Browsing by Author "Fernandes, Susana"
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- Actionable secondary findings following exome sequencing of 836 non-obstructive azoospermia cases and their value in patient managementPublication . Kasak, Laura; Lillepea, Kristiina; Nagirnaja, Liina; Aston, Kenneth I.; Schlegel, Peter N.; Gonçalves, João; Carvalho, Filipa; Moreno-Mendoza, Daniel; Almstrup, Kristian; Eisenberg, Michael L.; Jarvi, Keith A.; O’Bryan, Moira K.; Lopes, Alexandra M.; Conrad, Donald F.; Nagirnaja, Liina; Aston, Kenneth I.; Carrell, Douglas T.; Hotaling, James M.; Jenkins, Timothy G.; McLachlan, Rob; O’Bryan, Moira K.; Schlegel, Peter N.; Eisenberg, Michael L.; Sandlow, Jay I.; Jungheim, Emily S.; Omurtag, Kenan R.; Lopes, Alexandra M.; Seixas, Susana; Carvalho, Filipa; Fernandes, Susana; Barros, Alberto; Laan, Maris; Punab, Margus; Rajpert-De Meyts, Ewa; Jørgensen, Niels; Almstrup, Kristian; Krausz, Csilla G.; Jarvi, Keith A.; Punab, Margus; Laan, MarisStudy question: What is the load, distribution and added clinical value of secondary findings (SFs) identified in exome sequencing (ES) of patients with non-obstructive azoospermia (NOA)? Summary answer: One in 28 NOA cases carried an identifiable, medically actionable SF. What is known already: In addition to molecular diagnostics, ES allows assessment of clinically actionable disease-related gene variants that are not connected to the patient's primary diagnosis, but the knowledge of which may allow the prevention, delay or amelioration of late-onset monogenic conditions. Data on SFs in specific clinical patient groups, including reproductive failure, are currently limited. Study design, size, duration: The study group was a retrospective cohort of patients with NOA recruited in 10 clinics across six countries and formed in the framework of the international GEMINI (The GEnetics of Male INfertility Initiative) study. Participants/materials, setting, methods: ES data of 836 patients with NOA were exploited to analyze SFs in 85 genes recommended by the American College of Medical Genetics and Genomics (ACMG), Geisinger's MyCode, and Clinical Genome Resource. The identified 6374 exonic variants were annotated with ANNOVAR and filtered for allele frequency, retaining 1381 rare or novel missense and loss-of-function variants. After automatic assessment of pathogenicity with ClinVar and InterVar, 87 variants were manually curated. The final list of confident disease-causing SFs was communicated to the corresponding GEMINI centers. When patient consent had been given, available family health history and non-andrological medical data were retrospectively assessed. Main results and the role of chance: We found a 3.6% total frequency of SFs, 3.3% from the 59 ACMG SF v2.0 genes. One in 70 patients carried SFs in genes linked to familial cancer syndromes, whereas 1 in 60 cases was predisposed to congenital heart disease or other cardiovascular conditions. Retrospective assessment confirmed clinico-molecular diagnoses in several cases. Notably, 37% (11/30) of patients with SFs carried variants in genes linked to male infertility in mice, suggesting that some SFs may have a co-contributing role in spermatogenic impairment. Further studies are needed to determine whether these observations represent chance findings or the profile of SFs in NOA patients is indeed different from the general population. Limitations, reasons for caution: One limitation of our cohort was the low proportion of non-Caucasian ethnicities (9%). Additionally, as comprehensive clinical data were not available retrospectively for all men with SFs, we were not able to confirm a clinico-molecular diagnosis and assess the penetrance of the specific variants. Wider implications of the findings: For the first time, this study analyzed medically actionable SFs in men with spermatogenic failure. With the evolving process to incorporate ES into routine andrology practice for molecular diagnostic purposes, additional assessment of SFs can inform about future significant health concerns for infertility patients. Timely detection of SFs and respective genetic counseling will broaden options for disease prevention and early treatment, as well as inform choices and opportunities regarding family planning. A notable fraction of SFs was detected in genes implicated in maintaining genome integrity, essential in both mitosis and meiosis. Thus, potential genetic pleiotropy may exist between certain adult-onset monogenic diseases and NOA.
