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Aretini P, Presciuttini S, Pastore A, Galli A, Panepinto S, Tancredi M, Ghilli M, Guglielmi C, Sidoti D, Congregati C, Caligo MA. The BRCA1 c.4096+1G>A Is a Founder Variant Which Originated in Ancient Times. Int J Mol Sci 2023; 24:15507. [PMID: 37958491 PMCID: PMC10648645 DOI: 10.3390/ijms242115507] [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: 08/23/2023] [Revised: 10/17/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023] Open
Abstract
Approximately 30-50% of hereditary breast and ovarian cancer (HBOC) is due to the presence of germline pathogenic variants in the BRCA1 (OMIM 113705) and BRCA2 (OMIM 600185) onco-suppressor genes, which are involved in DNA damage response. Women who carry pathogenic BRCA1 variants are particularly likely to develop breast cancer (BC) and ovarian cancer (OC), with a 45-79 percent and 39-48 percent chance, respectively. The BRCA1 c.4096+1G>A variant has been frequently ascertained in Tuscany, Italy, and it has also been detected in other Italian regions and other countries. Its pathogenetic status has been repeatedly changed from a variant of uncertain significance, to pathogenic, to likely pathogenic. In our study, 48 subjects (38 of whom are carriers) from 27 families were genotyped with the Illumina OncoArray Infinium platform (533,531 SNPs); a 20 Mb region (24.6 cM) around BRCA1, including 4130 SNPs (21 inside BRCA1) was selected for haplotype analysis. We used a phylogenetic method to estimate the time to the most recent common ancestor (MRCA) of BRCA1 c.4096+1G>A founder pathogenic variant. This analysis suggests that the MRCA lived about 155 generations ago-around 3000 years ago.
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Affiliation(s)
- Paolo Aretini
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy;
| | - Silvano Presciuttini
- Dipartimento di Ricerca Traslazionale e Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, 56126 Pisa, Italy;
| | - Aldo Pastore
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy;
- Laboratorio NEST, Scuola Normale Superiore, 56126 Pisa, Italy
| | - Alvaro Galli
- Istituto di Fisiologia Clinica, Consiglio Nazionale delle Ricerche (CNR), 56124 Pisa, Italy;
| | - Sara Panepinto
- Laboratorio di Genetica Molecolare, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy; (S.P.); (M.T.); (C.G.); (D.S.)
| | - Mariella Tancredi
- Laboratorio di Genetica Molecolare, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy; (S.P.); (M.T.); (C.G.); (D.S.)
| | - Matteo Ghilli
- Breast Unit, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy;
| | - Chiara Guglielmi
- Laboratorio di Genetica Molecolare, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy; (S.P.); (M.T.); (C.G.); (D.S.)
| | - Diletta Sidoti
- Laboratorio di Genetica Molecolare, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy; (S.P.); (M.T.); (C.G.); (D.S.)
| | - Caterina Congregati
- Genetica Medica, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy;
| | - Maria Adelaide Caligo
- Laboratorio di Genetica Molecolare, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy; (S.P.); (M.T.); (C.G.); (D.S.)
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Bellè F, Mercatanti A, Lodovichi S, Congregati C, Guglielmi C, Tancredi M, Caligo MA, Cervelli T, Galli A. Validation and Data-Integration of Yeast-Based Assays for Functional Classification of BRCA1 Missense Variants. Int J Mol Sci 2022; 23:ijms23074049. [PMID: 35409408 PMCID: PMC8999655 DOI: 10.3390/ijms23074049] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 11/23/2022] Open
Abstract
Germline mutations in the BRCA1 gene have been reported to increase the lifetime risk of developing breast and/or ovarian cancer (BOC). By new sequencing technologies, numerous variants of uncertain significance (VUS) are identified. It is mandatory to develop new tools to evaluate their functional impact and pathogenicity. As the expression of pathogenic BRCA1 variants in Saccharomyces cerevisiae increases the frequency of intra- and inter-chromosomal homologous recombination (HR), and gene reversion (GR), we validated the two HR and the GR assays by testing 23 benign and 23 pathogenic variants and compared the results with those that were obtained in the small colony phenotype (SCP) assay, an additional yeast-based assay, that was validated previously. We demonstrated that they scored high accuracy, sensitivity, and sensibility. By using a classifier that was based on majority of voting, we have integrated data from HR, GR, and SCP assays and developed a reliable method, named yBRCA1, with high sensitivity to obtain an accurate VUS functional classification (benign or pathogenic). The classification of BRCA1 variants, important for assessing the risk of developing BOC, is often difficult to establish with genetic methods because they occur rarely in the population. This study provides a new tool to get insights on the functional impact of the BRCA1 variants.
