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Berres S, Gromoll J, Wöste M, Sandmann S, Laurentino S. OGRE: calculate, visualize, and analyze overlap between genomic input regions and public annotations. BMC Bioinformatics 2023; 24:300. [PMID: 37496002 PMCID: PMC10369718 DOI: 10.1186/s12859-023-05422-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/18/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND Modern genome sequencing leads to an ever-growing collection of genomic annotations. Combining these elements with a set of input regions (e.g. genes) would yield new insights in genomic associations, such as those involved in gene regulation. The required data are scattered across different databases making a manual approach tiresome, unpractical, and prone to error. Semi-automatic approaches require programming skills in data parsing, processing, overlap calculation, and visualization, which most biomedical researchers lack. Our aim was to develop an automated tool providing all necessary algorithms, benefiting both bioinformaticians and researchers without bioinformatic training. RESULTS We developed overlapping annotated genomic regions (OGRE) as a comprehensive tool to associate and visualize input regions with genomic annotations. It does so by parsing regions of interest, mining publicly available annotations, and calculating possible overlaps between them. The user can thus identify location, type, and number of associated regulatory elements. Results are presented as easy to understand visualizations and result tables. We applied OGRE to recent studies and could show high reproducibility and potential new insights. To demonstrate OGRE's performance in terms of running time and output, we have conducted a benchmark and compared its features with similar tools. CONCLUSIONS OGRE's functions and built-in annotations can be applied as a downstream overlap association step, which is compatible with most genomic sequencing outputs, and can thus enrich pre-existing analyses pipelines. Compared to similar tools, OGRE shows competitive performance, offers additional features, and has been successfully applied to two recent studies. Overall, OGRE addresses the lack of tools for automatic analysis, local genomic overlap calculation, and visualization by providing an easy to use, end-to-end solution for both biologists and computational scientists.
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Affiliation(s)
- Sven Berres
- Centre of Reproductive Medicine and Andrology, University of Münster, Albert-Schweitzer-Campus 1 Building D11, 48149, Munster, Germany
| | - Jörg Gromoll
- Centre of Reproductive Medicine and Andrology, University of Münster, Albert-Schweitzer-Campus 1 Building D11, 48149, Munster, Germany
| | - Marius Wöste
- Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1 Building A11, 48149, Munster, Germany
| | - Sarah Sandmann
- Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1 Building A11, 48149, Munster, Germany
| | - Sandra Laurentino
- Centre of Reproductive Medicine and Andrology, University of Münster, Albert-Schweitzer-Campus 1 Building D11, 48149, Munster, Germany.
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Siebert-Kuss LM, Krenz H, Tekath T, Wöste M, Di Persio S, Terwort N, Wyrwoll MJ, Cremers JF, Wistuba J, Dugas M, Kliesch S, Schlatt S, Tüttelmann F, Gromoll J, Neuhaus N, Laurentino S. Transcriptome analyses in infertile men reveal germ cell-specific expression and splicing patterns. Life Sci Alliance 2023; 6:6/2/e202201633. [PMID: 36446526 PMCID: PMC9713473 DOI: 10.26508/lsa.202201633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/30/2022] Open
Abstract
The process of spermatogenesis-when germ cells differentiate into sperm-is tightly regulated, and misregulation in gene expression is likely to be involved in the physiopathology of male infertility. The testis is one of the most transcriptionally rich tissues; nevertheless, the specific gene expression changes occurring during spermatogenesis are not fully understood. To better understand gene expression during spermatogenesis, we generated germ cell-specific whole transcriptome profiles by systematically comparing testicular transcriptomes from tissues in which spermatogenesis is arrested at successive steps of germ cell differentiation. In these comparisons, we found thousands of differentially expressed genes between successive germ cell types of infertility patients. We demonstrate our analyses' potential to identify novel highly germ cell-specific markers (TSPY4 and LUZP4 for spermatogonia; HMGB4 for round spermatids) and identified putatively misregulated genes in male infertility (RWDD2A, CCDC183, CNNM1, SERF1B). Apart from these, we found thousands of genes showing germ cell-specific isoforms (including SOX15, SPATA4, SYCP3, MKI67). Our approach and dataset can help elucidate genetic and transcriptional causes for male infertility.
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Affiliation(s)
- Lara M Siebert-Kuss
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University of Münster, Münster, Germany
| | - Henrike Krenz
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Tobias Tekath
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Marius Wöste
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Sara Di Persio
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University of Münster, Münster, Germany
| | - Nicole Terwort
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University of Münster, Münster, Germany
| | - Margot J Wyrwoll
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Jann-Frederik Cremers
- Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital of Münster, Münster, Germany
| | - Joachim Wistuba
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University of Münster, Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster, Germany.,Institute of Medical Informatics, Heidelberg University Hospital, Heidelberg, Germany
| | - Sabine Kliesch
- Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital of Münster, Münster, Germany
| | - Stefan Schlatt
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University of Münster, Münster, Germany
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Jörg Gromoll
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University of Münster, Münster, Germany
| | - Nina Neuhaus
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University of Münster, Münster, Germany
| | - Sandra Laurentino
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University of Münster, Münster, Germany
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Wyrwoll MJ, Wabschke R, Röpke A, Wöste M, Ruckert C, Perrey S, Rotte N, Hardy J, Astica L, Lupiáñez DG, Wistuba J, Westernströer B, Schlatt S, Berman AJ, Müller AM, Kliesch S, Yatsenko AN, Tüttelmann F, Friedrich C. Analysis of copy number variation in men with non-obstructive azoospermia. Andrology 2022; 10:1593-1604. [PMID: 36041235 PMCID: PMC9605881 DOI: 10.1111/andr.13267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Recent findings demonstrate that single nucleotide variants can cause non-obstructive azoospermia (NOA). In contrast, copy number variants (CNVs) were only analysed in few studies in infertile men. Some have reported a higher prevalence of CNVs in infertile versus fertile men. OBJECTIVES This study aimed to elucidate if CNVs are associated with NOA. MATERIALS AND METHODS We performed array-based comparative genomic hybridisation (aCGH) in 37 men with meiotic arrest, 194 men with Sertoli cell-only phenotype, and 21 control men. We filtered our data for deletions affecting genes and prioritised the affected genes according to the literature search. Prevalence of CNVs was compared between all groups. Exome data of 2,030 men were screened to detect further genetic variants in prioritised genes. Modelling was performed for the protein encoded by the novel candidate gene TEKT5 and we stained for TEKT5 in human testicular tissue. RESULTS We determined the cause of infertility in two individuals with homozygous deletions of SYCE1 and in one individual with a heterozygous deletion of SYCE1 combined with a likely pathogenic missense variant on the second allele. We detected heterozygous deletions affecting MLH3, EIF2B2, SLX4, CLPP and TEKT5, in one subject each. CNVs were not detected more frequently in infertile men compared with controls. DISCUSSION While SYCE1 and MLH3 encode known meiosis-specific proteins, much less is known about the proteins encoded by the other identified candidate genes, warranting further analyses. We were able to identify the cause of infertility in one out of the 231 infertile men by aCGH and in two men by using exome sequencing data. CONCLUSION As aCGH and exome sequencing are both expensive methods, combining both in a clinical routine is not an effective strategy. Instead, using CNV calling from exome data has recently become more precise, potentially making aCGH dispensable.