- An Alu-mediated 1Mb deletion removes Wilms’ tumor 1 (WT1) but not PAX6 in a patient with isolated cryptorchidismPublication . Seabra, Catarina; Quental, Sofia; Neto, Ana; Carvalho, Filipa; Gonçalves, João; Fernandes, Susana; Sousa, Mário; Barros, Alberto; Amorim, António; Lopes, Alexandra MObjective: We have recently performed an array-based genome-wide analysis of structural variants in a cohort of patients with non-obstructive azoospermia (NOA) and found a cryptic deletion of approximately 1Mb in 11p13, spanning the WT1 gene but not PAX6, in a Portuguese patient with clinical history of cryptorchidism during childhood?. Here we performed the molecular characterization of this novel deletion, to precisely map the breakpoints of this deletion, and evaluated the prevalence of focal WT1 genetic alterations in infertile Portuguese patients with cryptorchidism. Design: Fine molecular characterization of a heterozygous large deletion in 11p13 in one azoospermic patient (with clinical history of cryptorchidism) and screening for WT1 exonic microdeletions and mutations in a group of 31 Portuguese patients with uni- or bi-lateral cryptorchidism. Materials and Methods: Multiplex ligation-dependent probe amplification (MLPA), Long Range PCR; PCR amplification of the WT1 exons and proximal flanking sequences followed by Sanger sequencing. Results: We confirmed by MLPA the ~1Mb deletions at 11p13 spanning six genes - WT1, PRRG4, QSER1, TCP11L1, CSTF3 and HIPK3. Examination of the deletion breakpoint showed that it lies within highly homologous Alu Y sequences. Therefore the likely mechanism for this deletion was Alu-mediated non-allelic homologous recombination (NAHR). No mutations were found in the single allele present in this patient suggesting that the phenotype probably results from WT1 haploinsufficiency. We found no additional WT1 alterations in our group of patients with cryptorchidism. Conclusions: To our knowledge this is the smallest as yet described deletion encompassing the WT1 gene, which results in a non-syndromic clinical presentation of infertility. Repeat-mediated non-allelic recombination is an alternative mechanism for 11p13 deletions spanning WT1. Based on our results WT1 genetic defects are not frequently involved in isolated cryptorchidism, even though more patients should be analyzed. Support: This work was partially funded by the Portuguese Foundation for Science and Technology FCT/MCTES (PIDDAC) and co-financed by European funds (FEDER) through the COMPETE program, research grant PTDC/SAU-GMG/101229/2008 to AML. IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Science, Technology, and Higher Education and is partially supported by FCT. AML is the recipient of a postdoctoral fellowship from FCT (SFRH/BPD/73366/2010).