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Affiliation(s)
- Francesca Bellè
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR via Moruzzi 1, 56125 Pisa, Italy; (F.B.); (A.M.); (S.L.); (T.C.)
| | - Alberto Mercatanti
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR via Moruzzi 1, 56125 Pisa, Italy; (F.B.); (A.M.); (S.L.); (T.C.)
| | - Samuele Lodovichi
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR via Moruzzi 1, 56125 Pisa, Italy; (F.B.); (A.M.); (S.L.); (T.C.)
| | - Caterina Congregati
- Division of Internal Medicine, University Hospital of Pisa, 56125 Pisa, Italy;
| | - Chiara Guglielmi
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, 56125 Pisa, Italy; (C.G.); (M.T.)
| | - Mariella Tancredi
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, 56125 Pisa, Italy; (C.G.); (M.T.)
| | - Maria Adelaide Caligo
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, 56125 Pisa, Italy; (C.G.); (M.T.)
- Correspondence: (M.A.C.); (A.G.)
| | - Tiziana Cervelli
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR via Moruzzi 1, 56125 Pisa, Italy; (F.B.); (A.M.); (S.L.); (T.C.)
| | - Alvaro Galli
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR via Moruzzi 1, 56125 Pisa, Italy; (F.B.); (A.M.); (S.L.); (T.C.)
- Correspondence: (M.A.C.); (A.G.)
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Guglielmi C, Scarpitta R, Gambino G, Conti E, Bellè F, Tancredi M, Cervelli T, Falaschi E, Cosini C, Aretini P, Congregati C, Marino M, Patruno M, Pilato B, Spina F, Balestrino L, Tenedini E, Carnevali I, Cortesi L, Tagliafico E, Tibiletti MG, Tommasi S, Ghilli M, Vivanet C, Galli A, Caligo MA. Detection of Germline Variants in 450 Breast/Ovarian Cancer Families with a Multi-Gene Panel Including Coding and Regulatory Regions. Int J Mol Sci 2021; 22:ijms22147693. [PMID: 34299313 PMCID: PMC8305371 DOI: 10.3390/ijms22147693] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/10/2021] [Accepted: 07/14/2021] [Indexed: 12/24/2022] Open
Abstract
With the progress of sequencing technologies, an ever-increasing number of variants of unknown functional and clinical significance (VUS) have been identified in both coding and non-coding regions of the main Breast Cancer (BC) predisposition genes. The aim of this study is to identify a mutational profile of coding and intron-exon junction regions of 12 moderate penetrance genes (ATM, BRIP1, CDH1, CHEK2, NBN, PALB2, PTEN, RAD50, RAD51C, RAD51D, STK11, TP53) in a cohort of 450 Italian patients with Hereditary Breast/Ovarian Cancer Syndrome, wild type for germline mutation in BRCA1/2 genes. The analysis was extended to 5′UTR and 3′UTR of all the genes listed above and to the BRCA1 and BRCA2 known regulatory regions in a subset of 120 patients. The screening was performed through NGS target resequencing on the Illumina platform MiSeq. 8.7% of the patients analyzed is carriers of class 5/4 coding variants in the ATM (3.6%), BRIP1 (1.6%), CHEK2 (1.8%), PALB2 (0.7%), RAD51C (0.4%), RAD51D (0.4%), and TP53 (0.2%) genes, while variants of uncertain pathological significance (VUSs)/class 3 were identified in 9.1% of the samples. In intron-exon junctions and in regulatory regions, variants were detected respectively in 5.1% and in 32.5% of the cases analyzed. The average age of disease onset of 44.4 in non-coding variant carriers is absolutely similar to the average age of disease onset in coding variant carriers for each proband’s group with the same cancer type. Furthermore, there is not a statistically significant difference in the proportion of cases with a tumor onset under age of 40 between the two groups, but the presence of multiple non-coding variants in the same patient may affect the aggressiveness of the tumor and it is worth underlining that 25% of patients with an aggressive tumor are carriers of a PTEN 3′UTR-variant. This data provides initial information on how important it might be to extend mutational screening to the regulatory regions in clinical practice.