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Affiliation(s)
- M. J. Wyrwoll
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - R. Wabschke
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - A. Röpke
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - M. Wöste
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - C. Ruckert
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - S. Perrey
- Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, Recklinghausen, Germany
| | - N. Rotte
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - J. Hardy
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Women Research Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - L. Astica
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - D. G. Lupiáñez
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - J. Wistuba
- Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - B. Westernströer
- Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - S. Schlatt
- Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - A. J. Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - A. M. Müller
- Practice for Pathology and Centre for Pediatric Pathology, University Hospital of Cologne, Cologne, Germany
| | - S. Kliesch
- Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - A. N. Yatsenko
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Women Research Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - F. Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - C. Friedrich
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
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Schubert M, Pérez Lanuza L, Wöste M, Dugas M, Carmona FD, Palomino-Morales RJ, Rassam Y, Heilmann-Heimbach S, Tüttelmann F, Kliesch S, Gromoll J. A GWAS in Idiopathic/Unexplained Infertile Men Detects a Genomic Region Determining Follicle-Stimulating Hormone Levels. J Clin Endocrinol Metab 2022; 107:2350-2361. [PMID: 35305013 PMCID: PMC9282256 DOI: 10.1210/clinem/dgac165] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Indexed: 11/19/2022]
Abstract
CONTEXT Approximately 70% of infertile men are diagnosed with idiopathic (abnormal semen parameters) or unexplained (normozoospermia) infertility, with the common feature of lacking etiologic factors. Follicle-stimulating hormone (FSH) is essential for initiation and maintenance of spermatogenesis. Certain single-nucleotide variations (SNVs; formerly single-nucleotide polymorphisms [SNPs]) (ie, FSHB c.-211G > T, FSHR c.2039A > G) are associated with FSH, testicular volume, and spermatogenesis. It is unknown to what extent other variants are associated with FSH levels and therewith resemble causative factors for infertility. OBJECTIVE We aimed to identify further genetic determinants modulating FSH levels in a cohort of men presenting with idiopathic or unexplained infertility. METHODS We retrospectively (2010-2018) selected 1900 men with idiopathic/unexplained infertility. In the discovery study (n = 760), a genome-wide association study (GWAS) was performed (Infinium PsychArrays) in association with FSH values (Illumina GenomeStudio, v2.0). Minor allele frequencies (MAFs) were analyzed for the discovery and an independent normozoospermic cohort. In the validation study (n = 1140), TaqMan SNV polymerase chain reaction was conducted for rs11031005 and rs10835638 in association with andrological parameters. RESULTS Imputation revealed 9 SNVs in high linkage disequilibrium, with genome-wide significance (P < 4.28e-07) at the FSHB locus 11p.14.1 being associated with FSH. The 9 SNVs accounted for up to a 4.65% variance in FSH level. In the oligozoospermic subgroup, this was increased up to 6.95% and the MAF was enhanced compared to an independent cohort of normozoospermic men. By validation, a significant association for rs11031005/rs10835638 with FSH (P = 4.71e-06/5.55e-07) and FSH/luteinizing hormone ratio (P = 2.08e-12/6.4e-12) was evident. CONCLUSIONS This GWAS delineates the polymorphic FSHB genomic region as the main determinant of FSH levels in men with unexplained or idiopathic infertility. Given the essential role of FSH, molecular detection of one of the identified SNVs that causes lowered FSH and therewith decreases spermatogenesis could resolve the idiopathic/unexplained origin by this etiologic factor.
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Affiliation(s)
| | | | - Marius Wöste
- Institute of Medical Informatics, University of Münster, Münster, North Rhine-Westphalia 48149, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster, North Rhine-Westphalia 48149, Germany
- Institute of Medical Informatics, Heidelberg University Hospital, D-69120 Heidelberg, Germany
| | - F David Carmona
- Department of Genetics and Institute of Biotechnology, University of Granada, Granada, Andalusia 18016, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Andalusia 18012, Spain
| | - Rogelio J Palomino-Morales
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Andalusia 18012, Spain
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Granada, Andalusia 18071, Spain
| | - Yousif Rassam
- Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University of Münster, Münster, North Rhine-Westphalia 48149, Germany
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital, Bonn, North Rhine-Westphalia 53127, Germany
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, North Rhine-Westphalia 48149, Germany
| | - Sabine Kliesch
- Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University of Münster, Münster, North Rhine-Westphalia 48149, Germany
| | - Jörg Gromoll
- Correspondence: Jörg Gromoll, Dr. rer. nat., Institute of Reproductive and Regenerative Biology, Centre of Reproductive Medicine and Andrology, University of Münster, Albert-Schweitzer-Campus 1, Geb. D11, 48149 Münster, Germany.
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5
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Wyrwoll MJ, Köckerling N, Vockel M, Dicke AK, Rotte N, Pohl E, Emich J, Wöste M, Ruckert C, Wabschke R, Seggewiss J, Ledig S, Tewes AC, Stratis Y, Cremers JF, Wistuba J, Krallmann C, Kliesch S, Röpke A, Stallmeyer B, Friedrich C, Tüttelmann F. Genetic Architecture of Azoospermia-Time to Advance the Standard of Care. Eur Urol 2022; 83:452-462. [PMID: 35690514 DOI: 10.1016/j.eururo.2022.05.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/26/2022] [Accepted: 05/17/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND Crypto- and azoospermia (very few/no sperm in the semen) are main contributors to male factor infertility. Genetic causes for spermatogenic failure (SPGF) include Klinefelter syndrome and Y-chromosomal azoospermia factor microdeletions, and CFTR mutations for obstructive azoospermia (OA). However, the majority of cases remain unexplained because monogenic causes are not analysed. OBJECTIVE To elucidate the monogenic contribution to azoospermia by prospective exome sequencing and strict application of recent clinical guidelines. DESIGN, SETTING, AND PARTICIPANTS Since January 2017, we studied crypto- and azoospermic men without chromosomal aberrations and Y-chromosomal microdeletions attending the Centre of Reproductive Medicine and Andrology, Münster. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS We performed exome sequencing in 647 men, analysed 60 genes having at least previous limited clinical validity, and strictly assessed variants according to clinical guidelines. RESULTS AND LIMITATIONS Overall, 55 patients (8.5%) with diagnostic genetic variants were identified. Of these patients, 20 (3.1%) carried mutations in CFTR or ADGRG2, and were diagnosed with OA. In 35 patients (5.4%) with SPGF, mutations in 20 different genes were identified. According to ClinGen criteria, 19 of the SPGF genes now reach at least moderate clinical validity. As limitations, only one transcript per gene was considered, and the list of genes is increasing rapidly so cannot be exhaustive. CONCLUSIONS The number of diagnostic genes in crypto-/azoospermia was almost doubled to 21 using exome-based analyses and clinical guidelines. Application of this procedure in routine diagnostics will significantly improve the diagnostic yield and clinical workup as the results indicate the success rate of testicular sperm extraction. PATIENT SUMMARY When no sperm are found in the semen, a man cannot conceive naturally. The causes are often unknown, but genetics play a major role. We searched for genetic variants in a large group of patients and found causal mutations for one in 12 men; these predict the chances for fatherhood.
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Affiliation(s)
- Margot J Wyrwoll
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Nils Köckerling
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Matthias Vockel
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - Ann-Kristin Dicke
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Nadja Rotte
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Eva Pohl
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Jana Emich
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Marius Wöste
- Institute of Medical Informatics, University Hospital Münster, Münster, Germany
| | - Christian Ruckert
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - Rebecca Wabschke
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Jochen Seggewiss
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - Susanne Ledig
- Institute of Human Genetics, University of Münster, Münster, Germany
| | | | - Yvonne Stratis
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - Jann F Cremers
- Centre of Reproductive Medicine and Andrology (CeRA), University Hospital Münster, Münster, Germany
| | - Joachim Wistuba
- Centre of Reproductive Medicine and Andrology (CeRA), University Hospital Münster, Münster, Germany
| | - Claudia Krallmann
- Centre of Reproductive Medicine and Andrology (CeRA), University Hospital Münster, Münster, Germany
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology (CeRA), University Hospital Münster, Münster, Germany
| | - Albrecht Röpke
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - Birgit Stallmeyer
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Corinna Friedrich
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany.
