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1.
Cancer Res ; 80(7): 1374-1386, 2020 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-32046981

RESUMO

Germline nonsense and canonical splice site variants identified in disease-causing genes are generally considered as loss-of-function (LoF) alleles and classified as pathogenic. However, a fraction of such variants could maintain function through their impact on RNA splicing. To test this hypothesis, we used the alternatively spliced BRCA2 exon 12 (E12) as a model system because its in-frame skipping leads to a potentially functional protein. All E12 variants corresponding to putative LoF variants or predicted to alter splicing (n = 40) were selected from human variation databases and characterized for their impact on splicing in minigene assays and, when available, in patient lymphoblastoid cell lines. Moreover, a selection of variants was analyzed in a mouse embryonic stem cell-based functional assay. Using these complementary approaches, we demonstrate that a subset of variants, including nonsense variants, induced in-frame E12 skipping through the modification of splice sites or regulatory elements and, consequently, led to an internally deleted but partially functional protein. These data provide evidence, for the first time in a cancer-predisposition gene, that certain presumed null variants can retain function due to their impact on splicing. Further studies are required to estimate cancer risk associated with these hypomorphic variants. More generally, our findings highlight the need to exercise caution in the interpretation of putative LoF variants susceptible to induce in-frame splicing modifications. SIGNIFICANCE: This study presents evidence that certain presumed loss-of-function variants in a cancer predisposition gene can retain function due to their direct impact on RNA splicing.


Assuntos
Processamento Alternativo , Proteína BRCA2/genética , Predisposição Genética para Doença , Síndrome Hereditária de Câncer de Mama e Ovário/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , Animais , Linhagem Celular Tumoral , Células-Tronco Embrionárias , Éxons/genética , Feminino , Humanos , Mutação com Perda de Função , Masculino , Camundongos , Pessoa de Meia-Idade , Linhagem , Polimorfismo de Nucleotídeo Único , Proteínas Recombinantes/genética
2.
Oncotarget ; 9(25): 17334-17348, 2018 Apr 03.
Artigo em Inglês | MEDLINE | ID: mdl-29707112

RESUMO

Germline pathogenic variants in the BRCA2 gene are associated with a cumulative high risk of breast/ovarian cancer. Several BRCA2 variants result in complete loss of the exon-3 at the transcript level. The pathogenicity of these variants and the functional impact of loss of exon 3 have yet to be established. As a collaboration of the COVAR clinical trial group (France), and the ENIGMA consortium for investigating breast cancer gene variants, this study evaluated 8 BRCA2 variants resulting in complete deletion of exon 3. Clinical information for 39 families was gathered from Portugal, France, Denmark and Sweden. Multifactorial likelihood analyses were conducted using information from 293 patients, for 7 out of the 8 variants (including 6 intronic). For all variants combined the likelihood ratio in favor of causality was 4.39*1025. These results provide convincing evidence for the pathogenicity of all examined variants that lead to a total exon 3 skipping, and suggest that other variants that result in complete loss of exon 3 at the molecular level could be associated with a high risk of cancer comparable to that associated with classical pathogenic variants in BRCA1 or BRCA2 gene. In addition, our functional study shows, for the first time, that deletion of exon 3 impairs the ability of cells to survive upon Mitomycin-C treatment, supporting lack of function for the altered BRCA2 protein in these cells. Finally, this study demonstrates that any variant leading to expression of only BRCA2 delta-exon 3 will be associated with an increased risk of breast and ovarian cancer.