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Affiliation(s)
- Chiara Guglielmi
- SOD Molecular Genetics, University Hospital of Pisa, 56126 Pisa, Italy; (C.G.); (E.C.); (M.T.); (E.F.); (C.C.)
| | - Rosa Scarpitta
- Division of Pathology, University of Pisa, 56126 Pisa, Italy;
| | - Gaetana Gambino
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy;
| | - Eleonora Conti
- SOD Molecular Genetics, University Hospital of Pisa, 56126 Pisa, Italy; (C.G.); (E.C.); (M.T.); (E.F.); (C.C.)
| | - Francesca Bellè
- Functional Genetics and Genomics Laboratory, Institute of Clinical Physiology, IFC-CNR, 56127 Pisa, Italy; (F.B.); (T.C.)
| | - Mariella Tancredi
- SOD Molecular Genetics, University Hospital of Pisa, 56126 Pisa, Italy; (C.G.); (E.C.); (M.T.); (E.F.); (C.C.)
| | - Tiziana Cervelli
- Functional Genetics and Genomics Laboratory, Institute of Clinical Physiology, IFC-CNR, 56127 Pisa, Italy; (F.B.); (T.C.)
| | - Elisabetta Falaschi
- SOD Molecular Genetics, University Hospital of Pisa, 56126 Pisa, Italy; (C.G.); (E.C.); (M.T.); (E.F.); (C.C.)
| | - Cinzia Cosini
- SOD Molecular Genetics, University Hospital of Pisa, 56126 Pisa, Italy; (C.G.); (E.C.); (M.T.); (E.F.); (C.C.)
| | - Paolo Aretini
- Section of Oncological Genomics, Fondazione Pisana per la Scienza, 56017 Pisa, Italy;
| | - Caterina Congregati
- Division of Internal Medicine, University Hospital of Pisa, 56126 Pisa, Italy;
| | - Marco Marino
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (M.M.); (E.T.); (E.T.)
| | - Margherita Patruno
- IRCCS Istituto Tumori “Giovanni Paolo II”, 70124 Bari, Italy; (M.P.); (B.P.); (S.T.)
| | - Brunella Pilato
- IRCCS Istituto Tumori “Giovanni Paolo II”, 70124 Bari, Italy; (M.P.); (B.P.); (S.T.)
| | - Francesca Spina
- SC Medical Genetics, ASSL Cagliari, 09126 Cagliari, Italy; (F.S.); (L.B.); (C.V.)
| | - Luisa Balestrino
- SC Medical Genetics, ASSL Cagliari, 09126 Cagliari, Italy; (F.S.); (L.B.); (C.V.)
| | - Elena Tenedini
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (M.M.); (E.T.); (E.T.)
| | - Ileana Carnevali
- Ospedale di Circolo ASST Settelaghi, 21100 Varese, Italy; (I.C.); (M.G.T.)
| | - Laura Cortesi
- Department of Oncology, Haematology and Respiratory Diseases, University Hospital of Modena, 41124 Modena, Italy;
| | - Enrico Tagliafico
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (M.M.); (E.T.); (E.T.)
| | | | - Stefania Tommasi
- IRCCS Istituto Tumori “Giovanni Paolo II”, 70124 Bari, Italy; (M.P.); (B.P.); (S.T.)
| | - Matteo Ghilli
- Breast Cancer Center, University Hospital, 56126 Pisa, Italy;
| | - Caterina Vivanet
- SC Medical Genetics, ASSL Cagliari, 09126 Cagliari, Italy; (F.S.); (L.B.); (C.V.)
| | - Alvaro Galli
- Functional Genetics and Genomics Laboratory, Institute of Clinical Physiology, IFC-CNR, 56127 Pisa, Italy; (F.B.); (T.C.)
- Correspondence: (A.G.); (M.A.C.)
| | - Maria Adelaide Caligo
- SOD Molecular Genetics, University Hospital of Pisa, 56126 Pisa, Italy; (C.G.); (E.C.); (M.T.); (E.F.); (C.C.)
- Correspondence: (A.G.); (M.A.C.)
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Scarpitta R, Zanna I, Aretini P, Gambino G, Scatena C, Mei B, Ghilli M, Rossetti E, Roncella M, Congregati C, Bonci F, Naccarato AG, Palli D, Caligo MA. Germline investigation in male breast cancer of DNA repair genes by next-generation sequencing. Breast Cancer Res Treat 2019; 178:557-564. [PMID: 31512090 DOI: 10.1007/s10549-019-05429-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 02/18/2019] [Accepted: 08/29/2019] [Indexed: 02/03/2023]
Abstract
PURPOSE In order to better define the breast cancer (BC) genetic risk factors in men, a germline investigation was carried out on 81 Male BC cases by screening the 24 genes involved in BC predisposition, genome stability maintenance and DNA repair mechanisms by next-generation sequencing. METHODS Germline DNAs were tested in a custom multi-gene panel focused on all coding exons and exon-intron boundaries of 24 selected genes using two amplicon-based assays on PGM-Ion Torrent (ThermoFisher Scientific) and MiSeq (Illumina) platforms. All variants were recorded and classified by using a custom pipeline. RESULTS Clinical pathological data and the family history of 81 Male BC cases were gathered and analysed, revealing the average age of onset to be 61.3 years old and that in 35 cases there was a family history of BC. Our genetic screening allowed us to identify a germline mutation in 22 patients (23%) in 4 genes: BRCA2, BRIP1, MUTYH and PMS2. Moreover, 12 variants of unknown clinical significance (VUS) in 9 genes (BARD1, BRCA1, BRIP1, CHEK2, ERCC1, NBN, PALB2, PMS1, RAD50) were predicted as potentially pathogenic by in silico analysis bringing the mutation detection rate up to 40%. CONCLUSION As expected, a positive family history is a strong predictor of germline BRCA2 mutations in male BC. Understanding the potential pathogenicity of VUS represents an extremely urgent need for the management of BC risk in Male BC cases and their own families.