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Wyrwoll MJ, van Walree ES, Hamer G, Rotte N, Motazacker MM, Meijers-Heijboer H, Alders M, Meißner A, Kaminsky E, Wöste M, Krallmann C, Kliesch S, Hunt TJ, Clark AT, Silber S, Stallmeyer B, Friedrich C, van Pelt AMM, Mathijssen IB, Tüttelmann F. Bi-allelic variants in DNA mismatch repair proteins MutS Homolog MSH4 and MSH5 cause infertility in both sexes. Hum Reprod 2021; 37:178-189. [PMID: 34755185 DOI: 10.1093/humrep/deab230] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/27/2021] [Indexed: 11/14/2022] Open
Abstract
STUDY QUESTION Do bi-allelic variants in the genes encoding the MSH4/MSH5 heterodimer cause male infertility? SUMMARY ANSWER We detected biallelic, (likely) pathogenic variants in MSH5 (4 men) and MSH4 (3 men) in six azoospermic men, demonstrating that genetic variants in these genes are a relevant cause of male infertility. WHAT IS KNOWN ALREADY MSH4 and MSH5 form a heterodimer, which is required for prophase of meiosis I. One variant in MSH5 and two variants in MSH4 have been described as causal for premature ovarian insufficiency (POI) in a total of five women, resulting in infertility. Recently, pathogenic variants in MSH4 have been reported in infertile men. So far, no pathogenic variants in MSH5 had been described in males. STUDY DESIGN, SIZE, DURATION We utilized exome data from 1305 men included in the Male Reproductive Genomics (MERGE) study, including 90 males with meiotic arrest (MeiA). Independently, exome sequencing was performed in a man with MeiA from a large consanguineous family. PARTICIPANTS/MATERIALS, SETTING, METHODS Assuming an autosomal-recessive mode of inheritance, we screened the exome data for rare, biallelic coding variants in MSH4 and MSH5. If possible, segregation analysis in the patients' families was performed. The functional consequences of identified loss-of-function (LoF) variants in MSH5 were studied using heterologous expression of the MSH5 protein in HEK293T cells. The point of arrest during meiosis was determined by γH2AX staining. MAIN RESULTS AND THE ROLE OF CHANCE We report for the first time (likely) pathogenic, homozygous variants in MSH5 causing infertility in 2 out of 90 men with MeiA and overall in 4 out of 902 azoospermic men. Additionally, we detected biallelic variants in MSH4 in two men with MeiA and in the sister of one proband with POI. γH2AX staining revealed an arrest in early prophase of meiosis I in individuals with pathogenic MSH4 or MSH5 variants. Heterologous in vitro expression of the detected LoF variants in MSH5 showed that the variant p.(Ala620GlnTer9) resulted in MSH5 protein truncation and the variant p.(Ser26GlnfsTer42) resulted in a complete loss of MSH5. LARGE SCALE DATA All variants have been submitted to ClinVar (SCV001468891-SCV001468896 and SCV001591030) and can also be accessed in the Male Fertility Gene Atlas (MFGA). LIMITATIONS, REASONS FOR CAUTION By selecting for variants in MSH4 and MSH5, we were able to determine the cause of infertility in six men and one woman, leaving most of the examined individuals without a causal diagnosis. WIDER IMPLICATIONS OF THE FINDINGS Our findings have diagnostic value by increasing the number of genes associated with non-obstructive azoospermia with high clinical validity. The analysis of such genes has prognostic consequences for assessing whether men with azoospermia would benefit from a testicular biopsy. We also provide further evidence that MeiA in men and POI in women share the same genetic causes. STUDY FUNDING/COMPETING INTEREST(S) This study was carried out within the frame of the German Research Foundation sponsored Clinical Research Unit 'Male Germ Cells: from Genes to Function' (DFG, CRU326), and supported by institutional funding of the Research Institute Amsterdam Reproduction and Development and funds from the LucaBella Foundation. The authors declare no conflict of interest.
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Affiliation(s)
- M J Wyrwoll
- Institute of Reproductive Genetics, University of Münster, Münster, Germany.,Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - E S van Walree
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands
| | - G Hamer
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Research Institute Amsterdam Reproduction and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - N Rotte
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - M M Motazacker
- Laboratory of Genome Diagnostics, Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - H Meijers-Heijboer
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - M Alders
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - A Meißner
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - E Kaminsky
- Praxis für Humangenetik, Hamburg, Germany
| | - M Wöste
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - C Krallmann
- Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - S Kliesch
- Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - T J Hunt
- Department of Molecular, Cell and Developmental Biology, Los Angeles, CA, USA
| | - A T Clark
- Department of Molecular, Cell and Developmental Biology, Los Angeles, CA, USA
| | - S Silber
- Infertility Center of St Louis, St Luke's Hospital, St Louis, MO, USA
| | - B Stallmeyer
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - C Friedrich
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - A M M van Pelt
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Research Institute Amsterdam Reproduction and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - I B Mathijssen
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - F Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
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7
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Di Persio S, Leitão E, Wöste M, Tekath T, Cremers JF, Dugas M, Li X, Meyer Zu Hörste G, Kliesch S, Laurentino S, Neuhaus N, Horsthemke B. Whole-genome methylation analysis of testicular germ cells from cryptozoospermic men points to recurrent and functionally relevant DNA methylation changes. Clin Epigenetics 2021; 13:160. [PMID: 34419158 PMCID: PMC8379757 DOI: 10.1186/s13148-021-01144-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/01/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Several studies have reported an association between male infertility and aberrant sperm DNA methylation patterns, in particular in imprinted genes. In a recent investigation based on whole methylome and deep bisulfite sequencing, we have not found any evidence for such an association, but have demonstrated that somatic DNA contamination and genetic variation confound methylation studies in sperm of severely oligozoospermic men. To find out whether testicular germ cells (TGCs) of such patients might carry aberrant DNA methylation, we compared the TGC methylomes of four men with cryptozoospermia (CZ) and four men with obstructive azoospermia, who had normal spermatogenesis and served as controls (CTR). RESULTS There was no difference in DNA methylation at the whole genome level or at imprinted regions between CZ and CTR samples. However, using stringent filters to identify group-specific methylation differences, we detected 271 differentially methylated regions (DMRs), 238 of which were hypermethylated in CZ (binominal test, p < 2.2 × 10-16). The DMRs were enriched for distal regulatory elements (p = 1.0 × 10-6) and associated with 132 genes, 61 of which are differentially expressed at various stages of spermatogenesis. Almost all of the 67 DMRs associated with the 61 genes (94%) are hypermethylated in CZ (63/67, p = 1.107 × 10-14). As judged by single-cell RNA sequencing, 13 DMR-associated genes, which are mainly expressed during meiosis and spermiogenesis, show a significantly different pattern of expression in CZ patients. In four of these genes, the promoter is hypermethylated in CZ men, which correlates with a lower expression level in these patients. In the other nine genes, eight of which downregulated in CZ, germ cell-specific enhancers may be affected. CONCLUSIONS We found that impaired spermatogenesis is associated with DNA methylation changes in testicular germ cells at functionally relevant regions of the genome. We hypothesize that the described DNA methylation changes may reflect or contribute to premature abortion of spermatogenesis and therefore not appear in the mature, motile sperm.
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Affiliation(s)
- Sara Di Persio
- Centre of Reproductive Medicine and Andrology, University Hospital of Münster, 48149, Münster, Germany
| | - Elsa Leitão
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Marius Wöste
- Institute of Medical Informatics, University Hospital of Münster, 48149, Münster, Germany
| | - Tobias Tekath
- Institute of Medical Informatics, University Hospital of Münster, 48149, Münster, Germany
| | - Jann-Frederik Cremers
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital of Münster, 48149, Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University Hospital of Münster, 48149, Münster, Germany
| | - Xiaolin Li
- Department of Neurology, Institute of Translational Neurology, University Hospital of Münster, 48149, Münster, Germany
| | - Gerd Meyer Zu Hörste
- Department of Neurology, Institute of Translational Neurology, University Hospital of Münster, 48149, Münster, Germany
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital of Münster, 48149, Münster, Germany
| | - Sandra Laurentino
- Centre of Reproductive Medicine and Andrology, University Hospital of Münster, 48149, Münster, Germany
| | - Nina Neuhaus
- Centre of Reproductive Medicine and Andrology, University Hospital of Münster, 48149, Münster, Germany.
| | - Bernhard Horsthemke
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
- Institute of Human Genetics, University Hospital Münster, Münster, Germany
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8
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Schubert M, Pérez Lanuza L, Wöste M, Dugas M, Rassam Y, Heilmann-Heimbach S, Tüttelmann F, Kliesch S, Gromoll J. O-089 A Genome Wide Association Study in men with unexplained infertility identifies nine SNPs at the FSHB locus to be associated with Follicle Stimulating Hormone level. Hum Reprod 2021. [DOI: 10.1093/humrep/deab125.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Study question
Which single nucleotide polymorphisms (SNPs) are associated with Follicle stimulating hormone (FSH) levels in men with unexplained infertility and can affect FSH action and spermatogenesis?
