, I2 = 42%); this difference was significant for WGS vs CMA (P < 0.0001). In conclusion, in children with suspected genetic diseases, the diagnostic and clinical utility of WGS/WES were greater than CMA. Subgroups with higher WGS/WES diagnostic utility were trios and those receiving hospital-based interpretation. WGS/WES should be considered a first-line genomic test for children with suspected genetic diseases.
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Affiliation(s)
- Michelle M Clark
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
| | - Zornitza Stark
- 2Murdoch Children's Research Institute, Melbourne, Australia
| | - Lauge Farnaes
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
- 3Department of Pediatrics, University of California San Diego, San Diego, CA USA
| | - Tiong Y Tan
- 2Murdoch Children's Research Institute, Melbourne, Australia
- 4Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Susan M White
- 2Murdoch Children's Research Institute, Melbourne, Australia
- 4Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
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Rath M, Jenssen SE, Schwefel K, Spiegler S, Kleimeier D, Sperling C, Kaderali L, Felbor U. High-throughput sequencing of the entire genomic regions of CCM1/KRIT1 , CCM2 and CCM3/PDCD10 to search for pathogenic deep-intronic splice mutations in cerebral cavernous malformations. Eur J Med Genet 2017. [DOI: 10.1016/j.ejmg.2017.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Ahmad Z, Xing C, Panach K, Kittler R, McPhaul MJ, Wilson JD. Identification of the Underlying Androgen Receptor Defect in the Dallas Reifenstein Family. J Endocr Soc 2017; 1:836-842. [PMID: 29264534 PMCID: PMC5686667 DOI: 10.1210/js.2017-00124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/16/2017] [Indexed: 11/19/2022] Open
Abstract
CONTEXT The Dallas Reifenstein family - first described in 1965 - includes 14 known members with partial androgen insensitivity syndrome (PAIS). However, the underlying molecular defect was never identified. OBJECTIVE To identify the underlying genetic defect for PAIS in the Dallas Reifenstein family. DESIGN DNA was purified from scrotal skin fibroblasts, and whole exome sequencing was then performed in four affected men in the family. Additional family members - both affected and unaffected - were subsequently recruited to confirm segregation of the candidate mutations with the PAIS phenotype. PATIENTS The affected men have PAIS with infertility associated with azoospermia, hypospadias, and gynecomastia. RESULTS All four men harbored an intronic variant NC_000023.10:g.66788676A>C between exon 1 and exon 2 of the androgen receptor (AR) canonical transcript NM_000044 (complementary DNA position NM_000044: c.1616+22072A>C) predicted to cause an alternatively spliced AR transcript. Reverse transcription (RT) polymerase chain (PCR) experiments detected the predicted PCR product of the alternatively spliced AR transcript, and the mutation segregated with the PAIS phenotype in this family. The transcript includes the insertion of 185 nucleotides with a premature stop codon at chrX:66863131-66863133, likely resulting in a reduction in AR protein expression due to nonsense-mediated decay. CONCLUSIONS An intronic AR mutation was identified in the Dallas Reifenstein family. The findings suggest that in cases of PAIS without identifiable AR mutations in coding regions, intronic AR mutations should be considered.