- A de novo paradigm for male infertilityPublication . Oud, M.S.; Smits, R.M.; Smith, H.E.; Mastrorosa, F.K.; Holt, G.S.; Houston, B.J.; de Vries, P.F.; Alobaidi, B.K.S.; Batty, L.E.; Ismail, H.; Greenwood, J.; Sheth, H.; Mikulasova, A.; Astuti, G.D.N.; Gilissen, C.; McEleny, K.; Turner, H.; Coxhead, J.; Cockell, S.; Braat, D.D.M.; Fleischer, K.; D’Hauwers, K.W.M.; Schaafsma, E.; Conrad, Donald F.; Nagirnaja, Liina; Aston, Kenneth I.; Carrell, Douglas T.; Hotaling, James M.; Jenkins, Timothy G.; McLachlan, Rob; O’Bryan, Moira K.; Schlegel, Peter N.; Eisenberg, Michael L.; Sandlow, Jay I.; Jungheim, Emily S.; Omurtag, Kenan R.; Lopes, Alexandra M.; Seixas, Susana; Carvalho, Filipa; Fernandes, Susana; Barros, Alberto; Gonçalves, João; Caetano, Iris; Pinto, Graça; Correia, Sónia; Laan, Maris; Punab, Margus; Meyts, Ewa Rajpert-De; Jørgensen, Niels; Almstrup, Kristian; Krausz, Csilla G.; Jarvi, Keith A.; Nagirnaja, L.; Conrad, D.F.; Friedrich, C.; Kliesch, S.; Aston, K.I.; Riera-Escamilla, A.; Krausz, C.; Gonzaga-Jauregui, C.; Santibanez-Koref, M.; Elliott, D. J.; Vissers, L.E.L.M.; Tüttelmann, F.; O’Bryan, M.K.; Ramos, L.; Xavier, M.J.; van der Heijden, G.W.; Veltman, J.A.De novo mutations are known to play a prominent role in sporadic disorders with reduced fitness. We hypothesize that de novo mutations play an important role in severe male infertility and explain a portion of the genetic causes of this understudied disorder. To test this hypothesis, we utilize trio-based exome sequencing in a cohort of 185 infertile males and their unaffected parents. Following a systematic analysis, 29 of 145 rare (MAF < 0.1%) protein-altering de novo mutations are classified as possibly causative of the male infertility phenotype. We observed a significant enrichment of loss-of-function de novo mutations in loss-of-function-intolerant genes (p-value = 1.00 × 10−5) in infertile men compared to controls. Additionally, we detected a significant increase in predicted pathogenic de novo missense mutations affecting missense-intolerant genes (p-value = 5.01 × 10−4) in contrast to predicted benign de novo mutations. One gene we identify, RBM5, is an essential regulator of male germ cell pre-mRNA splicing and has been previously implicated in male infertility in mice. In a follow-up study, 6 rare pathogenic missense mutations affecting this gene are observed in a cohort of 2,506 infertile patients, whilst we find no such mutations in a cohort of 5,784 fertile men (p-value = 0.03). Our results provide evidence for the role of de novo mutations in severe male infertility and point to new candidate genes affecting fertility.
- Diverse monogenic subforms of human spermatogenic failurePublication . Nagirnaja, Liina; Lopes, Alexandra M.; Charng, Wu-Lin; Miller, Brian; Stakaitis, Rytis; Golubickaite, Ieva; Stendahl, Alexandra; Luan, Tianpengcheng; Friedrich, Corinna; Mahyari, Eisa; Fadial, Eloise; Kasak, Laura; Vigh-Conrad, Katinka; Oud, Manon S.; Xavier, Miguel J.; Cheers, Samuel R.; James, Emma R.; Guo, Jingtao; Jenkins, Timothy G.; Riera-Escamilla, Antoni; Barros, Alberto; Carvalho, Filipa; Fernandes, Susana; Gonçalves, João; Gurnett, Christina A.; Jørgensen, Niels; Jezek, Davor; Jungheim, Emily S.; Kliesch, Sabine; McLachlan, Robert I.; Omurtag, Kenan R.; Pilatz, Adrian; Sandlow, Jay I.; Smith, James; Eisenberg, Michael L.; Hotaling, James M.; Jarvi, Keith A.; Punab, Margus; Rajpert-De Meyts, Ewa; Carrell, Douglas T.; Krausz, Csilla; Laan, Maris; O’Bryan, Moira K.; Schlegel, Peter N.; Tüttelmann, Frank; Veltman, Joris A.; Almstrup, Kristian; Aston, Kenneth I.; Conrad, Donald F.Non-obstructive azoospermia (NOA) is the most severe form of male infertility and typically incurable. Defining the genetic basis of NOA has