Summary answer
We identified a genomic region at chromosome 11p.14.1, including nine SNPs, that are significantly associated with FSH levels in men with unexplained infertility.
What is known already
FSH action is essential for the initiation and maintenance of human spermatogenesis. One well-studied SNP, FSHB c.-211G>T (rs10835638), is associated with FSHB mRNA transcription and directly affects FSH serum levels, testicular volume and spermatogenesis. Carriers of a T-allele in this promoter are diagnosed with functional secondary hypogonadism with isolated FSH deficiency.
Other genetic variants, for example at the FSHR have been shown to slightly modulate FSH action, however the clinical impact in these variants seems to
be low. The so far identified FSH-associated SNPs revealed an impact of up to 2.3 % on FSH serum level variance.
Study design, size, duration
A Genome wide association study (GWAS) was performed on a clinically well characterized cohort of 742 men with unexplained infertility (discovery study). Of the nine identified SNPs, validation was performed for rs11031005 and the already described rs10835638 in an independent cohort of 1123 men with unexplained infertility (validation study).
Participants/materials, setting, methods
Patients were retrospectively selected from our CeRA database Androbase® applying strict selection criteria; DNA was isolated from stored EDTA-blood samples. Informative genetic variants were identified using Illumina PsychArray v1.3. Illumina®GenomeStudio v2.0, PLINK v1.90 and R 3.6.3 were used to perform quantitative association analysis based on normalized FSH values. The validation study was performed using TaqMan PCR for SNP detection and R 3.6.3 for quantitative association to analyze the impact of each SNP on FSH level.
Main results and the role of chance
Imputation of the GWAS data revealed 94 SNPs with suggestive significance (p < 8.56e-06) and nine SNPs (including rs10835638) with genome-wide significance (p < 4.28e-07). The nine SNPs are all located at the FSHB locus on Chromosome 11p.14.1 and are in high linkage disequilibrium (LD). The validation study of 1123 patients with unexplained infertility for the SNPs rs11003005 and rs10835638 revealed a significant association with FSH (p = 4.71e-06 and p = 5.55e-07) and FSH/LH ratio (p = 2.08e-12 and p = 6.4e-12).The nine significant SNPs accounted for 3.60 –4.65 % variance in FSH serum level each in the entire discovery cohort. In an oligozoospermic subgroup (n = 249) this effect was increased to 4.89 – 6.95 %.
This the first GWAS in men with unexplained infertility. This study shows that not one single SNP, but rather a genomic region has an impact on FSH serum level in men with unexplained male infertility. This effect is even more pronounced in the more severe phenotype of oligozoospermic men.
Limitations, reasons for caution
The study is restricted to men with unexplained infertility, which might cause a selection bias. Validation and functional evaluation of the eight newly identified SNPs in independent cohorts would emphasize the results more. The sample size of 742 limits detection of loci with smaller effect on FSH levels.
Wider implications of the findings
The determination of one of the nine SNPs can improve diagnostic precision in identifying men with secondary functional hypogonadism with isolated FSH deficiency. An oligozoospermic subgroup of these men would putatively benefit from FSH treatment and has to be proven in randomized controlled trials.
Trial registration number
German Research Foundation CRU326
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Affiliation(s)
- M Schubert
- Centre of Reproductive Medicine and Andrology CeRA- University Münster, Department of Clinical and Surgical Andrology, Münster, Germany
| | - L Pérez Lanuza
- University Childreńs Hospital Münster, Department of Pediatric Hematology and Oncology, Münster, Germany
| | - M Wöste
- University of Münster, Institute of Medical Informatics, Münster, Germany
| | - M Dugas
- University of Münster, Institute of Medical Informatics, Münster, Germany
| | - Y Rassam
- Centre of Reproductive Medicine and Andrology CeRA- University Münster, Department of Clinical and Surgical Andrology, Münster, Germany
| | - S Heilmann-Heimbach
- University of Bonn- School of Medicine & University Hospital Bonn, Institute of Human Genetics, Bonn, Germany
| | - F Tüttelmann
- University of Münster, Institute of Reproductive Genetics, Münster, Germany
| | - S Kliesch
- Centre of Reproductive Medicine and Andrology CeRA- University Münster, Department of Clinical and Surgical Andrology, Münster, Germany
| | - J Gromoll
- Centre of Reproductive Medicine and Andrology CeRA- University of Münster, Institute of Reproductive and Regenerative Biology, Münster, Germany
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9
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Persio SD, Leitão E, Wöste M, Tekath T, Cremers JF, Dugas M, Xiaolin L, Meye. z. Hörste G, Kliesch S, Laurentino S, Horsthemke B, Neuhaus N. P–529 Whole-genome methylation analysis of testicular germ cells from cryptozoospermic men points to recurrent and functionally relevant DNA methylation changes. Hum Reprod 2021. [DOI: 10.1093/humrep/deab130.528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Study question
Do DNA methylation changes occur in testicular germ cells (TGCs) from patients with impaired spermatogenesis?
Summary answer
TGCs from men with cryptozoospermia exhibit altered DNA methylation levels at several genomic regions, many of which are associated with genes involved in spermatogenesis.
What is known already
In the last 15 years, several studies have described DNA methylation changes in sperm of infertile men. More recently, using whole genome bisulfite sequencing (WGBS) we were able to refute these findings by demonstrating that somatic DNA contamination and genetic variation confound methylation studies in swim-up purified sperm of severely oligozoospermic men. However, it remains unknown whether altered DNA methylation plays a role during the development of the germ cells in the testes of these patients.
Study design, size, duration
For identifying DNA methylation differences associated with impaired spermatogenesis, we compared the TGC methylomes of men with cryptozoospermia (CZ) and men with obstructive azoospermia (n = 4 each), who had normal spermatogenesis and served as controls (CTR). Study participants were selected among an age-matched cohort of 24 CTR and 10 CZ. The selection was based on similar composition of the TGC suspension evaluated by ploidy analysis and absence of somatic DNA.
Participants/materials, setting, methods
TGCs were isolated from biopsies after short-term cell culture. Presence of somatic DNA was evaluated by analyzing the DNA methylation levels of H19, MEST, DDX4 and XIST. WGBS was performed at ∼14× coverage. Bioinformatic tools were used to compare global DNA methylation levels, identify differentially methylated regions (DMRs) and functionally annotate the DMRs. Single-cell RNA sequencing (scRNA-seq) was used to associate the DNA methylation changes to gene expression.
Main results and the role of chance
We could not identify any difference in the global DNA methylation level or at imprinted regions between CZ and CTR samples. However, using stringent filters to identify group-specific methylation differences, we detected 271 DMRs, 238 of which were hypermethylated in CZ (binominal test, p < 2.2 × 10–16). The DMRs are associated with 132 genes, 61 of which are known to be differentially expressed at various stages of spermatogenesis according to scRNA-seq studies. Almost all of the DMRs associated with the 61 genes are hypermethylated in CZ (63/67, p = 1.107 × 10–14). As assessed by scRNA-seq, 13 DMR-associated genes, which were mainly expressed during meiosis and spermiogenesis, show a significantly different pattern of expression in CZ patients. In four of these genes, the promoter was hypermethylated in CZ men, which correlates with a lower expression level in these patients. In the other nine genes, most of which downregulated in CZ, germ cell-specific enhancers may be affected.
Limitations, reasons for caution
The small sample size constitutes a limitation of this study. Furthermore, even though the cellular composition of samples was similar by ploidy analysis, we cannot rule out that the observed DNA methylation changes might be due to differences in the relative proportion of different germ cell types.
