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Hernando-Calvo A, Vila-Casadesús M, Bareche Y, Gonzalez-Medina A, Abbas-Aghababazadeh F, Lo Giacco D, Martin A, Saavedra O, Brana I, Vieito M, Fasani R, Stagg J, Mancuso F, Haibe-Kains B, Han M, Berche R, Pugh TJ, Mirallas O, Jimenez J, Gonzalez NS, Valverde C, Muñoz-Couselo E, Suarez C, Diez M, Élez E, Capdevila J, Oaknin A, Saura C, Macarulla T, Galceran JC, Felip E, Dienstmann R, Bedard PL, Nuciforo P, Seoane J, Tabernero J, Garralda E, Vivancos A. A pan-cancer clinical platform to predict immunotherapy outcomes and prioritize immuno-oncology combinations in early-phase trials. Med 2023; 4:710-727.e5. [PMID: 37572657 DOI: 10.1016/j.medj.2023.07.006] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 06/01/2023] [Accepted: 07/14/2023] [Indexed: 08/14/2023]
Abstract
BACKGROUND Immunotherapy is effective, but current biomarkers for patient selection have proven modest sensitivity. Here, we developed VIGex, an optimized gene signature based on the expression level of 12 genes involved in immune response with RNA sequencing. METHODS We implemented VIGex using the nCounter platform (Nanostring) on a large clinical cohort encompassing 909 tumor samples across 45 tumor types. VIGex was developed as a continuous variable, with cutoffs selected to detect three main categories (hot, intermediate-cold and cold) based on the different inflammatory status of the tumor microenvironment. FINDINGS Hot tumors had the highest VIGex scores and exhibited an increased abundance of tumor-infiltrating lymphocytes as compared with the intermediate-cold and cold. VIGex scores varied depending on tumor origin and anatomic site of metastases, with liver metastases showing an immunosuppressive tumor microenvironment. The predictive power of VIGex-Hot was observed in a cohort of 98 refractory solid tumor from patients treated in early-phase immunotherapy trials and its clinical performance was confirmed through an extensive metanalysis across 13 clinically annotated gene expression datasets from 877 patients treated with immunotherapy agents. Last, we generated a pan-cancer biomarker platform that integrates VIGex categories with the expression levels of immunotherapy targets under development in early-phase clinical trials. CONCLUSIONS Our results support the clinical utility of VIGex as a tool to aid clinicians for patient selection and personalized immunotherapy interventions. FUNDING BBVA Foundation; 202-2021 Division of Medical Oncology and Hematology Fellowship award; Princess Margaret Cancer Center.
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Affiliation(s)
- Alberto Hernando-Calvo
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain; Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G2C4, Canada; Departamento de Medicina, Universidad Autónoma de Barcelona (UAB), 08035 Barcelona, Spain
| | | | - Yacine Bareche
- Institut du Cancer de Montréal, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, QC H2X0A9, Canada; Faculty of Pharmacy, Université de Montréal, Montréal, QC H3T1J4, Canada
| | | | | | | | - Agatha Martin
- Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Omar Saavedra
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Irene Brana
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Maria Vieito
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Roberta Fasani
- Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - John Stagg
- Institut du Cancer de Montréal, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, QC H2X0A9, Canada; Faculty of Pharmacy, Université de Montréal, Montréal, QC H3T1J4, Canada
| | | | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G2C4, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S2E4, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada; Vector Institute for Artificial Intelligence, Toronto, ON M5G1M1, Canada
| | - Ming Han
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G2C4, Canada
| | - Roger Berche
- Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G2C4, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Oriol Mirallas
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Jose Jimenez
- Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Nadia Saoudi Gonzalez
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Claudia Valverde
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Eva Muñoz-Couselo
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Cristina Suarez
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Marc Diez
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Elena Élez
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Jaume Capdevila
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Ana Oaknin
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Cristina Saura
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Teresa Macarulla
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Joan Carles Galceran
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Enriqueta Felip
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | | | - Philippe L Bedard
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G2C4, Canada
| | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Joan Seoane
- Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Josep Tabernero
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Elena Garralda
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Ana Vivancos
- Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain.