proven chal lenging, and the most advanced classification of NOA subforms is not based on genetics, but simple description of testis histology. In this study, we exome sequenced over 1000 clinically diagnosed NOA cases and identified a plausible recessive Mendelian cause in 20%. We find further support for 21 genes in a 2-stage burden test with 2072 cases and 11,587 fertile controls. The disrupted genes are primarily on the autosomes, enriched for undescribed human “knockouts”, and, for the most part, have yet to be linked to a Mendelian trait. Integration with single-cell RNA sequencing data shows that azoospermia genes can be grouped into molecular subforms with synchronized expression patterns, and analogs of these subforms exist in mice. This analysis framework identifies groups of genes with known roles in spermatogenesis but also reveals unrecognized subforms, such as a set of genes expressed across mitotic divisions of differentiating spermatogonia. Our findings highlight NOA as an understudied Mendelian disorder and provide a conceptual structure for organizing the complex genetics of male infertility, which may provide a rational basis for disease classification
- Human spermatogenic failure purges deleterious mutation load from the autosomes and both sex chromosomes, including the gene DMRT1Publication . Lopes, Alexandra; Aston, Kenneth I.; Thompson, Emma E; Carvalho, Filipa; Gonçalves, João; Huang, N.; Matthiesen, Rune; Noordam, Michiel J.; Quintela, Ines; Ramu, Avinash; Seabra, Catarina; Wilfert, Amy B.; Dai, Juncheng; Downie, Jonathan; Fernandes, Susana; Guo, Xuejiang; Shah, Jiahao; Amorim, Antonio; Barros, Alberto; Carracedo, A.; Hu, Z.; Hurles, M.E.; Moskovtsev, S.; Ober, C.; Paduch, D.A.; Schiffman, J.D.; Schlegel, P.N.; Sousa, M.; Carrell, D.T.; Conrad, D.F.Gonadal failure, along with early pregnancy loss and perinatal death, may be an important filter that limits the propagation of harmful mutations in the human population. We hypothesized that men with spermatogenic impairment, a disease with unknown genetic architecture and a common cause of male infertility, are enriched for rare deleterious mutations compared to men with normal spermatogenesis. After assaying genomewide SNPs and CNVs in 323 Caucasian men with idiopathic spermatogenic impairment and more than 1,100 controls, we estimate that each rare autosomal deletion detected in our study multiplicatively changes a man’s risk of disease by 10% (OR 1.10 [1.04–1.16], p,261023), rare X-linked CNVs by 29%, (OR 1.29 [1.11–1.50], p,161023), and rare Y-linked duplications by 88% (OR 1.88 [1.13–3.13], p,0.03). By contrasting the properties of our case-specific CNVs with those of CNV callsets from cases of autism, schizophrenia, bipolar disorder, and intellectual disability, we propose that the CNV burden in spermatogenic impairment is distinct from the burden of large, dominant mutations described for neurodevelopmental disorders. We identified two patients with deletions of DMRT1, a gene on chromosome 9p24.3 orthologous to the putative sex determination locus of the avian ZW chromosome system. In an independent sample of Han Chinese men, we identified 3 more DMRT1 deletions in 979 cases of idiopathic azoospermia and none in 1,734 controls, and found none in an additional 4,519 controls from public databases. The combined results indicate that DMRT1 loss-of-function mutations are a risk factor and potential genetic cause of human spermatogenic failure (frequency of 0.38% in 1306 cases and 0% in 7,754 controls, p = 6.261025). Our study identifies other recurrent CNVs as potential causes of idiopathic azoospermia and generates hypotheses for directing future studies on the genetic basis of male infertility and IVF outcomes.