Wider implications of the findings: Impaired spermatogenesis is associated with DNA methylation changes in testicular germ cells at functionally relevant regions of the genome, which points to an important role of DNA methylation in normal spermatogenesis. The DNA methylation changes may contribute to premature abortion of spermatogenesis and therefore not appear in mature sperm.
Trial registration number
N/A
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Affiliation(s)
- S D Persio
- University Hospital of Münster, Centre of Reproductive Medicine and Andrology, Münster, Germany
| | - E Leitão
- Essen University Hospital, Institute of Human Genetics, Essen, Germany
| | - M Wöste
- University Hospital of Münster, Institute of Medical Informatics, Münster, Germany
| | - T Tekath
- University Hospital of Münster, Institute of Medical Informatics, Münster, Germany
| | - J F Cremers
- University Hospital of Münster, Centre of Reproductive Medicine and Andrology- Department of Clinical and Surgical Andrology, Münster, Germany
| | - M Dugas
- University Hospital of Münster, Institute of Medical Informatics, Münster, Germany
| | - L Xiaolin
- University Hospital of Münster, Institute of Translational Neurology- Department of Neurology, Münster, Germany
| | - G Meye. z. Hörste
- University Hospital of Münster, Institute of Translational Neurology- Department of Neurology, Münster, Germany
| | - S Kliesch
- University Hospital of Münster, Centre of Reproductive Medicine and Andrology- Department of Clinical and Surgical Andrology, Münster, Germany
| | - S Laurentino
- University Hospital of Münster, Centre of Reproductive Medicine and Andrology, Münster, Germany
| | - B Horsthemke
- Essen University Hospital, Institute of Human Genetics, Essen, Germany
| | - N Neuhaus
- University Hospital of Münster, Centre of Reproductive Medicine and Andrology, Münster, Germany
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10
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Schubert M, Pérez Lanuza L, Wöste M, Dugas M, Rassam Y, Heilmann-Heimbach S, Tüttelmann F, Kliesch S, Gromoll J. Identifying a genomic region at Chromosome 11p.14.1 that is associated to FSH serum level in men with unexplained male infertility. Eur Urol 2021. [DOI: 10.1016/s0302-2838(21)00883-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Torres-Fernández LA, Emich J, Port Y, Mitschka S, Wöste M, Schneider S, Fietz D, Oud MS, Di Persio S, Neuhaus N, Kliesch S, Hölzel M, Schorle H, Friedrich C, Tüttelmann F, Kolanus W. TRIM71 Deficiency Causes Germ Cell Loss During Mouse Embryogenesis and Is Associated With Human Male Infertility. Front Cell Dev Biol 2021; 9:658966. [PMID: 34055789 PMCID: PMC8155544 DOI: 10.3389/fcell.2021.658966] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/30/2021] [Indexed: 12/21/2022] Open
Abstract
Mutations affecting the germline can result in infertility or the generation of germ cell tumors (GCT), highlighting the need to identify and characterize the genes controlling germ cell development. The RNA-binding protein and E3 ubiquitin ligase TRIM71 is essential for embryogenesis, and its expression has been reported in GCT and adult mouse testes. To investigate the role of TRIM71 in mammalian germ cell embryonic development, we generated a germline-specific conditional Trim71 knockout mouse (cKO) using the early primordial germ cell (PGC) marker Nanos3 as a Cre-recombinase driver. cKO mice are infertile, with male mice displaying a Sertoli cell-only (SCO) phenotype which in humans is defined as a specific subtype of non-obstructive azoospermia characterized by the absence of germ cells in the seminiferous tubules. Infertility in male Trim71 cKO mice originates during embryogenesis, as the SCO phenotype was already apparent in neonatal mice. The in vitro differentiation of mouse embryonic stem cells (ESCs) into PGC-like cells (PGCLCs) revealed reduced numbers of PGCLCs in Trim71-deficient cells. Furthermore, TCam-2 cells, a human GCT-derived seminoma cell line which was used as an in vitro model for PGCs, showed proliferation defects upon TRIM71 knockdown. Additionally, in vitro growth competition assays, as well as proliferation assays with wild type and CRISPR/Cas9-generated TRIM71 mutant NCCIT cells showed that TRIM71 also promotes proliferation in this malignant GCT-derived non-seminoma cell line. Importantly, the PGC-specific markers BLIMP1 and NANOS3 were consistently downregulated in Trim71 KO PGCLCs, TRIM71 knockdown TCam-2 cells and TRIM71 mutant NCCIT cells. These data collectively support a role for TRIM71 in PGC development. Last, via exome sequencing analysis, we identified several TRIM71 variants in a cohort of infertile men, including a loss-of-function variant in a patient with an SCO phenotype. Altogether, our work reveals for the first time an association of TRIM71 deficiency with human male infertility, and uncovers further developmental roles for TRIM71 in the germline during mouse embryogenesis.
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Affiliation(s)
| | - Jana Emich
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Yasmine Port
- Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Sibylle Mitschka
- Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Marius Wöste
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Simon Schneider
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Daniela Fietz
- Institute for Veterinary Anatomy, Histology and Embryology, Justus Liebig University Gießen, Gießen, Germany
- Hessian Centre of Reproductive Medicine (HZRM), Justus Liebig University Gießen, Gießen, Germany
| | - Manon S. Oud
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sara Di Persio
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University Hospital Münster, Münster, Germany
| | - Nina Neuhaus
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University Hospital Münster, Münster, Germany
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital Münster, Münster, Germany
| | - Michael Hölzel
- Institute of Experimental Oncology, University Hospital Bonn, Bonn, Germany
| | - Hubert Schorle
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Corinna Friedrich
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Waldemar Kolanus
- Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
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12
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Salas-Huetos A, Tüttelmann F, Wyrwoll MJ, Kliesch S, Lopes AM, Goncalves J, Boyden SE, Wöste M, Hotaling JM, Nagirnaja L, Conrad DF, Carrell DT, Aston KI. Disruption of human meiotic telomere complex genes TERB1, TERB2 and MAJIN in men with non-obstructive azoospermia. Hum Genet 2020; 140:217-227. [PMID: 33211200 DOI: 10.1007/s00439-020-02236-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/03/2020] [Indexed: 12/14/2022]
Abstract
Non-obstructive azoospermia (NOA), the lack of spermatozoa in semen due to impaired spermatogenesis affects nearly 1% of men. In about half of cases, an underlying cause for NOA cannot be identified. This study aimed to identify novel variants associated with idiopathic NOA. We identified a nonconsanguineous family in which multiple sons displayed the NOA phenotype. We performed whole-exome sequencing in three affected brothers with NOA, their two unaffected brothers and their father, and identified compound heterozygous frameshift variants (one novel and one extremely rare) in Telomere Repeat Binding Bouquet Formation Protein 2 (TERB2) that segregated perfectly with NOA. TERB2 interacts with TERB1 and Membrane Anchored Junction Protein (MAJIN) to form the tripartite meiotic telomere complex (MTC), which has been shown in mouse models to be necessary for the completion of meiosis and both male and female fertility. Given our novel findings of TERB2 variants in NOA men, along with the integral role of the three MTC proteins in spermatogenesis, we subsequently explored exome sequence data from 1495 NOA men to investigate the role of MTC gene variants in spermatogenic impairment. Remarkably, we identified two NOA patients with likely damaging rare homozygous stop and missense variants in TERB1 and one NOA patient with a rare homozygous missense variant in MAJIN. Available testis histology data from three of the NOA patients indicate germ cell maturation arrest, consistent with mouse phenotypes. These findings suggest that variants in MTC genes may be an important cause of NOA in both consanguineous and outbred populations.