3.
Genet Med ; 20(12): 1589-1599, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-29790873

RESUMO

PURPOSE: Constitutional epimutations are an alternative to genetic mutations in the etiology of genetic diseases. Some of these epimutations, termed secondary, correspond to the epigenetic effects of cis-acting genetic defects transmitted to the offspring following a Mendelian inheritance pattern. In Lynch syndrome, a few families with such apparently heritable MLH1 epimutations have been reported so far. METHODS: We designed a long-range polymerase chain reaction next-generation sequencing strategy to screen MLH1 entire gene and applied it to 4 French families with heritable epimutations and 10 additional patients with no proven transmission of their epimutations. RESULTS: This strategy successfully detected the insertion of an Alu element in MLH1 coding sequence in one family. Two previously unreported MLH1 variants were also identified in other epimutation carriers: a nucleotide substitution within intron 1 and a single-nucleotide deletion in the 5'-UTR. Detection of a partial MLH1 duplication in another family required multiplex ligation-dependent probe amplification technology. We demonstrated the segregation of these variants with MLH1 methylation and studied the functional consequences of these defects on transcription. CONCLUSION: This is the largest cohort of patients with MLH1 secondary epimutations associated with a broad spectrum of genetic defects. This study provides further insight into the complexity of molecular mechanisms leading to secondary epimutations.


Assuntos
Neoplasias Colorretais Hereditárias sem Polipose/genética , Epigênese Genética , Predisposição Genética para Doença , Proteína 1 Homóloga a MutL/genética , Adulto , Alelos , Elementos Alu/genética , Neoplasias Colorretais Hereditárias sem Polipose/epidemiologia , Neoplasias Colorretais Hereditárias sem Polipose/patologia , Metilação de DNA/genética , Feminino , Haplótipos , Heterozigoto , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Íntrons/genética , Masculino , Pessoa de Meia-Idade , Mutação , Linhagem , Polimorfismo de Nucleotídeo Único/genética , Regiões Promotoras Genéticas/genética
4.
Hum Mutat ; 37(12): 1318-1328, 2016 12.
Artigo em Inglês | MEDLINE | ID: mdl-27633797

RESUMO

As next-generation sequencing increases access to human genetic variation, the challenge of determining clinical significance of variants becomes ever more acute. Germline variants in the BRCA1 and BRCA2 genes can confer substantial lifetime risk of breast and ovarian cancer. Assessment of variant pathogenicity is a vital part of clinical genetic testing for these genes. A database of clinical observations of BRCA variants is a critical resource in that process. This article describes BRCA Share™, a database created by a unique international alliance of academic centers and commercial testing laboratories. By integrating the content of the Universal Mutation Database generated by the French Unicancer Genetic Group with the testing results of two large commercial laboratories, Quest Diagnostics and Laboratory Corporation of America (LabCorp), BRCA Share™ has assembled one of the largest publicly accessible collections of BRCA variants currently available. Although access is available to academic researchers without charge, commercial participants in the project are required to pay a support fee and contribute their data. The fees fund the ongoing curation effort, as well as planned experiments to functionally characterize variants of uncertain significance. BRCA Share™ databases can therefore be considered as models of successful data sharing between private companies and the academic world.


Assuntos
Proteína BRCA1/genética , Proteína BRCA2/genética , Neoplasias da Mama/genética , Bases de Dados Factuais , Neoplasias Ovarianas/genética , Curadoria de Dados , Bases de Dados Factuais/economia , Feminino , Predisposição Genética para Doença , Humanos , Mutação
5.
Eur J Hum Genet ; 24(1): 99-105, 2016 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-25873010