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Hernando-Calvo A, Yang SYC, Vila-Casadesús M, Berman HK, Spreafico A, Abdul Razak AR, Lheureux S, Hansen AR, Lo Giacco D, Matito J, Pugh TJ, Bratman SV, Berché R, Saavedra Santa Gadea O, Garralda E, Elston S, Siu LL, Ohashi PS, Vivancos A, Bedard PL. External validation of the VIGex gene-expression signature (GES) as a novel predictive biomarker for immune checkpoint treatment (ICT). J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.2510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2510 Background: VIGex is a 12- gene GES classifier initially developed on the Nanostring platform and validated for RNA-seq. VIGex classifies samples into Hot, intermediate-Cold (I-Cold) and Cold subgroups. The Hot subgroup as defined by VIGex has been associated with better (PFS) in patients (pts) treated on phase 1 ICT trials at Vall D’Hebron Hospital (VH) (ESMO2020). We investigated the performance of VIGex in pts treated with Pembrolizumab (P) in the INSPIRE clinical trial (NCT02644369) at Princess Margaret Cancer Centre (PM) and compared VIGex with other predictive ICT biomarkers. Methods: Pts with advanced solid tumors were treated with P 200 mg IV Q3wks. RNA-seq from baseline biopsies was performed using the Illumina NextSeq550 platform. Tumor RNA-seq data were transferred from PM to VH and classified by the VIGex algorithm blinded to clinical data. Bespoke circulating tumor DNA (ctDNA) was assayed at baseline (B) and start of cycle 3 (C3) using a pt-specific amplicon-based NGS assay (Signatera). Tumor mutational burden (TMB) was defined as the number of non-synonymous mutations per megabase and PD-L1 was assessed by immunohistochemistry (22C3). Hot subgroup (HOT) was compared to I-Cold + Cold (COLD). We defined 4 groups based on the combination of VIGex subgroups and the change in ctDNA at cycle 3 from baseline (ΔctDNA). Survival times were calculated with the Kaplan–Meier method and Cox proportional-hazard models were constructed. Results: Out of 76 pts, median age was 55y (range 21-81y), M:F 31:45, all ECOG 0-1, 16 High-grade serous ovarian, 12 triple negative breast, 12 head and neck, 10 melanoma and 26 other. Median no. of P cycles was 3 (range 1–35); follow up was 14m (range 1-67); Median PFS 10.9m and median overall survival (OS) 14m. Overall response rate (RECIST 1.1) was 24% in HOT and 10% in COLD (p = 0.22 two-sided Fisher's exact test). The HOT subgroup was significantly associated with higher OS and PFS when included in a multivariate model adjusted by tumor histology, TMB and PD-L1 (HR 0.43; 95%CI 0.23-0.81; p = 0.009) and (HR: 0.48; 95%CI 0.25-0.95; p = 0.036) respectively. A total of 57 pts had both VIGex and ΔctDNA data. The addition of ΔctDNA further improved the predictive performance of VIGex for OS (Table). Conclusions: VIGex maintained its predictive power for ICT outcomes when applied to an independent external dataset using RNA-seq. The predictive information provided by VIGex was independent of PD-L1 and TMB. Our data indicates that the addition of ΔctDNA to baseline VIGex may refine prediction for ICT outcomes. [Table: see text]
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Affiliation(s)
- Alberto Hernando-Calvo
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - S Y Cindy Yang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Maria Vila-Casadesús
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Hal K. Berman
- Department of Pathology and Laboratory Medicine, University Health Network, Toronto, ON, Canada
| | - Anna Spreafico
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | | | - Stephanie Lheureux
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Aaron Richard Hansen
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Deborah Lo Giacco
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Judit Matito
- Cancer Genomics Group, Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Trevor John Pugh
- Princess Margaret Cancer Centre, University Health Network. Ontario Institute for Cancer Research. Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Scott Victor Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Roger Berché
- Oncology Data Science (ODysSey) Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Elena Garralda
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Sawako Elston
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Lillian L. Siu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Pamela S. Ohashi
- Princess Margaret Cancer Centre, University Health Network, Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Ana Vivancos
- Cancer Genomics Group, Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
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Ortiz C, Argilés G, Élez E, Matito J, Mendizabal L, Lo Giacco D, Mancuso FM, Sanz-Garcia E, Macarulla T, Alsina M, Capdevila J, Saurí T, Azaro A, Cruz C, Hierro C, Ramon y Cajal S, Nuciforo P, Rodón J, Tabernero J, Vivancos A. Measuring the impact of Next Generation Sequencing (NGS) technique implementation in metastatic colorectal cancer (mCRC) drug development program. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.3598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | - Elena Élez
- Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Judit Matito
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Leire Mendizabal
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Deborah Lo Giacco
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Francesco M Mancuso