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Affiliation(s)
- Albert Salas-Huetos
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, 48149, Münster, Germany
| | - Margot J Wyrwoll
- Institute of Reproductive Genetics, University of Münster, 48149, Münster, Germany.,Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital Münster, 48149, Münster, Germany
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital Münster, 48149, Münster, Germany
| | - Alexandra M Lopes
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135, Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135, Porto, Portugal
| | - João Goncalves
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, 1649-016, Lisbon, Portugal.,ToxOmics-Centro de Toxicogenómica e Saúde Humana, Nova Medical School, 1169-056, Lisbon, Portugal
| | - Steven E Boyden
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.,Utah Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Marius Wöste
- Institute of Medical Informatics, University of Münster, 48149, Munster, Germany
| | - James M Hotaling
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA.,Department of Obstetrics and Gynecology, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA
| | | | - Liina Nagirnaja
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
| | - Donald F Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Douglas T Carrell
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA.,Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Kenneth I Aston
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA.
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13
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Sandmann S, Wöste M, de Graaf AO, Burkhardt B, Jansen JH, Dugas M. CopyDetective: Detection threshold-aware copy number variant calling in whole-exome sequencing data. Gigascience 2020; 9:giaa118. [PMID: 33135740 PMCID: PMC7604644 DOI: 10.1093/gigascience/giaa118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/17/2020] [Accepted: 10/02/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Copy number variants (CNVs) are known to play an important role in the development and progression of several diseases. However, detection of CNVs with whole-exome sequencing (WES) experiments is challenging. Usually, additional experiments have to be performed. FINDINGS We developed a novel algorithm for somatic CNV calling in matched WES data called "CopyDetective". Different from other approaches, CNV calling with CopyDetective consists of a 2-step procedure: first, quality analysis is performed, determining individual detection thresholds for every sample. Second, actual CNV calling on the basis of the previously determined thresholds is performed. Our algorithm evaluates the change in variant allele frequency of polymorphisms and reports the fraction of affected cells for every CNV. Analyzing 4 WES data sets (n = 100) we observed superior performance of CopyDetective compared with ExomeCNV, VarScan2, ControlFREEC, ExomeDepth, and CNV-seq. CONCLUSIONS Individual detection thresholds reveal that not every WES data set is equally apt for CNV calling. Initial quality analyses, determining individual detection thresholds-as realized by CopyDetective-can and should be performed prior to actual variant calling.
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Affiliation(s)
- Sarah Sandmann
- Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1, Building A11, Münster 48149, Germany
| | - Marius Wöste
- Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1, Building A11, Münster 48149, Germany
| | - Aniek O de Graaf
- Laboratory Hematology, RadboudUMC, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, Netherlands
| | - Birgit Burkhardt
- Paediatric Hematology & Oncology, University Hospital Münster, Albert-Schweitzer-Campus 1, Building A1, Münster 48149, Germany
| | - Joop H Jansen
- Laboratory Hematology, RadboudUMC, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, Netherlands
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1, Building A11, Münster 48149, Germany
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14
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van der Bijl N, Röpke A, Biswas U, Wöste M, Jessberger R, Kliesch S, Friedrich C, Tüttelmann F. Mutations in the stromal antigen 3 (STAG3) gene cause male infertility due to meiotic arrest. Hum Reprod 2020; 34:2112-2119. [PMID: 31682730 DOI: 10.1093/humrep/dez204] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/18/2019] [Indexed: 01/18/2023] Open
Abstract
STUDY QUESTION Are sequence variants in the stromal antigen 3 (STAG3) gene a cause for non-obstructive azoospermia (NOA) in infertile human males? SUMMARY ANSWER Sequence variants affecting protein function of STAG3 cause male infertility due to meiotic arrest. WHAT IS KNOWN ALREADY In both women and men, STAG3 encodes for a meiosis-specific protein that is crucial for the functionality of meiotic cohesin complexes. Sequence variants in STAG3 have been reported to cause meiotic arrest in male and female mice and premature ovarian failure in human females, but not in infertile human males so far. STUDY DESIGN, SIZE, DURATION The full coding region of STAG3 was sequenced directly in a cohort of 28 men with NOA due to meiotic arrest. In addition, a larger group of 275 infertile men that underwent whole-exome sequencing (WES) was screened for potential STAG3 sequence variants. Furthermore, meiotic spreads, immunohistochemistry, WES and population sampling probability (PSAP) have been conducted in the index case. PARTICIPANTS/MATERIALS, SETTING, METHODS This study included 28 infertile but otherwise healthy human males who underwent Sanger sequencing of the full coding region of STAG3. Additionally, WES data of 275 infertile human males with different infertility phenotypes have been screened for relevant STAG3 variants. All participants underwent karyotype analysis and azoospermia factor (AZF) screening in advance. In the index patient, segregation analysis, WES data, PSAP, lab parameters, testis histology and nuclear spreads have been added to suplort the findings. MAIN RESULTS AND THE ROLE OF CHANCE Two compound-heterozygous variants in STAG3 (c.[1262T>G];[1312C>T], p.[(Leu421Arg)];[(Arg438Ter)]) have been found to cause male infertility due to complete bilateral meiotic arrest in an otherwise healthy human male. Compound heterozygosity was confirmed by Sanger sequencing of the parents and the patient's brother. Other variants which may affect spermatogenesis have been ruled out through analysis of the patient's WES data and application of the PSAP pipeline. As expected from Stag3 knockout-mice meiotic spreads, germ cells did not develop further than zygotene and showed drastic chromosome aberrations. No rare variants in STAG3 were found in the 275 infertile males with other phenotypes. Our results indicate that STAG3 variants that negatively affect its protein function are a rare cause of NOA (<1% of cases). LIMITATIONS, REASONS FOR CAUTION We identified only one patient with compound-heterozygous variants in STAG3 causing NOA due to meiotic arrest. Future studies should evaluate STAG3 variants in larger cohorts to support this finding. WIDER IMPLICATIONS OF THE FINDINGS Identification of STAG3 sequence variants in infertile human males should improve genetic counselling as well as diagnostics and treatment. Especially before testicular sperm extraction (TESE) for ICSI, STAG3 variants should be ruled out to prevent unnecessary interventions with frustrating outcomes for both patients and clinicians. STUDY FUNDING/COMPETING INTEREST(S) This work was carried out within the frame of the German Research Foundation (DFG) Clinical Research Unit 'Male Germ Cells: from Genes to Function' (CRU326). Work in the laboratory of R.J. is supported by a grant of the European Union H2020 program GermAge. The authors declare no conflicts of interest. TRIAL REGISTRATION NUMBER Not applicable.
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Affiliation(s)
- N van der Bijl
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany
| | - A Röpke
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany
| | - U Biswas
- Institute of Physiological Chemistry, TU Dresden, 01307 Dresden, Germany
| | - M Wöste
- Institute of Medical Informatics, University of Münster, 48149 Münster, Germany
| | - R Jessberger
- Institute of Physiological Chemistry, TU Dresden, 01307 Dresden, Germany
| | - S Kliesch
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital Münster, 48149 Münster, Germany
| | - C Friedrich
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany
| | - F Tüttelmann
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany
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15
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Wyrwoll MJ, Temel ŞG, Nagirnaja L, Oud MS, Lopes AM, van der Heijden GW, Heald JS, Rotte N, Wistuba J, Wöste M, Ledig S, Krenz H, Smits RM, Carvalho F, Gonçalves J, Fietz D, Türkgenç B, Ergören MC, Çetinkaya M, Başar M, Kahraman S, McEleny K, Xavier MJ, Turner H, Pilatz A, Röpke A, Dugas M, Kliesch S, Neuhaus N, Aston KI, Conrad DF, Veltman JA, Friedrich C, Tüttelmann F. Bi-allelic Mutations in M1AP Are a Frequent Cause of Meiotic Arrest and Severely Impaired Spermatogenesis Leading to Male Infertility. Am J Hum Genet 2020; 107:342-351. [PMID: 32673564 PMCID: PMC7413853 DOI: 10.1016/j.ajhg.2020.06.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 06/12/2020] [Indexed: 01/08/2023] Open
Abstract
Male infertility affects ∼7% of men, but its causes remain poorly understood. The most severe form is non-obstructive azoospermia (NOA), which is, in part, caused by an arrest at meiosis. So far, only a few validated disease-associated genes have been reported. To address this gap, we performed whole-exome sequencing in 58 men with unexplained meiotic arrest and identified the same homozygous frameshift variant c.676dup (p.Trp226LeufsTer4) in M1AP, encoding meiosis 1 associated protein, in three unrelated men. This variant most likely results in a truncated protein as shown in vitro by heterologous expression of mutant M1AP. Next, we screened four large cohorts of infertile men and identified three additional individuals carrying homozygous c.676dup and three carrying combinations of this and other likely causal variants in M1AP. Moreover, a homozygous missense variant, c.1166C>T (p.Pro389Leu), segregated with infertility in five men from a consanguineous Turkish family. The common phenotype between all affected men was NOA, but occasionally spermatids and rarely a few spermatozoa in the semen were observed. A similar phenotype has been described for mice with disruption of M1ap. Collectively, these findings demonstrate that mutations in M1AP are a relatively frequent cause of autosomal recessive severe spermatogenic failure and male infertility with strong clinical validity.