- A novel Alu-mediated microdeletion at 11p13 removes WT1 in a patient with cryptorchidism and azoospermiaPublication . Seabra, Catarina M.; Quental, Sofia; Paula Neto, Ana; Carvalho, Filipa; Gonçalves, João; Paulo Oliveira, João; Fernandes, Susana; Sousa, Mário; Barros, Alberto; Amorim, António; Lopes, Alexandra M.This article describes a patient with cryptorchidism and nonobstructive azoospermia presenting a novel microdeletion of approximately 1 Mb at 11p13. It was confirmed by multiplex ligation-dependent probe amplification that this heterozygous deletion spanned nine genes (WT1, EIF3M, CCDC73, PRRG4, QSER1, DEPDC7, TCP11L1, CSTF3 and HIPK3) and positioned the breakpoints within highly homologous repetitive elements. As far as is known, this is the smallest deletion as-yet described encompassing the WT1 gene and was detected only once in a total of 32 Portuguese patients with isolated uni- or bilateral cryptorchidism. These findings suggest that molecular analysis in patients with genitourinary features suggestive of WT1 impairment, namely cryptorchidism and renal abnormalities, may reveal cryptic genetic defects.
- The mutational spectrum of WT1 in male infertilityPublication . Seabra, Catarina M.; Quental, Sofia; Lima, Ana C; Carvalho, Filipa; Gonçalves, João; Fernandes, Susana; Pereira, Iris; Silva, Júlia; Marques, Patrícia I.; Sousa, Mário; Barros, Alberto; Seixas, Susana; Amorim, António; Lopes, Alexandra M.PURPOSE: We evaluated the impact of WT1 mutations in isolated severe spermatogenic impairment in a population of European ancestry. WT1 was first identified as the gene responsible for Wilms tumor. It was later associated with a plethora of clinical phenotypes often accompanied by urogenital defects and male infertility. The recent finding of WT1 missense mutations in Chinese azoospermic males without major gonadal malformations broadened the phenotypic spectrum of WT1 defects and motivated this study. MATERIALS AND METHODS: We analyzed the WT1 coding region in a cohort of 194 Portuguese patients with nonobstructive azoospermia and in 188 with severe oligozoospermia with increased depth for the exons encoding the regulatory region of the protein. We also analyzed a group of 31 infertile males with a clinical history of unilateral or bilateral cryptorchidism and 1 patient with anorchia. RESULTS: We found 2 WT1 missense substitutions at higher frequency in patients than in controls. 1) A novel variant in exon 1 (p.Pro130Leu) that disrupted a mammalian specific polyproline stretch in the self-association domain was more frequent in azoospermia cases (0.27% vs 0.13%, p = 0.549). 2) A rare variant in a conserved residue in close proximity to the first zinc finger (pCys350Arg) was more frequent in severe oligozoospermia cases (0.80% vs 0.13%, p = 0.113). CONCLUSIONS: Results suggest a role for rare WT1 damaging variants in severe spermatogenic failure in populations of European ancestry. Large multicenter studies are needed to fully assess the contribution of WT1 genetic alterations to male infertility in the absence of other disease phenotypes.
- Validation of Rare Structural Variants in Portuguese Azoospermic PatientsPublication . Seabra, Catarina; Carvalho, Filipa; Gonçalves, João; Matthiesen, Rune; Fernandes, Susana; Ana, Neto; de Sousa, Mário; Barros, Alberto; Amorim, António; Donald, Conrad; Lopes, AlexandraAzoospermia affects approximately 15% of infertile males. Despite considerable research efforts in the last decades, in the majority of cases the cause remains unidentified. Chromosomal abnormalities and Yq microdeletions have been thoroughly studied, yet only account for 17% of azoospermic men. In fact, little is known about the contribution of the hemizygous X-linked and autosomal genes to male infertility. This study focuses on the validation of rare deletions encompassing candidate genes on the X chromosome and on the autosomes, previously identified by Affymetrix 6.0 SNP Array, in a cohort of 166 Portuguese individuals with severe spermatogenic impairment (non-obstructive azoospermia and severe oligozoospermia). As expected, the protein-coding genes CXORF48, and MAGEA8, as well as a miRNA (hsa-mir-4330) could not be amplified by PCR from the single X chromosome of the patients suspected of carrying deletions. These rearrangements will be further validated by aCGH (array Comparative Genomic Hybridization). Additionally, by MLPA analysis on 11p13 we confirmed a large deletion (~1Mb) spanning the WT1 gene - a conserved transcription factor known to play a crucial role in gonadal differentiation. A retrospective clinical evaluation of this patient revealed partial gonadal dysgenesis, consistent with a causal role for the newly discovered deletion. These results reveal new candidate genes for a role in spermatogenic pathways and suggest that haploinsufficiency of proteins important for the development of the male reproductive system can lead to spermatogenic dysfunction.