RESUMO

To determine if the at-risk single-nucleotide polymorphism (SNP) alleles for colorectal cancer (CRC) could contribute to clinical situations suggestive of an increased genetic risk for CRC, we performed a prospective national case-control study based on highly selected patients (CRC in two first-degree relatives, one before 61 years of age; or CRC diagnosed before 51 years of age; or multiple primary CRCs, the first before 61 years of age; exclusion of Lynch syndrome and polyposes) and controls without personal or familial history of CRC. SNPs were genotyped using SNaPshot, and statistical analyses were performed using Pearson's χ(2) test, Cochran-Armitage test of trend and logistic regression. We included 1029 patients and 350 controls. We confirmed the association of CRC risk with four SNPs, with odds ratio (OR) higher than previously reported: rs16892766 on 8q23.3 (OR: 1.88, 95% confidence interval (CI): 1.30-2.72; P=0.0007); rs4779584 on 15q13.3 (OR: 1.42, CI: 1.11-1.83; P=0.0061) and rs4939827 and rs58920878/Novel 1 on 18q21.1 (OR: 1.49, CI: 1.13-1.98; P=0.007 and OR: 1.49, CI: 1.14-1.95; P=0.0035). We found a significant (P<0.0001) cumulative effect of the at-risk alleles or genotypes with OR at 1.62 (CI: 1.10-2.37), 2.09 (CI: 1.43-3.07), 2.87 (CI: 1.76-4.70) and 3.88 (CI: 1.72-8.76) for 1, 2, 3 and at least 4 at-risk alleles, respectively, and OR at 1.71 (CI: 1.18-2.46), 2.29 (CI: 1.55-3.38) and 6.21 (CI: 2.67-14.42) for 1, 2 and 3 at-risk genotypes, respectively. Combination of SNPs may therefore explain a fraction of clinical situations suggestive of an increased risk for CRC.


Assuntos
Cromossomos Humanos Par 15 , Cromossomos Humanos Par 18 , Cromossomos Humanos Par 8 , Neoplasias Colorretais/genética , Predisposição Genética para Doença , Polimorfismo de Nucleotídeo Único , Adulto , Alelos , Estudos de Casos e Controles , Neoplasias Colorretais/diagnóstico , Neoplasias Colorretais/patologia , Feminino , Frequência do Gene , Loci Gênicos , Estudo de Associação Genômica Ampla , Técnicas de Genotipagem , Humanos , Masculino , Pessoa de Meia-Idade , Razão de Chances , Estudos Prospectivos , Fatores de Risco
7.
Eur J Hum Genet ; 22(8): 979-87, 2014 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-24301060

RESUMO

Fanconi anaemia (FA) is characterized by progressive bone marrow failure, congenital anomalies, and predisposition to malignancy. In a minority of cases, FA results from biallelic FANCD1/BRCA2 mutations that are associated with early-onset leukaemia and solid tumours. Here, we describe the clinical and molecular features of a remarkable family presenting with multiple primary colorectal cancers (CRCs) without detectable mutations in genes involved in the Mendelian predisposition to CRCs. We unexpectedly identified, despite the absence of clinical cardinal features of FA, a biallelic mutation of the FANCD1/BRCA2 corresponding to a frameshift alteration (c.1845_1846delCT, p.Asn615Lysfs*6) and a missense mutation (c.7802A>G, p.Tyr2601Cys). The diagnosis of FA was confirmed by the chromosomal analysis of lymphocytes. Reverse transcriptase (RT)-PCR analysis revealed that the c.7802A>G BRCA2 variation was in fact a splicing mutation that creates an aberrant splicing donor site and results partly into an aberrant transcript encoding a truncated protein (p.Tyr2601Trpfs*46). The atypical FA phenotype observed within this family was probably explained by the residual amount of BRCA2 with the point mutation c.7802A>G in the patients harbouring the biallelic FANCD1/BRCA2 mutations. Although this report is based in a single family, it suggests that CRCs may be part of the tumour spectrum associated with FANCD1/BRCA2 biallelic mutations and that the presence of such mutations should be considered in families with CRCs, even in the absence of cardinal features of FA.