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Affiliation(s)
- Margot J Wyrwoll
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany
| | - Şehime G Temel
- Bursa Uludag University, Faculty of Medicine, Department of Medical Genetics & Department of Histology & Embryology & Health Sciences Institute, Department of Translational Medicine, 16059 Bursa, Turkey
| | - Liina Nagirnaja
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Manon S Oud
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Alexandra M Lopes
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), 4200-804 Porto, Portugal; Instituto de Investigação e Inovação em Saúde (i3s), Universidade do Porto, 4099-002 Porto, Portugal
| | - Godfried W van der Heijden
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 Nijmegen, the Netherlands; Department of Obstetrics and Gynecology, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - James S Heald
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Nadja Rotte
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany; Centre of Reproductive Medicine and Andrology, Institute of Reproductive Medicine, University of Münster, 48149 Münster, Germany
| | - Joachim Wistuba
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive Medicine, University of Münster, 48149 Münster, Germany
| | - Marius Wöste
- Institute of Medical Informatics, University of Münster, 48149 Münster, Germany
| | - Susanne Ledig
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany
| | - Henrike Krenz
- Institute of Medical Informatics, University of Münster, 48149 Münster, Germany
| | - Roos M Smits
- Department of Obstetrics and Gynecology, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Filipa Carvalho
- Instituto de Investigação e Inovação em Saúde (i3s), Universidade do Porto, 4099-002 Porto, Portugal; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, 4099-002 Porto, Portugal
| | - João Gonçalves
- Departmento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, 1649-016 Lisboa, Portugal; ToxOmics - Centro de Toxicogenómica e Saúde Humana, Nova Medical School, 1169-056 Lisboa, Portugal
| | - Daniela Fietz
- Institute of Veterinary Anatomy, Histology and Embryology, Justus Liebig University, 35392 Gießen, Germany
| | - Burcu Türkgenç
- University of Acibadem, Acibadem Genetic Diagnostic Centre, 34662 Istanbul, Turkey
| | - Mahmut C Ergören
- Near East University, Faculty of Medicine, Department of Medical Biology, 99138 Nicosia, Cyprus
| | - Murat Çetinkaya
- Istanbul Memorial Hospital, Assisted Reproductive Technologies and Reproductive Genetics Centre, 34385 Istanbul, Turkey
| | - Murad Başar
- Istanbul Memorial Hospital, Department of Urology & Andrology, 34385 Istanbul, Turkey
| | - Semra Kahraman
- Istanbul Memorial Hospital, Assisted Reproductive Technologies and Reproductive Genetics, 34385 Istanbul, Turkey
| | - Kevin McEleny
- Newcastle Fertility Centre, The Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4EP Newcastle upon Tyne, UK
| | - Miguel J Xavier
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Helen Turner
- Department of Cellular Pathology, The Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4LP Newcastle upon Tyne, UK
| | - Adrian Pilatz
- Clinic for Urology, Pediatric Urology and Andrology, Justus Liebig University, 35392 Gießen, Germany
| | - Albrecht Röpke
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, 48149 Münster, Germany
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital Münster, 48149 Münster, Germany
| | - Nina Neuhaus
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive Medicine, University of Münster, 48149 Münster, Germany
| | - Kenneth I Aston
- Andrology and IVF Laboratories, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Donald F Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Joris A Veltman
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 Nijmegen, the Netherlands; Biosciences Institute, Faculty of Medical Sciences, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Corinna Friedrich
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany
| | - Frank Tüttelmann
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany.
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16
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Leitão E, Di Persio S, Laurentino S, Wöste M, Dugas M, Kliesch S, Neuhaus N, Horsthemke B. The sperm epigenome does not display recurrent epimutations in patients with severely impaired spermatogenesis. Clin Epigenetics 2020; 12:61. [PMID: 32375885 PMCID: PMC7204326 DOI: 10.1186/s13148-020-00854-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/17/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND In the past 15 years, numerous studies have described aberrant DNA methylation of imprinted genes (e.g. MEST and H19) in sperm of oligozoospermic men, but the prevalence and genomic extent of abnormal methylation patterns have remained unknown. RESULTS Using deep bisulfite sequencing (DBS), we screened swim-up sperm samples from 40 normozoospermic and 93 patients diagnosed as oligoasthenoteratozoospermic, oligoteratozoospermic or oligozoospermic, which are termed OATs throughout the manuscript, for H19 and MEST methylation. Based on this screening, we defined three patient groups: normal controls (NC), abnormally methylated oligozoospermic (AMO; n = 7) and normally methylated oligozoospermic (NMO; n = 86). Whole-genome bisulfite sequencing (WGBS) of five NC and five AMO samples revealed abnormal methylation levels of all 50 imprinting control regions in each AMO sample. To investigate whether this finding reflected epigenetic germline mosaicism or the presence of residual somatic DNA, we made a genome-wide inventory of soma-germ cell-specific DNA methylation. We found that > 2000 germ cell-specific genes are promoter-methylated in blood and that AMO samples had abnormal methylation levels at these genes, consistent with the presence of somatic cell DNA. The comparison between the five NC and six NMO samples revealed 19 differentially methylated regions (DMRs), none of which could be validated in an independent cohort of 40 men. Previous studies reported a higher incidence of epimutations at single CpG sites in the CTCF-binding region 6 of H19 in infertile patients. DBS analysis of this locus, however, revealed an association between DNA methylation levels and genotype (rs2071094), but not fertility phenotype. CONCLUSIONS Our results suggest that somatic DNA contamination and genetic variation confound methylation studies in sperm of infertile men. While we cannot exclude the existence of rare patients with slightly abnormal sperm methylation at non-recurrent CpG sites, the prevalence of aberrant methylation in swim-up purified sperm of infertile men has likely been overestimated, which is reassuring for patients undergoing assisted reproduction.
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Affiliation(s)
- Elsa Leitão
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Sara Di Persio
- Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - Sandra Laurentino
- Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - Marius Wöste
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital Münster, Münster, Germany
| | - Nina Neuhaus
- Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany.
| | - Bernhard Horsthemke
- Institute of Human Genetics, University Hospital Essen, Essen, Germany.,Institute of Human Genetics, University Hospital Münster, Münster, Germany
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17
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Wöste M, Leitão E, Laurentino S, Horsthemke B, Rahmann S, Schröder C. wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data. BMC Bioinformatics 2020; 21:169. [PMID: 32357829 PMCID: PMC7195798 DOI: 10.1186/s12859-020-3470-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/24/2020] [Indexed: 11/20/2022] Open
Abstract
Background Analysing whole genome bisulfite sequencing datasets is a data-intensive task that requires comprehensive and reproducible workflows to generate valid results. While many algorithms have been developed for tasks such as alignment, comprehensive end-to-end pipelines are still sparse. Furthermore, previous pipelines lack features or show technical deficiencies, thus impeding analyses. Results We developed wg-blimp (whole genome bisulfite sequencing methylation analysis pipeline) as an end-to-end pipeline to ease whole genome bisulfite sequencing data analysis. It integrates established algorithms for alignment, quality control, methylation calling, detection of differentially methylated regions, and methylome segmentation, requiring only a reference genome and raw sequencing data as input. Comparing wg-blimp to previous end-to-end pipelines reveals similar setups for common sequence processing tasks, but shows differences for post-alignment analyses. We improve on previous pipelines by providing a more comprehensive analysis workflow as well as an interactive user interface. To demonstrate wg-blimp’s ability to produce correct results we used it to call differentially methylated regions for two publicly available datasets. We were able to replicate 112 of 114 previously published regions, and found results to be consistent with previous findings. We further applied wg-blimp to a publicly available sample of embryonic stem cells to showcase methylome segmentation. As expected, unmethylated regions were in close proximity of transcription start sites. Segmentation results were consistent with previous analyses, despite different reference genomes and sequencing techniques. Conclusions wg-blimp provides a comprehensive analysis pipeline for whole genome bisulfite sequencing data as well as a user interface for simplified result inspection. We demonstrated its applicability by analysing multiple publicly available datasets. Thus, wg-blimp is a relevant alternative to previous analysis pipelines and may facilitate future epigenetic research.