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Affiliation(s)
- Zahid Ahmad
- Division of Nutrition and Metabolic Diseases, Center for Human Nutrition, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Chao Xing
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Kamaldeep Panach
- Division of Endocrinology and Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Ralf Kittler
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Michael J. McPhaul
- Division of Endocrinology and Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas 75390
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California 92665
| | - Jean D. Wilson
- Division of Endocrinology and Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas 75390
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Baetens D, Mendonça BB, Verdin H, Cools M, De Baere E. Non-coding variation in disorders of sex development. Clin Genet 2017; 91:163-172. [PMID: 27801941 DOI: 10.1111/cge.12911] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/27/2016] [Accepted: 10/27/2016] [Indexed: 01/26/2023]
Abstract
Genetic studies in Disorders of Sex Development (DSD), representing a wide spectrum of developmental or functional conditions of the gonad, have mainly been oriented towards the coding genome. Application of genomic technologies, such as whole-exome sequencing, result in a molecular genetic diagnosis in ∼50% of cases with DSD. Many of the genes mutated in DSD encode transcription factors such as SRY, SOX9, NR5A1, and FOXL2, characterized by a strictly regulated spatiotemporal expression. Hence, it can be hypothesized that at least part of the missing genetic variation in DSD can be explained by non-coding mutations in regulatory elements that alter gene expression, either by reduced, mis- or overexpression of their target genes. In addition, structural variations such as translocations, deletions, duplications or inversions can affect the normal chromatin conformation by different mechanisms. Here, we review non-coding defects in human DSD phenotypes and in animal models. The wide variety of non-coding defects found in DSD emphasizes that the regulatory landscape of known and to be discovered DSD genes has to be taken into consideration when investigating the molecular pathogenesis of DSD.
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Affiliation(s)
- D Baetens
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - B B Mendonça
- Laboratório de Hormônios e Genética Molecular, LIM/42, Unidade de Adrenal, Disc. de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - H Verdin
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - M Cools
- Department of Pediatrics, Division of Pediatric Endocrinology, Ghent University Hospital and Ghent University, Ghent, Belgium
| | - E De Baere
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
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Clinically Focused Molecular Investigation of 1000 Consecutive Families with Inherited Retinal Disease. Ophthalmology 2017; 124:1314-1331. [PMID: 28559085 DOI: 10.1016/j.ophtha.2017.04.008] [Citation(s) in RCA: 285] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 12/30/2022] Open
Abstract
PURPOSE To devise a comprehensive multiplatform genetic testing strategy for inherited retinal disease and to describe its performance in 1000 consecutive families seen by a single clinician. DESIGN Retrospective series. PARTICIPANTS One thousand consecutive families seen by a single clinician. METHODS The clinical records of all patients seen by a single retina specialist between January 2010 and June 2016 were reviewed, and all patients who met the clinical criteria for a diagnosis of inherited retinal disease were included in the study. Each patient was assigned to 1 of 62 diagnostic categories, and this clinical diagnosis was used to define the scope and order of the molecular investigations that were performed. The number of nucleotides evaluated in a given subject ranged from 2 to nearly 900 000. MAIN OUTCOME MEASURES Sensitivity and false genotype rate. RESULTS Disease-causing genotypes were identified in 760 families (76%). These genotypes were distributed across 104 different genes. More than 75% of these 104 genes have coding sequences small enough to be packaged efficiently into an adeno-associated virus. Mutations in ABCA4 were the most common cause of disease in this cohort (173 families), whereas mutations in 80 genes caused disease in 5 or fewer families (i.e., 0.5% or less). Disease-causing genotypes were identified in 576 of the families without next-generation sequencing (NGS). This included 23 families with mutations in the repetitive region of RPGR exon 15 that would have been missed by NGS. Whole-exome sequencing of the remaining 424 families revealed mutations in an additional 182 families, and whole-genome sequencing of 4 of the remaining 242 families revealed 2 additional genotypes that were invisible by the other methods. Performing the testing in a clinically focused tiered fashion would be 6.1% more sensitive and 17.7% less expensive and would have a significantly lower average false genotype rate than using whole-exome sequencing to assess more than 300 genes in all patients (7.1% vs. 128%; P < 0.001). CONCLUSIONS Genetic testing for inherited retinal disease is now more than 75% sensitive. A clinically directed tiered testing strategy can increase sensitivity and improve statistical significance without increasing cost.
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Deep intronic mutations and human disease. Hum Genet 2017; 136:1093-1111. [DOI: 10.1007/s00439-017-1809-4] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/05/2017] [Indexed: 12/22/2022]
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