- Variants in GCNA, X-linked germ-cell genome integrity gene, identified in men with primary spermatogenic failurePublication . Hardy, Jimmaline J.; Wyrwoll, Margot J.; Mcfadden, William; Malcher, Agnieszka; Rotte, Nadja; Pollock, Nijole C.; Munyoki, Sarah; Veroli, Maria V.; Houston, Brendan J.; Xavier, Miguel J.; Kasak, Laura; Punab, Margus; Laan, Maris; Kliesch, Sabine; Schlegel, Peter; Jaffe, Thomas; Hwang, Kathleen; Vukina, Josip; Brieño-Enríquez, Miguel A.; Orwig, Kyle; Yanowitz, Judith; Buszczak, Michael; Veltman, Joris A.; Oud, Manon; Nagirnaja, Liina; Olszewska, Marta; O’Bryan, Moira K.; Conrad, Donald F.; Kurpisz, Maciej; Tüttelmann, Frank; Yatsenko, Alexander N.; Conrad, Donald F.; Nagirnaja, Liina; Aston, Kenneth I.; Carrell, Douglas T.; Hotaling, James M.; Jenkins, Timothy G.; McLachlan, Rob; O’Bryan, Moira K.; Schlegel, Peter N.; Eisenberg, Michael L.; Sandlow, Jay I.; Jungheim, Emily S.; Omurtag, Kenan R.; Lopes, Alexandra M.; Seixas, Susana; Carvalho, Filipa; Fernandes, Susana; Barros, Alberto; Gonçalves, João; Caetano, Iris; Pinto, Graça; Correia, Sónia; Laan, Maris; Punab, Margus; Meyts, Ewa Rajpert-De; Jørgensen, Niels; Almstrup, Kristian; Krausz, Csilla G.; Jarvi, Keith A.; on behalf of GEMINI ConsortiumMale infertility impacts millions of couples yet, the etiology of primary infertility remains largely unknown. A critical element of successful spermatogenesis is maintenance of genome integrity. Here, we present a genomic study of spermatogenic failure (SPGF). Our initial analysis (n=176) did not reveal known gene-candidates but identifed a potentially signifcant single-nucleotide variant (SNV) in X-linked germ-cell nuclear antigen (GCNA). Together with a larger follow-up study (n=2049), 7 likely clinically relevant GCNA variants were identifed. GCNA is critical for genome integrity in male meiosis and knockout models exhibit impaired spermatogenesis and infertility. Single-cell RNA-seq and immunohistochemistry confrm human GCNA expression from spermatogonia to elongated spermatids. Five identifed SNVs were located in key functional regions, including N-terminal SUMO-interacting motif and C-terminal Spartan-like protease domain. Notably, variant p.Ala115ProfsTer7 results in an early frameshift, while Spartan-like domain missense variants p.Ser659Trp and p.Arg664Cys change conserved residues, likely afecting 3D structure. For variants within GCNA’s intrinsically disordered region, we performed computational modeling for consensus motifs. Two SNVs were predicted to impact the structure of these consensus motifs. All identifed variants have an extremely low minor allele frequency in the general population and 6 of 7 were not detected in>5000 biological fathers. Considering evidence from animal models, germ-cell-specifc expression, 3D modeling, and computational predictions for SNVs, we propose that identifed GCNA variants disrupt structure and function of the respective protein domains, ultimately arresting germ-cell division. To our knowledge, this is the frst study implicating GCNA, a key genome integrity factor, in human male infertility.