6 results on '"Inés Llinares-Burguet"'
Search Results
2. Minigene-based splicing analysis and ACMG/AMP-based tentative classification of 56 ATM variants
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Elena Bueno‐Martínez, Lara Sanoguera‐Miralles, Alberto Valenzuela‐Palomo, Ada Esteban‐Sánchez, Víctor Lorca, Inés Llinares‐Burguet, Jamie Allen, Alicia García‐Álvarez, Pedro Pérez‐Segura, Mercedes Durán, Douglas F Easton, Peter Devilee, Maaike PG Vreeswijk, Miguel de la Hoya, Eladio A Velasco‐Sampedro, de la Hoya, Miguel [0000-0002-8113-1410], Velasco-Sampedro, Eladio A [0000-0002-9682-5589], Apollo - University of Cambridge Repository, European Commission, Instituto de Salud Carlos III, Junta de Castilla y León, CSIC-UVA - Instituto de Biología y Genética Molecular (IBGM), Universidad de Valladolid, Asociación Española Contra el Cáncer, Comunidad de Madrid, and Easton, Douglas [0000-0003-2444-3247]
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Susceptibility genes ,RNA Splicing ,Minigenes ,hereditary breast cancer ,Ataxia Telangiectasia Mutated Proteins ,Splicing ,Aberrant splicing ,Pathology and Forensic Medicine ,VUS ,aberrant splicing ,splicing ,Alternative Splicing ,Ataxia Telangiectasia ,splicing assay ,Splicing assay ,Variant classification ,ATM ,MCF-7 Cells ,Humans ,minigenes ,susceptibility genes ,variant classification ,Hereditary breast cancer ,HeLa Cells - Abstract
The ataxia telangiectasia-mutated (ATM) protein is a major coordinator of the DNA damage response pathway. ATM loss-of-function variants are associated with 2-fold increased breast cancer risk. We aimed at identifying and classifying spliceogenic ATM variants detected in subjects of the large-scale sequencing project BRIDGES. A total of 381 variants at the intron-exon boundaries were identified, 128 of which were predicted to be spliceogenic. After further filtering, we ended up selecting 56 variants for splicing analysis. Four functional minigenes (mgATM) spanning exons 4-9, 11-17, 25-29, and 49-52 were constructed in the splicing plasmid pSAD. Selected variants were genetically engineered into the four constructs and assayed in MCF-7/HeLa cells. Forty-eight variants (85.7%) impaired splicing, 32 of which did not show any trace of the full-length (FL) transcript. A total of 43 transcripts were identified where the most prevalent event was exon/multi-exon skipping. Twenty-seven transcripts were predicted to truncate the ATM protein. A tentative ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme that integrates mgATM data allowed us to classify 29 ATM variants as pathogenic/likely pathogenic and seven variants as likely benign. Interestingly, the likely pathogenic variant c.1898+2T>G generated 13% of the minigene FL-transcript due to the use of a noncanonical GG-5'-splice-site (0.014% of human donor sites). Circumstantial evidence in three ATM variants (leakiness uncovered by our mgATM analysis together with clinical data) provides some support for a dosage-sensitive expression model in which variants producing ¿30% of FL-transcripts would be predicted benign, while variants producing ¿13% of FL-transcripts might be pathogenic., PD, MPGV, DFE, MdlH and EAV received funding from the European Union's Horizon 2020 research and innovation program under grant agreement no. 634935. The EAV lab is supported by grants from the Spanish Ministry of Science and Innovation, Plan Nacional de I+D+I 2013-2016, ISCIII (PI17/00227 and PI20/00225) co-funded by the FEDER from Regional Development European Funds (European Union) and from the Consejería de Educación, Junta de Castilla y León, ref. CSI242P18 (actuación cofinanciada P.O. FEDER 2014-2020 de Castilla y León). The MdlH lab is supported by a grant from the Spanish Ministry of Science and Innovation, Plan Nacional de I+D+I 2013-2016, ISCIII (PI20/00110) co-funded by FEDER from Regional Development European Funds (European Union). Programa Estratégico Instituto de Biología y Genética Molecular (IBGM), Escalera de Excelencia, Junta de Castilla y León (Ref. CLU-2019-2002). EB-M is a postdoctoral researcher funded by the University of Valladolid (POSTDOC-UVA05, 2022-2025). AV-P and IL-B are supported by predoctoral fellowships from the Consejería de Educación, Junta de Castilla y León. LS-M is supported by a predoctoral fellowship from the AECC-Scientific Foundation, Sede Provincial de Valladolid (2019–2023). AE-S is supported through the Operational Program for Youth Employment and Youth Employment Initiative (YEI), called by the Community of Madrid in 2020, and co-financed by the European Social Fund.