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Affiliation(s)
- R Scarpitta
- Section of Genetic Oncology, University Hospital, Pisa, Italy
| | - I Zanna
- Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Via Delle Oblate 4, 50141, Florence, Italy
| | - P Aretini
- Section of Cancer Genomics, Fondazione Pisana per la Scienza, Pisa, Italy
| | - G Gambino
- Section of Genetic Oncology, University Hospital, Pisa, Italy
| | - C Scatena
- Division of Pathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - B Mei
- Section of Genetic Oncology, University Hospital, Pisa, Italy
| | - M Ghilli
- Breast Cancer Center, University Hospital, Pisa, Italy
| | - E Rossetti
- Breast Cancer Center, University Hospital, Pisa, Italy
| | - M Roncella
- Breast Cancer Center, University Hospital, Pisa, Italy
| | - C Congregati
- Division of Internal Medicine, University Hospital, Pisa, Italy
| | - F Bonci
- Unit of Medical Oncology 2, University Hospital, Pisa, Italy
| | - A G Naccarato
- Division of Pathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - D Palli
- Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Via Delle Oblate 4, 50141, Florence, Italy
| | - M A Caligo
- Section of Genetic Oncology, University Hospital, Pisa, Italy.
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Maresca L, Lodovichi S, Lorenzoni A, Cervelli T, Monaco R, Spugnesi L, Tancredi M, Falaschi E, Zavaglia K, Landucci E, Roncella M, Congregati C, Gadducci A, Naccarato AG, Caligo MA, Galli A. Functional Interaction Between BRCA1 and DNA Repair in Yeast May Uncover a Role of RAD50, RAD51, MRE11A, and MSH6 Somatic Variants in Cancer Development. Front Genet 2018; 9:397. [PMID: 30283497 PMCID: PMC6156519 DOI: 10.3389/fgene.2018.00397] [Citation(s) in RCA: 16] [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: 05/02/2018] [Accepted: 08/31/2018] [Indexed: 01/07/2023] Open
Abstract
In this study, we determined if BRCA1 partners involved in DNA double-strand break (DSB) and mismatch repair (MMR) may contribute to breast and ovarian cancer development. Taking advantage the functional conservation of DNA repair pathways between yeast and human, we expressed several BRCA1 missense variants in DNA repair yeast mutants to identify functional interaction between BRCA1 and DNA repair in BRCA1-induced genome instability. The pathogenic p.C61G, pA1708E, p.M775R, and p.I1766S, and the neutral pS1512I BRCA1 variants increased intra-chromosomal recombination in the DNA-repair proficient strain RSY6. In the mre11, rad50, rad51, and msh6 deletion strains, the BRCA1 variants p.C61G, pA1708E, p.M775R, p.I1766S, and pS1215I did not increase intra-chromosomal recombination suggesting that a functional DNA repair pathway is necessary for BRCA1 variants to determine genome instability. The pathogenic p.C61G and p.I1766S and the neutral p.N132K, p.Y179C, and p.N550H variants induced a significant increase of reversion in the msh2Δ strain; the neutral p.Y179C and the pathogenic p.I1766S variant induced gene reversion also, in the msh6Δ strain. These results imply a functional interaction between MMR and BRCA1 in modulating genome instability. We also performed a somatic mutational screening of MSH6, RAD50, MRE11A, and RAD51 genes in tumor samples from 34 patients and identified eight pathogenic or predicted pathogenic rare missense variants: four in MSH6, one in RAD50, one in MRE11A, and two in RAD51. Although we found no correlation between BRCA1 status and these somatic DNA repair variants, this study suggests that somatic missense variants in DNA repair genes may contribute to breast and ovarian tumor development.