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | | | | | - Maria Alsina
- Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | | | - Tamara Saurí
- Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Analia Azaro
- Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Cristina Cruz
- Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Cinta Hierro
- Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | | | - Paolo Nuciforo
- Molecular Pathology Group, Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Jordi Rodón
- Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | | | - Ana Vivancos
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
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Chianese C, Gunning AC, Giachini C, Daguin F, Balercia G, Ars E, Giacco DL, Ruiz-Castañé E, Forti G, Krausz C. X chromosome-linked CNVs in male infertility: discovery of overall duplication load and recurrent, patient-specific gains with potential clinical relevance. PLoS One 2014; 9:e97746. [PMID: 24914684 PMCID: PMC4051606 DOI: 10.1371/journal.pone.0097746] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 04/24/2014] [Indexed: 12/13/2022] Open
Abstract
Introduction Spermatogenesis is a highly complex process involving several thousand genes, only a minority of which have been studied in infertile men. In a previous study, we identified a number of Copy Number Variants (CNVs) by high-resolution array-Comparative Genomic Hybridization (a-CGH) analysis of the X chromosome, including 16 patient-specific X chromosome-linked gains. Of these, five gains (DUP1A, DUP5, DUP20, DUP26 and DUP40) were selected for further analysis to evaluate their clinical significance. Materials and Methods The copy number state of the five selected loci was analyzed by quantitative-PCR on a total of 276 idiopathic infertile patients and 327 controls in a conventional case-control setting (199 subjects belonged to the previous a-CGH study). For one interesting locus (intersecting DUP1A) additional 338 subjects were analyzed. Results and Discussion All gains were confirmed as patient-specific and the difference in duplication load between patients and controls is significant (p = 1.65×10−4). Two of the CNVs are private variants, whereas 3 are found recurrently in patients and none of the controls. These CNVs include, or are in close proximity to, genes with testis-specific expression. DUP1A, mapping to the PAR1, is found at the highest frequency (1.4%) that was significantly different from controls (0%) (p = 0.047 after Bonferroni correction). Two mechanisms are proposed by which DUP1A may cause spermatogenic failure: i) by affecting the correct regulation of a gene with potential role in spermatogenesis; ii) by disturbing recombination between PAR1 regions during meiosis. This study allowed the identification of novel spermatogenesis candidate genes linked to the 5 CNVs and the discovery of the first recurrent, X-linked gain with potential clinical relevance.
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Affiliation(s)
- Chiara Chianese
- Department of Experimental and Clinical Biomedical Sciences, University of Florence and Centre of Excellence DeNothe, Florence, Italy
- Molecular Biology Laboratory, Fundació Puigvert, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Adam C. Gunning
- Department of Experimental and Clinical Biomedical Sciences, University of Florence and Centre of Excellence DeNothe, Florence, Italy
| | - Claudia Giachini
- Department of Experimental and Clinical Biomedical Sciences, University of Florence and Centre of Excellence DeNothe, Florence, Italy
| | - Fabrice Daguin
- Department of Experimental and Clinical Biomedical Sciences, University of Florence and Centre of Excellence DeNothe, Florence, Italy
| | - Giancarlo Balercia
- Division of Endocrinology, Department of Clinical and Molecular Sciences, Umberto I Hospital, Polytechnic University of Marche, Ancona, Italy
| | - Elisabet Ars
- Molecular Biology Laboratory, Fundació Puigvert, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Deborah Lo Giacco
- Molecular Biology Laboratory, Fundació Puigvert, Universitat Autonoma de Barcelona, Barcelona, Spain
- Andrology Service, Fundació Puigvert, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Eduard Ruiz-Castañé
- Andrology Service, Fundació Puigvert, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Gianni Forti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence and Centre of Excellence DeNothe, Florence, Italy
| | - Csilla Krausz
- Department of Experimental and Clinical Biomedical Sciences, University of Florence and Centre of Excellence DeNothe, Florence, Italy
- Andrology Service, Fundació Puigvert, Universitat Autonoma de Barcelona, Barcelona, Spain
- * E-mail:
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Lo Giacco D, Chianese C, Sánchez-Curbelo J, Bassas L, Ruiz P, Rajmil O, Sarquella J, Vives A, Ruiz-Castañé E, Oliva R, Ars E, Krausz C. Clinical relevance of Y-linked CNV screening in male infertility: new insights based on the 8-year experience of a diagnostic genetic laboratory. Eur J Hum Genet 2013; 22:754-61. [PMID: 24193344 DOI: 10.1038/ejhg.2013.253] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 09/28/2013] [Accepted: 10/04/2013] [Indexed: 11/09/2022] Open
Abstract