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- 2022
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3. Minigene Splicing Assays Identify 20 Spliceogenic Variants of the Breast/Ovarian Cancer Susceptibility Gene
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Lara, Sanoguera-Miralles, Elena, Bueno-Martínez, Alberto, Valenzuela-Palomo, Ada, Esteban-Sánchez, Inés, Llinares-Burguet, Pedro, Pérez-Segura, Alicia, García-Álvarez, Miguel, de la Hoya, and Eladio A, Velasco-Sampedro
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- 2022
4. Minigene splicing assays identify 20 spliceogenic variants of the breast/Ovarian cancer susceptibility gene RAD51C
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Lara Sanoguera-Miralles, Elena Bueno-Martínez, Alberto Valenzuela-Palomo, Ada Esteban-Sánchez, Inés Llinares-Burguet, Pedro Pérez-Segura, Alicia García-Álvarez, Miguel de la Hoya, Eladio A. Velasco-Sampedro, Ministerio de Ciencia e Innovación (España), Instituto de Salud Carlos III, European Commission, Junta de Castilla y León, CSIC-UVA - Instituto de Biología y Genética Molecular (IBGM), Asociación Española Contra el Cáncer, Universidad de Valladolid, and Comunidad de Madrid
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Cancer Research ,Oncology ,RAD51C ,Hereditary breast and ovarian cancer ,Minigenes ,Cancer susceptibility genes ,hereditary breast and ovarian cancer ,cancer susceptibility genes ,aberrant splicing ,functional assay ,minigenes ,clinical interpretation ,Functional assay ,Aberrant splicing ,Clinical interpretation - Abstract
RAD51C loss-of-function variants are associated with an increased risk of breast and ovarian cancers. Likewise, splicing disruptions are a frequent mechanism of gene inactivation. Taking advantage of a previous splicing-reporter minigene with exons 2-8 (mgR51C_ex2-8), we proceeded to check its impact on the splicing of candidate ClinVar variants. A total of 141 RAD51C variants at the intron/exon boundaries were analyzed with MaxEntScan. Twenty variants were selected and genetically engineered into the wild-type minigene. All the variants disrupted splicing, and 18 induced major splicing anomalies without any trace or minimal amounts (, The EAV lab is supported by grants from the Spanish Ministry of Science and Innovation, Plan Nacional de I+D+I 2013–2016, ISCIII (PI17/00227 and PI20/00225), co-funded by FEDER (the European Regional Development Fund, European Union) and the Consejería de Educación, Junta de Castilla y León, ref. CSI242P18 (actuación cofinanciada P.O. FEDER 2014–2020 de Castilla y León) and Programa Estratégico Instituto de Biología y Genética Molecular (IBGM), Escalera de Excelencia, Junta de Castilla y León (Ref. CLU-2019-02). The MdlH lab is supported by a grant from the Spanish Ministry of Science and Innovation, Plan Nacional de I+D+I 2013–2016, ISCIII (PI20/00110), cofunded by FEDER. LS-M is supported by a predoctoral fellowship from the AECC Scientific Foundation, Sede Provincial de Valladolid (2019–2023). EB-M is a postdoctoral researcher funded by the University of Valladolid (POSTDOC-UVA05, 2022–2025). IL-B is supported by a predoctoral fellowship from the Consejería de Educación, Junta de Castilla y León (2018–2022). AE-S is supported through the Operational Program for Youth Employment and the Youth Employment Initiative (YEI), set up by the Community of Madrid in 2020 and co-financed by the European Social Fund.