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Affiliation(s)
- Luisa Maresca
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Samuele Lodovichi
- Yeast Genetics and Genomics, Institute of Clinical Physiology, CNR Pisa, Pisa, Italy.,PhD Program in Clinical and Translational Sciences, University of Pisa, Pisa, Italy
| | - Alessandra Lorenzoni
- Yeast Genetics and Genomics, Institute of Clinical Physiology, CNR Pisa, Pisa, Italy
| | - Tiziana Cervelli
- Yeast Genetics and Genomics, Institute of Clinical Physiology, CNR Pisa, Pisa, Italy
| | - Rossella Monaco
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Laura Spugnesi
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Mariella Tancredi
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Elisabetta Falaschi
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Katia Zavaglia
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | | | | | - Caterina Congregati
- Department of Clinical and Experimental Medicine, Division of Internal Medicine, University Hospital of Pisa, Pisa, Italy
| | - Angiolo Gadducci
- Department of Clinical and Experimental Medicine, Division of Gynecology and Obstetrics, University Hospital of Pisa, Pisa, Italy
| | - Antonio Giuseppe Naccarato
- Department of Translational Research and New Technologies in Medicine and Surgery, University Hospital of Pisa, Pisa, Italy
| | - Maria Adelaide Caligo
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Alvaro Galli
- Yeast Genetics and Genomics, Institute of Clinical Physiology, CNR Pisa, Pisa, Italy
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6
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Franceschi S, Spugnesi L, Aretini P, Lessi F, Scarpitta R, Galli A, Congregati C, Caligo MA, Mazzanti CM. Whole-exome analysis of a Li-Fraumeni family trio with a novel TP53 PRD mutation and anticipation profile. Carcinogenesis 2017; 38:938-943. [PMID: 28911001 DOI: 10.1093/carcin/bgx069] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/23/2017] [Indexed: 12/12/2022] Open
Abstract
Li-Fraumeni syndrome is a clinically heterogeneous familial cancer predisposition syndrome with autosomal-dominant inheritance caused by heterozygous germline mutations in the TP53 gene. We here analyze the genetic background of a family with a 4-year-proband presented with a Li-Fraumeni tumor. The mother developed breast cancer at age 37 and the proband died at age 8. We performed Sanger sequencing and whole-exome sequencing on peripheral blood DNA from proband and relatives. Data analysis selected only high-quality score and depth reads, rare variants and protein impact involving missense, non-sense, frameshift and splice disrupt mutations. Disease implicated variants and predicted deleterious alterations were also chosen. TP53 genetic testing revealed a never reported TP53 deletion arose as de novo mutation in the mother and inherited by the proband. We then performed whole-exome analysis of the trio to uncover inherited variants from the father that potentially worsen the already altered genetic background in the proband. No pathogenic variants were inherited in autosomal recessive, de novo dominant or X-linked recessive manner. Comparing proband and father exome we detected 25 predicted deleterious variants including a nonsense mutation in ERCC3. Those inherited mutations are possible candidate modifiers linked to TP53, explaining the proband accelerated tumor onset compared to the mother and providing a possible explanation of the genetic anticipation event in this Li-Fraumeni family.
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Affiliation(s)
| | - Laura Spugnesi
- Section of Genetic Oncology, Department of Laboratory Medicine, University Hospital of Pisa, Pisa 56100, Italy
| | - Paolo Aretini
- FPS - Fondazione Pisana per la Scienza, Pisa 56121, Italy
| | | | - Rosa Scarpitta
- Section of Genetic Oncology, Department of Laboratory Medicine, University Hospital of Pisa, Pisa 56100, Italy
| | - Alvaro Galli
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, Pisa 56124, Italy
| | - Caterina Congregati
- Cytogenetics and Molecular Genetic Unit, University Hospital of Pisa, Pisa 56100, Italy
| | - Maria Adelaide Caligo
- UO Medical Genetics, Department of Laboratory Medicine, University Hospital of Pisa, Pisa 56100, Italy
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7
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Bruno R, Valetto A, Bertini V, Cosini C, Toschi B, Congregati C, Rossi S, Simi P. A 17q duplication prenatally detected. Taiwan J Obstet Gynecol 2015; 54:326-9. [PMID: 26166353 DOI: 10.1016/j.tjog.2014.05.008] [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] [Accepted: 05/27/2014] [Indexed: 10/23/2022] Open
Affiliation(s)
- Rossella Bruno
- Cytogenetics and Molecular Genetic Unit, Azienda Ospedaliera Universitaria Pisana, S. Chiara Hospital, 56100 Pisa, Italy
| | - Angelo Valetto
- Cytogenetics and Molecular Genetic Unit, Azienda Ospedaliera Universitaria Pisana, S. Chiara Hospital, 56100 Pisa, Italy.