Assuntos
Idade de Início , Alelos , Proteína BRCA2/genética , Neoplasias Colorretais/genética , Mutação , Adulto , Substituição de Aminoácidos , Quebra Cromossômica , Neoplasias Colorretais/diagnóstico , Biologia Computacional , Análise Mutacional de DNA , Feminino , Humanos , Linhagem , Sítios de Splice de RNA , Processamento de RNA
8.
Fam Cancer ; 11(4): 681-3, 2012 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-22890886

RESUMO

Several studies report an increased risk of breast/pancreatic cancer in MMR (DNA mismatch repair) mutation carriers that has significant consequences on standard cancer screening in such population. The French national network involved in Lynch syndrome molecular characterization registered 15 families with an identified MMR germline mutation and the occurrence of breast/pancreatic adenocarcinoma in mutations carriers. Corresponding tumors were investigated and the MMR function was shown to be intact. This observation tends to exclude breast/pancreatic cancers from Lynch tumor spectrum defined by a complete loss of the MMR function in tumor cells and to support the hypothesis of another causal factor.


Assuntos
Neoplasias da Mama/etiologia , Neoplasias Colorretais Hereditárias sem Polipose/complicações , Reparo de Erro de Pareamento de DNA/genética , Neoplasias Pancreáticas/etiologia , Proteínas Adaptadoras de Transdução de Sinal/genética , Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Neoplasias da Mama/diagnóstico , Neoplasias Colorretais Hereditárias sem Polipose/genética , Feminino , Mutação em Linhagem Germinativa/genética , Humanos , Técnicas Imunoenzimáticas , Instabilidade de Microssatélites , Proteína 1 Homóloga a MutL , Proteína 2 Homóloga a MutS/genética , Proteína 2 Homóloga a MutS/metabolismo , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Neoplasias Pancreáticas/diagnóstico , Prognóstico
10.
Hum Mutat ; 33(8): 1228-38, 2012 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-22505045

RESUMO

Assessing the impact of variants of unknown significance (VUS) on splicing is a key issue in molecular diagnosis. This impact can be predicted by in silico tools, but proper evaluation and user guidelines are lacking. To fill this gap, we embarked upon the largest BRCA1 and BRCA2 splice study to date by testing 272 VUSs (327 analyses) within the BRCA splice network of Unicancer. All these VUSs were analyzed by using six tools (splice site prediction by neural network, splice site finder (SSF), MaxEntScan (MES), ESE finder, relative enhancer and silencer classification by unanimous enrichment, and human splicing finder) and the predictions obtained were compared with transcript analysis results. Combining MES and SSF gave 96% sensitivity and 83% specificity for VUSs occurring in the vicinity of consensus splice sites, that is, the surrounding 11 and 14 bases for the 5' and 3' sites, respectively. This study was also an opportunity to define guidelines for transcript analysis along with a tentative classification of splice variants. The guidelines drawn from this large series should be useful for the whole community, particularly in the context of growing sequencing capacities that require robust pipelines for variant interpretation.


Assuntos
Proteína BRCA1/genética , Proteína BRCA2/genética , Patologia Molecular/métodos , Patologia Molecular/normas , Processamento de RNA/genética , Éxons/genética , Feminino , Humanos
11.
Am J Med Genet A ; 149A(11): 2493-500, 2009 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-19842196

RESUMO

Monosomy 1p36 is the most frequent terminal deletion known in Humans. Typical craniofacial features, developmental delay/mental retardation, seizures and sensorineural defects characterize 1p36 deletion syndrome. Aicardi syndrome (AIS) is a rare genetic disorder characterized by chorioretinal lacunae, corpus callosum agenesis and infantile spasms responsible for mental retardation. By screening DNA from diagnosed AIS patients with oligonucleotide array-based comparative genomic hybridization (aCGH), we report a 1p36 monosomy in this study. There were no other deletions or duplications. Regarding clinical criteria, the patient did not have the typical facial appearance commonly described for 1p36 monosomy patients. We showed that this 1p36 monosomy corresponded to combined interstitial and terminal de novo deletions of the chromosome 1 leading to an 11.73 Mb deletion confirmed with qPCR. By microsatellite markers and FISH analyses, we have concluded that this deletion occurred on maternal chromosome 1 during oogenesis. We did find some clinical features shared by the 1p36 monosomy and AIS: infantile spasms, corpus callosum dysgenesis, ophthalmological abnormalities, and skeletal malformations. To date, no relationship between these two phenotypes has been established. We conclude that the monosomy 1p36 should be considered in the differential diagnosis of AIS.