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- 2022
5. Splicing analysis of 16 PALB2 clinVar variants by minigene assays: identification of six likely pathogenic variants
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Alberto Valenzuela-Palomo, Lara Sanoguera-Miralles, Elena Bueno-Martínez, Ada Esteban-Sánchez, Inés Llinares-Burguet, Alicia García-Álvarez, Pedro Pérez-Segura, Susana Gómez-Barrero, Miguel de la Hoya, Eladio A. Velasco-Sampedro, Ministerio de Ciencia e Innovación (España), Instituto de Salud Carlos III, European Commission, Junta de Castilla y León, CSIC-UVA - Instituto de Biología y Genética Molecular (IBGM), Asociación Española Contra el Cáncer, Universidad de Valladolid, and Comunidad de Madrid
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Cancer Research ,Oncology ,PALB2 ,Minigenes ,hereditary breast cancer ,cancer susceptibility genes ,aberrant splicing ,functional assay ,minigenes ,clinical interpretation ,Cancer susceptibility genes ,Functional assay ,Aberrant splicing ,Clinical interpretation ,Hereditary breast cancer - Abstract
PALB2 loss-of-function variants are associated with significant increased risk of breast cancer as well as other types of tumors. Likewise, splicing disruptions are a common mechanism of disease susceptibility. Indeed, we previously showed, by minigene assays, that 35 out of 42 PALB2 variants impaired splicing. Taking advantage of one of these constructs (mgPALB2_ex1-3), we proceeded to analyze other variants at exons 1 to 3 reported at the ClinVar database. Thirty-one variants were bioinformatically analyzed with MaxEntScan and SpliceAI. Then, 16 variants were selected for subsequent RNA assays. We identified a total of 12 spliceogenic variants, 11 of which did not produce any trace of the expected minigene full-length transcript. Interestingly, variant c.49-1G > A mimicked previous outcomes in patient RNA (transcript ∆(E2p6)), supporting the reproducibility of the minigene approach. A total of eight variant-induced transcripts were characterized, three of which (∆(E1q17), ∆(E3p11), and ∆(E3)) were predicted to introduce a premature termination codon and to undergo nonsense-mediated decay, and five (▼(E1q9), ∆(E2p6), ∆(E2), ▼(E3q48)-a, and ▼(E3q48)-b) maintained the reading frame. According to an ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme, which integrates mgPALB2 data, six PALB2 variants were classified as pathogenic/likely pathogenic, five as VUS, and five as likely benign. Furthermore, five ±1,2 variants were catalogued as VUS because they produced significant proportions of in-frame transcripts of unknown impact on protein function., The EAV lab is supported by grants from the Spanish Ministry of Science and Innovation, Plan Nacional de I+D+I 2013–2016, ISCIII (PI20/00225), co‐funded by FEDER (the European Regional Development Fund, European Union) and the Consejería de Educación, Junta de Castilla Cancers 2022, 14, 4541 16 of 18 y León, ref. CSI242P18 (actuación cofinanciada P.O. FEDER 2014–2020 de Castilla y León) and Pro‐ grama Estratégico Instituto de Biología y Genética Molecular (IBGM), Escalera de Excelencia, Junta de Castilla y León (Ref. CLU‐2019‐02). The MdlH lab is supported by a grant from the Spanish Ministry of Science and Innovation, Plan Nacional de I+D+I 2013–2016, ISCIII (PI20/00110), co‐funded by FEDER. L.S.‐M. is supported by a predoctoral fellowship from the AECC Scientific Foundation, Sede Provincial de Valladolid (2019–2023). E.B.‐M. is a postdoctoral researcher funded by the University of Valladolid (POSTDOC‐UVA05, 2022–2025). I.L.‐B. is supported by a predoctoral fellowship from the Consejería de Educación, Junta de Castilla y León (2022–2025). A.E.‐S. is supported through the Operational Program for Youth Employment and the Youth Employment Initiative (YEI), set up by the Community of Madrid in 2020 and co‐financed by the European Social Fund.