| | - Veronica Bertini
- Cytogenetics and Molecular Genetic Unit, Azienda Ospedaliera Universitaria Pisana, S. Chiara Hospital, 56100 Pisa, Italy
| | - Cinzia Cosini
- Cytogenetics and Molecular Genetic Unit, Azienda Ospedaliera Universitaria Pisana, S. Chiara Hospital, 56100 Pisa, Italy
| | - Benedetta Toschi
- Cytogenetics and Molecular Genetic Unit, Azienda Ospedaliera Universitaria Pisana, S. Chiara Hospital, 56100 Pisa, Italy
| | - Caterina Congregati
- Cytogenetics and Molecular Genetic Unit, Azienda Ospedaliera Universitaria Pisana, S. Chiara Hospital, 56100 Pisa, Italy
| | - Simona Rossi
- Cytogenetics and Molecular Genetic Unit, Azienda Ospedaliera Universitaria Pisana, S. Chiara Hospital, 56100 Pisa, Italy
| | - Paolo Simi
- Cytogenetics and Molecular Genetic Unit, Azienda Ospedaliera Universitaria Pisana, S. Chiara Hospital, 56100 Pisa, Italy
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Caleca L, Putignano AL, Colombo M, Congregati C, Sarkar M, Magliery TJ, Ripamonti CB, Foglia C, Peissel B, Zaffaroni D, Manoukian S, Tondini C, Barile M, Pensotti V, Bernard L, Papi L, Radice P. Characterization of an Italian founder mutation in the RING-finger domain of BRCA1. PLoS One 2014; 9:e86924. [PMID: 24516540 PMCID: PMC3916327 DOI: 10.1371/journal.pone.0086924] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [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: 08/28/2013] [Accepted: 12/16/2013] [Indexed: 12/17/2022] Open
Abstract
The identification of founder mutations in cancer predisposing genes is important to improve risk assessment in geographically defined populations, since it may provide specific targets resulting in cost-effective genetic testing. Here, we report the characterization of the BRCA1 c.190T>C (p.Cys64Arg) mutation, mapped to the RING-finger domain coding region, that we detected in 43 hereditary breast/ovarian cancer (HBOC) families, for the large part originating from the province of Bergamo (Northern Italy). Haplotype analysis was performed in 21 families, and led to the identification of a shared haplotype extending over three BRCA1-associated marker loci (0.4 cM). Using the DMLE+2.2 software program and regional population demographic data, we were able to estimate the age of the mutation to vary between 3,100 and 3,350 years old. Functional characterization of the mutation was carried out at both transcript and protein level. Reverse transcriptase-PCR analysis on lymphoblastoid cells revealed expression of full length mRNA from the mutant allele. A green fluorescent protein (GFP)-fragment reassembly assay showed that the p.Cys64Arg substitution prevents the binding of the BRCA1 protein to the interacting protein BARD1, in a similar way as proven deleterious mutations in the RING-domain. Overall, 55 of 83 (66%) female mutation carriers had a diagnosis of breast and/or ovarian cancer. Our observations indicate that the BRCA1 c.190T>C is a pathogenic founder mutation present in the Italian population. Further analyses will evaluate whether screening for this mutation can be suggested as an effective strategy for the rapid identification of at-risk individuals in the Bergamo area.
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Affiliation(s)
- Laura Caleca
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), c/o Amadeolab, Milano, Italy
- * E-mail:
| | - Anna Laura Putignano
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
- FiorGen Foundation for Pharmacogenomics, Sesto Fiorentino, Italy
| | - Mara Colombo
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), c/o Amadeolab, Milano, Italy
| | - Caterina Congregati
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Mohosin Sarkar
- Department of Chemistry and Department of Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Thomas J. Magliery
- Department of Chemistry and Department of Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Carla B. Ripamonti
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), c/o Amadeolab, Milano, Italy
| | - Claudia Foglia
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), c/o Amadeolab, Milano, Italy
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Daniela Zaffaroni
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Carlo Tondini
- Unit of Medical Oncology, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy
| | - Monica Barile
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, Milan, Italy
| | - Valeria Pensotti
- COGENTECH-Cancer Genetic Testing Laboratory, Milan, Italy
- Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Loris Bernard
- COGENTECH-Cancer Genetic Testing Laboratory, Milan, Italy
- Department of Experimental Oncology, Istituto Europeo di Oncologia, Milan, Italy
| | - Laura Papi
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), c/o Amadeolab, Milano, Italy
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Toschi B, Valetto A, Bertini V, Congregati C, Cantinotti M, Assanta N, Simi P. Acro-cardio-facial syndrome: a microdeletion syndrome? Am J Med Genet A 2012; 158A:1994-9. [PMID: 22740423 DOI: 10.1002/ajmg.a.35444] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 04/07/2012] [Indexed: 11/06/2022]
Abstract
Acro-cardio-facial syndrome (ACFS) is an infrequently reported, variable condition characterized by split-hand and split-foot malformation and congenital heart defect (CHD), along with cleft lip and palate, genital anomalies, unusual face and intellectual disability. An autosomal recessive pattern of inheritance has been suggested because of affected sibs born to unaffected parents and parental consanguinity; the cause is unknown. We describe a newborn with the clinical manifestations of ACFS in whom a deletion of the region 6q21-q22.3 was detected by array CGH. We compare the clinical features of the present patient with earlier reported patients with similar 6q deletions and patients diagnosed with ACFS. The similarities between these patient groups suggest that ACFS may be a microdeletion syndrome caused by loss of the 6q21-22.3 region. The recurrence in families may be explained by prenatal germline mosaicism. Alternatively, ACFS may be a genetically heterogeneous disorder which can also be caused by biallelic mutations of an autosomal recessive gene.