AZF microdeletion screening is routinely performed in the diagnostic work-up for male infertility; however, some issues remain debated. In this study, we provide insights into the sperm concentration cutoff value for routine testing, the predictive value of AZFc deletion for testicular sperm retrieval and the Y-background contribution to the interpopulation variability of deletion frequencies. In the Spanish population, partial AZFc rearrangements have been poorly explored and no data exist on partial duplications. In our study, 27/806 (3.3%) patients carried complete AZF deletions. All were azoo/cryptozoospermic, except for one whose sperm concentration was 2 × 10(6)/ml. In AZFc-deleted men, we observed a lower sperm recovery rate upon conventional TESE (9.1%) compared with the literature (60-80% with microTESE). Haplogroup E was the most represented among non-Spanish and hgr P among Spanish AZF deletion carriers. The analysis of AZFc partial rearrangements included 330 idiopathic infertile patients and 385 controls of Spanish origin. Gr/gr deletion, but not AZFc partial duplications, was significantly associated with spermatogenic impairment. Our data integrated with the literature suggest that: (1) routine AZF microdeletion testing could eventually include only men with ≤2 × 10(6)/ml; (2) classical TESE is associated with low sperm recovery rate in azoospermic AZFc-deleted men, and therefore microTESE should be preferred; (3) Y background could partially explain the differences in deletion frequencies among populations. Finally, our data on gr/gr deletion further support the inclusion of this genetic test in the work-up of infertile men, whereas partial AZFc duplications do not represent a risk for spermatogenic failure in the Spanish population.
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Affiliation(s)
- Deborah Lo Giacco
- 1] Molecular Biology Laboratory, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain [2] Andrology Service, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Chiara Chianese
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Josvany Sánchez-Curbelo
- Andrology Service, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Lluis Bassas
- Andrology Service, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Patricia Ruiz
- Molecular Biology Laboratory, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Osvaldo Rajmil
- Andrology Service, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Joaquim Sarquella
- Andrology Service, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Alvaro Vives
- Andrology Service, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Eduard Ruiz-Castañé
- Andrology Service, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Rafael Oliva
- 1] Human Genetics Research Group, IDIBAPS, Faculty of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain [2] Biochemistry and Molecular Genetics Service, Clinic Hospital, Villarroel 170, 08036 Barcelona, Spain
| | - Elisabet Ars
- Molecular Biology Laboratory, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Csilla Krausz
- 1] Andrology Service, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain [2] Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
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Krausz C, Giachini C, Lo Giacco D, Daguin F, Chianese C, Ars E, Ruiz-Castane E, Forti G, Rossi E. High resolution X chromosome-specific array-CGH detects new CNVs in infertile males. PLoS One 2012; 7:e44887. [PMID: 23056185 PMCID: PMC3467283 DOI: 10.1371/journal.pone.0044887] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 08/15/2012] [Indexed: 11/18/2022] Open
Abstract
CONTEXT The role of CNVs in male infertility is poorly defined, and only those linked to the Y chromosome have been the object of extensive research. Although it has been predicted that the X chromosome is also enriched in spermatogenesis genes, no clinically relevant gene mutations have been identified so far. OBJECTIVES In order to advance our understanding of the role of X-linked genetic factors in male infertility, we applied high resolution X chromosome specific array-CGH in 199 men with different sperm count followed by the analysis of selected, patient-specific deletions in large groups of cases and normozoospermic controls. RESULTS We identified 73 CNVs, among which 55 are novel, providing the largest collection of X-linked CNVs in relation to spermatogenesis. We found 12 patient-specific deletions with potential clinical implication. Cancer Testis Antigen gene family members were the most frequently affected genes, and represent new genetic targets in relationship with altered spermatogenesis. One of the most relevant findings of our study is the significantly higher global burden of deletions in patients compared to controls due to an excessive rate of deletions/person (0.57 versus 0.21, respectively; p = 8.785×10(-6)) and to a higher mean sequence loss/person (11.79 Kb and 8.13 Kb, respectively; p = 3.435×10(-4)). CONCLUSIONS By the analysis of the X chromosome at the highest resolution available to date, in a large group of subjects with known sperm count we observed a deletion burden in relation to spermatogenic impairment and the lack of highly recurrent deletions on the X chromosome. We identified a number of potentially important patient-specific CNVs and candidate spermatogenesis genes, which represent novel targets for future investigations.
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Affiliation(s)
- Csilla Krausz
- Unit of Sexual Medicine and Andrology, Molecular Genetic Laboratory, Department of Clinical Physiopathology, University of Florence, Florence, Italy. c.krausz@ dfc.unifi.it
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