Browsing by Author "Lopes, Alexandra M"
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- 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).
- Changes in environmental exposures over decades may influence the genetic architecture of severe spermatogenic failurePublication . Cerván-Martín, Miriam; González-Muñoz, Sara; Guzmán-Jiménez, Andrea; Higueras-Serrano, Inmaculada; Castilla, José A.; Garrido, Nicolás; Luján, Saturnino; Bassas, Lluís; Seixas, Susana; Gonçalves, João; Lopes, Alexandra M; Larriba, Sara; Palomino-Morales, Rogelio J.; Bossini-Castillo, Lara; Carmona, F. DavidStudy question: Do the genetic determinants of idiopathic severe spermatogenic failure (SPGF) differ between generations? Summary answer: Our data support that the genetic component of idiopathic SPGF is impacted by dynamic changes in environmental exposures over decades. What is known already: The idiopathic form of SPGF has a multifactorial etiology wherein an interaction between genetic, epigenetic, and environmental factors leads to the disease onset and progression. At the genetic level, genome-wide association studies (GWASs) allow the analysis of millions of genetic variants across the genome in a hypothesis-free manner, as a valuable tool for identifying susceptibility risk loci. However, little is known about the specific role of non-genetic factors and their influence on the genetic determinants in this type of conditions. Study design, size, duration: Case-control genetic association analyses were performed including a total of 912 SPGF cases and 1360 unaffected controls. Participants/materials, setting, methods: All participants had European ancestry (Iberian and German). SPGF cases were diagnosed during the last decade either with idiopathic non-obstructive azoospermia (n = 547) or with idiopathic non-obstructive oligozoospermia (n = 365). Case-control genetic association analyses were performed by logistic regression models considering the generation as a covariate and by in silico functional characterization of the susceptibility genomic regions. Main results and the role of chance: This analysis revealed 13 novel genetic association signals with SPGF, with eight of them being independent. The observed associations were mostly explained by the interaction between each lead variant and the age-group. Additionally, we established links between these loci and diverse non-genetic factors, such as toxic or dietary habits, respiratory disorders, and autoimmune diseases, which might potentially influence the genetic architecture of idiopathic SPGF. Large scale data: GWAS data are available from the authors upon reasonable request. Limitations, reasons for caution: Additional independent studies involving large cohorts in ethnically diverse populations are warranted to confirm our findings. Wider implications of the findings: Overall, this study proposes an innovative strategy to achieve a more precise understanding of conditions such as SPGF by considering the interactions between a variable exposome through different generations and genetic predisposition to complex diseases.