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Affiliation(s)
- Benedetta Toschi
- U.O. Laboratorio Genetica Medica, Santa Chiara Hospital, Pisa, Italy.
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10
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Bacca A, Sellari Franceschini S, Carrara D, Bernini M, Zampa V, Taddei S, Miccoli P, Congregati C, Simi P, Ferrari M, Bernini G. Sporadic or familial head neck paragangliomas enrolled in a single center: clinical presentation and genotype/phenotype correlations. Head Neck 2012; 35:23-7. [PMID: 22290790 DOI: 10.1002/hed.22910] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2011] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND The purpose of this study was to investigate clinical features and prevalence of germline mutations of patients with head/neck paragangliomas. METHODS Genetic analysis on known susceptibility genes for paragangliomas (VHL, RET, SDHB, SDHC, SDHD, and SDHAF2) was performed in 17 consecutive patients with head/neck paraganglioma (age range, 14-82 years) and 17 relatives. RESULTS Head/neck paragangliomas were usually symptomatic with "mass effect" (88.2%), without family history (82.3%), often multifocal (41.2%), never functioning, and malignant. Germline mutations were detected in 7 of 17 patients (41%; 6 SDHD and 1 SDHB). Patients with mutations were younger, with head/neck paragangliomas usually multifocal and with higher biologic aggressiveness than wild-type subjects. To date, 4 families have been studied and the prevalence of carriers was elevated (58.8%). These mutated relatives (age range, 17-71 years) were disease-free, except 4 patients in whom multiple head/neck paragangliomas were detected. CONCLUSION Adequate morpho-functional screening and follow-up and, if possible, genetic testing is advisable in patients with head/neck paraganglioma.
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Affiliation(s)
- Alessandra Bacca
- Department of Internal Medicine, University of Pisa, Ospedale Santa Chiara, Pisa, Italy
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11
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Papi L, Palli D, Masi L, Putignano AL, Congregati C, Zanna I, Marini F, Giusti F, Luzi E, Tonelli F, Genuardi M, Brandi ML, Falchetti A. Germline mutations in MEN1 and BRCA1 genes in a woman with familial multiple endocrine neoplasia type 1 and inherited breast-ovarian cancer syndromes: a case report. ACTA ACUST UNITED AC 2009; 195:75-9. [PMID: 19837273 DOI: 10.1016/j.cancergencyto.2009.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Revised: 06/17/2009] [Accepted: 06/20/2009] [Indexed: 12/21/2022]
Abstract
The simultaneous occurrence of mutations in two different tumor suppressor genes in the same individual is a very rare event. Here we report the case of a woman in whom germline mutations in both MEN1 and BRCA1 were identified. The severity of MEN1-related biochemical and clinical findings did not significantly differ from that for other affected family members lacking the BRCA1 mutation, except for the development of an extremely large visceral lipoma; the proband has not developed any BRCA1-related malignancies. We explore genetic and molecular rationales for an association between these neoplastic processes.
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Affiliation(s)
- Laura Papi
- Medical Genetics Unit, Department of Clinical Pathophysiology, University of Florence, Florence, Italy
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12
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Papi L, Putignano AL, Congregati C, Piaceri I, Zanna I, Sera F, Morrone D, Genuardi M, Palli D. A PALB2 germline mutation associated with hereditary breast cancer in Italy. Fam Cancer 2009; 9:181-5. [PMID: 19763884 DOI: 10.1007/s10689-009-9295-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Accepted: 09/09/2009] [Indexed: 12/16/2022]
Abstract
Recently, it has been demonstrated that monoallelic PALB2 mutations predispose to familial breast cancer. We investigated the contribution of PALB2 mutations in a set of 132 Italian BRCA1/BRCA2-negative breast cancer families; one truncating PALB2 mutation, c.2257C>T, resulting in p.Arg753X, was identified in a woman and her daughter, with breast cancer diagnosed at 60 and 31 years old, respectively. This study supports the recent observation that PALB2 mutation are present, although infrequently, in familial BRCA1/BRCA2-negative breast cancer cases; moreover, it sustains latest evidences that some PALB2 mutations are associated with a substantially increased risk of breast cancer.