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- 2022
6. Evaluation of Male Fertility-Associated Loci in a European Population of Patients with Severe Spermatogenic Impairment
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F. Javier Vicente, Cláudia Pina Costa, Samuel Santos-Ribeiro, Alexandra M. Lopes, Rocio Rivera-Egea, M. Fernanda Peraza, Josvany Sánchez-Curbelo, João Gonçalves, Gema Romeu, Miguel Burgos, Ana Clavero, Iris Pereira-Caetano, Francisco J. Barrionuevo, F. David Carmona, Alberto Barros, Saturnino Luján, Olga López-Rodrigo, Nicolás Garrido, Lluís Bassas, Inés Llinares-Burguet, Susana Seixas, Filipa Carvalho, Rogelio Palomino-Morales, José A. Castilla, Patrícia Isabel Marques, Chiranan Khantham, Sara Larriba, Rafael Jiménez, Andrea Guzmán-Jiménez, Lara Bossini-Castillo, Miriam Cerván-Martín, M. Carmen Gonzalvo, Centre for Toxicogenomics and Human Health (ToxOmics), NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM), and Instituto de Investigação e Inovação em Saúde
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Infertility ,Physiology ,lcsh:Medicine ,Medicine (miscellaneous) ,Single-nucleotide polymorphism ,Biology ,Article ,genetic association analysis ,Male infertility ,Impaired Spermatogenesis ,Non-obstructive Azoospermia ,03 medical and health sciences ,0302 clinical medicine ,Genetic variation ,Genetic predisposition ,medicine ,Genetics ,non-obstructive azoospermia ,Allele frequency ,030304 developmental biology ,Genetic association ,Azoospermia ,0303 health sciences ,030219 obstetrics & reproductive medicine ,lcsh:R ,Severe Oligospermia ,medicine.disease ,impaired spermatogenesis ,Esterilitat ,severe oligospermia ,Genetic Association Analysis ,Doenças Genéticas ,infertility ,Genètica ,SNPs - Abstract
Infertility is a growing concern in developed societies. Two extreme phenotypes of male infertility are non-obstructive azoospermia (NOA) and severe oligospermia (SO), which are characterized by severe spermatogenic failure (SpF). We designed a genetic association study comprising 725 Iberian infertile men as a consequence of SpF and 1058 unaffected controls to evaluate whether five single-nucleotide polymorphisms (SNPs), previously associated with reduced fertility in Hutterites, are also involved in the genetic susceptibility to idiopathic SpF and specific clinical entities. A significant difference in the allele frequencies of USP8-rs7174015 was observed under the recessive model between the NOA group and both the control group (p = 0.0226, OR = 1.33) and the SO group (p = 0.0048, OR = 1.78). Other genetic associations for EPSTI1-rs12870438 and PSAT1-rs7867029 with SO and between TUSC1-rs10966811 and testicular sperm extraction (TESE) success in the context of NOA were observed. In silico analysis of functional annotations demonstrated cis-eQTL effects of such SNPs likely due to the modification of binding motif sites for relevant transcription factors of the spermatogenic process. The findings reported here shed light on the molecular mechanisms leading to severe phenotypes of idiopathic male infertility, and may help to better understand the contribution of the common genetic variation to the development of these conditions., Spanish Ministry of Economy and Competitiveness through the Spanish State Plan for Scientific and Technical Research and Innovation SAF201678722-R, Spanish Government RYC-2014-16458, "Juan de la Cierva Incorporacion" program IJC2018-038026-I, European Union (EU), Spanish Government FIS-ISCIII DTS18/00101, Generalitat de Catalunya 2017SGR191, "Plan Propio" program of the University of Granada ("Becas de Iniciacion a la Investigacion para estudiantes de Grado"), "Researchers Consolidation Program" from the SNS-Dpt. Salut Generalitat de Catalunya CES09/020, FCT/MCTES, through national funds attributed to Center for Toxicogenomics and Human Health-ToxOmics UIDB/00009/2020, Portuguese Foundation for Science and Technology SFRH/BPD/120777/2016, Portuguese State Budget of the Ministry for Science, Technology and High Education, European Social Fund through the Programa Operacional do Capital Humano, Portuguese Foundation for Science and Technology IF/01262/2014, FCT in the framework of the project "Institute for Research and Innovation in Health Sciences" POCI-01-0145-FEDER-007274
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- 2020
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