Assuntos
Anormalidades Múltiplas/genética , Cromossomos Humanos Par 1/genética , Monossomia/genética , Adulto , Criança , Deleção Cromossômica , Feminino , Rearranjo Gênico/genética , Humanos , Hibridização in Situ Fluorescente , Lactente , Masculino , Pais , Fenótipo , Reação em Cadeia da Polimerase , Síndrome
12.
Biochem J ; 384(Pt 2): 295-305, 2004 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-15312046

RESUMO

AMPK (AMP-activated protein kinase) responds to intracellular ATP depletion, while PPARalpha (peroxisome proliferator-activated receptor alpha) induces the expression of genes coding for enzymes and proteins involved in increasing cellular ATP yields. PPARalpha-mediated transcription is shown here to be co-activated by the alpha subunit of AMPK, as well as by kinase-deficient (Thr172Ala) and kinase-less (Asp157Ala, Asp139Ala) mutants of AMPKalpha. The Ser452Ala mutant of mPPARalpha mutated in its putative consensus AMPKalpha phosphorylation site is similarly co-activated by AMPKalpha. AMPKalpha or its kinase-less mutants bind to PPARalpha; binding is increased by MgATP, to a lesser extent by MgADP, but not at all by AMP or ZMP [AICAR (5-aminoimidazole-4-carboxamide ribonucleoside) monophosphate]. ATP-activated binding of AMPKalpha to PPARalpha is mediated primarily by the C-terminal regulatory domain of AMPKalpha. PPARalpha co-activation by AMPKalpha may, however, require its secondary interaction with the N-terminal catalytic domain of AMPKalpha, independently of its kinase activity. While AMPK catalytic activity is activated by AICAR, PPARalpha co-activation and PPARalpha-controlled transcription are robustly inhibited by AICAR, with concomitant translocation of nuclear AMPKalpha or its kinase-less mutants to the cytosol. In conclusion, AMPKalpha, independently of its kinase activity, co-activates PPARalpha both in primary rat hepatocytes and in PPARalpha-transfected cells. The kinase and transcriptional co-activation modes of AMPKalpha are both regulated by the cellular ATP/AMP ratio. Co-activation of PPARalpha by AMPKalpha may transcriptionally complement AMPK in maintaining cellular ATP status.


Assuntos
Aminoimidazol Carboxamida/análogos & derivados , Complexos Multienzimáticos/fisiologia , PPAR alfa/genética , Fosfotransferases/metabolismo , Proteínas Serina-Treonina Quinases/fisiologia , Ativação Transcricional/fisiologia , Proteínas Quinases Ativadas por AMP , Aminoimidazol Carboxamida/farmacologia , Animais , Células COS/química , Células COS/metabolismo , Linhagem Celular , Linhagem Celular Tumoral , Células Cultivadas , Chlorocebus aethiops , Células HeLa/química , Células HeLa/metabolismo , Hepatócitos/química , Hepatócitos/metabolismo , Humanos , Rim/citologia , Rim/embriologia , Complexos Multienzimáticos/antagonistas & inibidores , Complexos Multienzimáticos/genética , Complexos Multienzimáticos/metabolismo , PPAR alfa/metabolismo , Subunidades Proteicas/metabolismo , Proteínas Serina-Treonina Quinases/antagonistas & inibidores , Proteínas Serina-Treonina Quinases/genética , Proteínas Serina-Treonina Quinases/metabolismo , Ratos , Ribonucleotídeos/farmacologia , Transcrição Genética/efeitos dos fármacos , Transcrição Genética/fisiologia , Ativação Transcricional/efeitos dos fármacos , Transfecção
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