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Affiliation(s)
- Laura Papi
- Medical Genetics Unit, Department of Clinical Physiopathology, University of Florence, Viale Pieraccini, 6, 50139 Florence, Italy
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13
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Papi L, Putignano AL, Congregati C, Zanna I, Sera F, Morrone D, Falchetti M, Turco MRD, Ottini L, Palli D, Genuardi M. Founder mutations account for the majority of BRCA1-attributable hereditary breast/ovarian cancer cases in a population from Tuscany, Central Italy. Breast Cancer Res Treat 2008; 117:497-504. [PMID: 18821011 DOI: 10.1007/s10549-008-0190-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 09/05/2008] [Indexed: 12/12/2022]
Abstract
BACKGROUND Germline mutations in the BRCA1 and BRCA2 tumour-suppressor genes predispose to early-onset breast and ovarian cancer. Although both genes display a highly heterogeneous mutation spectrum, a number of alterations recur in some populations. Only a limited number of founder mutations have been identified in the Italian population so far. OBJECTIVE To investigate the spectrum of BRCA1/BRCA2 mutations in a set of families originary from the Central-Eastern part of Tuscany and to ascertain the presence of founder effects. We also wanted to approximate the age of the most frequent BRCA1 founder mutation. RESULTS Overall, four distinct BRCA1 mutations accounted for a large fraction (72.7%) of BRCA1-attributable hereditary breast/ovarian cancer in families originary from this area. We identified common haplotypes for two newly recognised recurrent BRCA1 mutations, c.3228_3229delAG and c.3285delA. The c.3228_3229delAG mutation was estimated to have originated about 129 generations ago. Interestingly, male breast cancer cases were present in 3 out of 11 families with the c.3228_3229delAG mutation. CONCLUSIONS The observation that a high proportion of families with BRCA1 alterations from Central-Eastern Tuscany harbours a limited number of founder mutations can have significant impact on clinical management of at risk subjects from this area. In addition, the identification of a large set of families carrying an identical mutation that predisposes to breast and ovarian cancer provides unique opportunities to study the effect of other genetic and environmental factors on penetrance and disease phenotype.
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Affiliation(s)
- Laura Papi
- Medical Genetics Unit, Department of Clinical Physiopathology, University of Florence, Viale Pieraccini, 6, 50139 Florence, Italy.
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14
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Tedde A, Laura Putignano A, Bagnoli S, Congregati C, Milla M, Sorbi S, Genuardi M, Papi L. Interleukin-10 promoter polymorphisms influence susceptibility to ulcerative colitis in a gender-specific manner. Scand J Gastroenterol 2008; 43:712-8. [PMID: 18569989 DOI: 10.1080/00365520701885507] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
OBJECTIVE Pathological evidence supports a potential role of the pro- and anti-inflammatory cytokine network in the pathogenesis of inflammatory bowel disease (IBD). Moreover, associated studies suggest a possible involvement of cytokine-related genes in IBD susceptibility. In this study, we evaluated the effect of the anti-inflammatory interleukin-10 (IL10) gene on ulcerative colitis (UC). MATERIAL AND METHODS Two functional single nucleotide polymorphisms (-1082 G/A, -819 T/C) in the IL10 promoter in 203 Italian sporadic UC patients and 391 controls were determined using high-resolution melting analysis. RESULTS The frequency of the -1082A allele was significantly higher in the UC patients than in controls (p=0.00003); -1082 genotype frequencies were also significantly different between UC patients and controls (p=0.0001). Allele and genotype frequencies of -819 T/C were not significantly associated with UC. Furthermore, the frequencies of haplotypes -1082A/-819C and -1082A/-819T, which have been reported to have a lower promoter activity, were significantly higher in UC patients than in controls (p=0.0004). After gender stratification, we found a significant difference in the -1082A allele (p=0.00004) and genotype (p=0.0002) frequencies only between female UC patients and controls; the same result was obtained for the -1082A/-819C and -1082A/-819T haplotypes (p=0.0006). CONCLUSIONS A gender effect is observed, with women of AG/AA IL10 genotypes and AC/AT haplotypes having a higher risk of developing UC at a younger age. This finding could be related to the previously documented lower IL10 production associated with the -1082A allele and to the IL10 down-regulating effect of estrogens.
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Affiliation(s)
- Andrea Tedde
- Neurogenetics Unit, Department of Neurological and Psychiatric Sciences, University of Florence, Italy
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