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Affiliation(s)
- Marius Wöste
- Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1, Münster, 48149, Germany.
| | - Elsa Leitão
- Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Hufelandstraße 55, Essen, 45147, Germany
| | - Sandra Laurentino
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University Hospital Münster, Albert-Schweitzer-Campus 1, Münster, 48149, Germany
| | - Bernhard Horsthemke
- Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Hufelandstraße 55, Essen, 45147, Germany.,Institute of Human Genetics, University of Münster, Vesaliusweg 12-14, Münster, 48149, Germany
| | - Sven Rahmann
- Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Hufelandstraße 55, Essen, 45147, Germany
| | - Christopher Schröder
- Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Hufelandstraße 55, Essen, 45147, Germany.,Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Hufelandstraße 55, Essen, 45147, Germany
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18
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Wallmeier J, Frank D, Shoemark A, Nöthe-Menchen T, Cindric S, Olbrich H, Loges NT, Aprea I, Dougherty GW, Pennekamp P, Kaiser T, Mitchison HM, Hogg C, Carr SB, Zariwala MA, Ferkol T, Leigh MW, Davis SD, Atkinson J, Dutcher SK, Knowles MR, Thiele H, Altmüller J, Krenz H, Wöste M, Brentrup A, Ahrens F, Vogelberg C, Morris-Rosendahl DJ, Omran H. De Novo Mutations in FOXJ1 Result in a Motile Ciliopathy with Hydrocephalus and Randomization of Left/Right Body Asymmetry. Am J Hum Genet 2019; 105:1030-1039. [PMID: 31630787 PMCID: PMC6849114 DOI: 10.1016/j.ajhg.2019.09.022] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 09/18/2019] [Indexed: 12/11/2022] Open
Abstract
Hydrocephalus is one of the most prevalent form of developmental central nervous system (CNS) malformations. Cerebrospinal fluid (CSF) flow depends on both heartbeat and body movement. Furthermore, it has been shown that CSF flow within and across brain ventricles depends on cilia motility of the ependymal cells lining the brain ventricles, which play a crucial role to maintain patency of the narrow sites of CSF passage during brain formation in mice. Using whole-exome and whole-genome sequencing, we identified an autosomal-dominant cause of a distinct motile ciliopathy related to defective ciliogenesis of the ependymal cilia in six individuals. Heterozygous de novo mutations in FOXJ1, which encodes a well-known member of the forkhead transcription factors important for ciliogenesis of motile cilia, cause a motile ciliopathy that is characterized by hydrocephalus internus, chronic destructive airway disease, and randomization of left/right body asymmetry. Mutant respiratory epithelial cells are unable to generate a fluid flow and exhibit a reduced number of cilia per cell, as documented by high-speed video microscopy (HVMA), transmission electron microscopy (TEM), and immunofluorescence analysis (IF). TEM and IF demonstrate mislocalized basal bodies. In line with this finding, the focal adhesion protein PTK2 displays aberrant localization in the cytoplasm of the mutant respiratory epithelial cells.
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Affiliation(s)
- Julia Wallmeier
- Department of General Pediatrics, University Children’s Hospital Muenster, 48149 Muenster, Germany
| | - Diana Frank
- Department of General Pediatrics, University Children’s Hospital Muenster, 48149 Muenster, Germany
| | - Amelia Shoemark
- Molecular & Clinical Medicine, University of Dundee, Dundee DD1 4HN, UK,Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Trust, London SW3 6NP, UK
| | - Tabea Nöthe-Menchen
- Department of General Pediatrics, University Children’s Hospital Muenster, 48149 Muenster, Germany
| | - Sandra Cindric
- Department of General Pediatrics, University Children’s Hospital Muenster, 48149 Muenster, Germany
| | - Heike Olbrich
- Department of General Pediatrics, University Children’s Hospital Muenster, 48149 Muenster, Germany
| | - Niki T. Loges
- Department of General Pediatrics, University Children’s Hospital Muenster, 48149 Muenster, Germany
| | - Isabella Aprea
- Department of General Pediatrics, University Children’s Hospital Muenster, 48149 Muenster, Germany
| | - Gerard W. Dougherty
- Department of General Pediatrics, University Children’s Hospital Muenster, 48149 Muenster, Germany
| | - Petra Pennekamp
- Department of General Pediatrics, University Children’s Hospital Muenster, 48149 Muenster, Germany
| | - Thomas Kaiser
- Department of General Pediatrics, University Children’s Hospital Muenster, 48149 Muenster, Germany
| | - Hannah M. Mitchison
- Genetics and Genomic Medicine, University College London (UCL) Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - Claire Hogg
- Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Trust, London SW3 6NP, UK
| | - Siobhán B. Carr
- Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Trust, London SW3 6NP, UK
| | - Maimoona A. Zariwala
- Department of Pathology and Laboratory Medicine, Marsico Lung Institute/UNC CF Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Thomas Ferkol
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Margaret W. Leigh
- Department of Pediatrics, Marsico Lung Institute/UNC CF Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie D. Davis
- Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeffrey Atkinson
- Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Susan K. Dutcher
- McDonnell Genome Institute, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Michael R. Knowles
- Department of Medicine, Marsico Lung Institute/UNC CF Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Holger Thiele
- Cologne Center for Genomics, Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Henrike Krenz
- Institute of Medical Informatics, University of Muenster, 48149 Muenster, Germany
| | - Marius Wöste
- Institute of Medical Informatics, University of Muenster, 48149 Muenster, Germany
| | - Angela Brentrup
- Department of Neurosurgery, University Hospital Muenster, 48149 Muenster, Germany
| | - Frank Ahrens
- Children’s Hospital “Altona,” 22763 Hamburg, Germany
| | - Christian Vogelberg
- Paediatric Department, University Hospital Carl Gustav Carus Dresden, TU Dresden, 01307 Dresden, Germany
| | - Deborah J. Morris-Rosendahl
- Clinical Genetics and Genomics, Royal Brompton and Harefield NHS Foundation Trust, SW3 6NP London, UK,National Heart and Lung Institute, Imperial College London, SW3 6LY London, UK
| | - Heymut Omran
- Department of General Pediatrics, University Children's Hospital Muenster, 48149 Muenster, Germany.
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19
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Abstract
Summary With the rapid development in next-generation sequencing, cost and time requirements for genomic sequencing are decreasing, enabling applications in many areas such as cancer research. Many tools have been developed to analyze genomic variation ranging from single nucleotide variants to whole chromosomal aberrations. As sequencing throughput increases, the number of variants called by such tools also grows. Often employed manual inspection of such calls is thus becoming a time-consuming procedure. We developed the Variant InsPector and Expert Rating tool (VIPER) to speed up this process by integrating the Integrative Genomics Viewer into a web application. Analysts can then quickly iterate through variants, apply filters and make decisions based on the generated images and variant metadata. VIPER was successfully employed in analyses with manual inspection of more than 10 000 calls. Availability and implementation VIPER is implemented in Java and Javascript and is freely available at https://github.com/MarWoes/viper. Contact marius.woeste@uni-muenster.de. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Marius Wöste
- Institute of Medical Informatics, University of Münster, Münster 48149, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster 48149, Germany
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