Exome sequencing and case-control analyses identify RCC1 as a candidate breast cancer susceptibility gene.

Breast cancer is a genetic disease but the known genes explain a minority of cases. To elucidate the molecular basis of breast cancer in the Tunisian population, we performed exome sequencing on six BRCA1/BRCA2 mutation-negative patients with familial breast cancer and identified a novel frameshift mutation in RCC1, encoding the Regulator of Chromosome Condensation 1. Subsequent genotyping detected the 19-bp deletion in additional 5 out of 153 (3%) breast cancer patients but in none of 400 female controls (p = 0.0015). The deletion was enriched in patients with a positive family history (5%, p = 0.0009) and co-segregated with breast cancer in the initial pedigree. The mutant allele was lost in 4/6 breast tumors from mutation carriers which may be consistent with the hypothesis that RCC1 dysfunction provides a selective disadvantage at the stage of tumor progression. In summary, we propose RCC1 as a likely breast cancer susceptibility gene in the Tunisian population.

STAT1 and STAT6 Act as Antagonistic Regulators of PPARγ in Diabetic Patients with and without Cardiovascular Diseases.

BACKGROUND: The processes that mediate an inflammatory environment and increase atherosclerosis in diabetes are not well understood. Peroxisome proliferator-activated receptors (PPARs) are a subgroup of the nuclear hormone receptor superfamily of ligand-activated transcription factors which play an important role in the pathogenesis of type 2 diabetes mellitus (T2DM) and atherosclerosis. PPARγ promotes changes in lipid metabolism, especially in fatty acid (FA) trafficking, and the activity of PPARγ could be modulated by diabetes phenotype patients. Fatty acid translocase CD36 is one of the advanced PPARγ targets to arbitrate this action. In the current study, we investigated the potential role of signal transducer and activator of transcription STAT1 and STAT6 signaling linked to PPARγ and its implication in the modulation of lipid metabolism. METHODS: Real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) was used to quantify target genes in Peripheral Blood Mononuclear Cells (PBMCs) isolated from two diabetic groups: diabetic patients with cardiovascular diseases (D.CVD) and without cardiovascular diseases (D). RESULTS: We demonstrated that PPARγ and CD36 mRNA expressions were downregulated along D.CVD compared to D (p = 0.002; p = 0.04; respectively). Decreased CD36 was accompanied by elevated levels of plasma triglyceride (TG) concentrations, 0.83 ± 0.29 vs. 2.46 ± 0.22), respectively. Furthermore, STAT1 was significantly more expressed in D.CVD (p = 0.01). On the other hand, we demonstrated that STAT6 induces a significant level of PPARγ mRNA expression in D patients (p = 0.01). CONCLUSIONS: Our results suggest that the expression and activity of PPARγ mediates CD36 in PBMCs and varies with respect to STAT6 and STAT1 trafficking in diabetic patients with and without cardiovascular diseases.

Molecular characterization, homology modeling and docking studies of the R2787H missense variation in BRCA2 gene: Association with breast cancer.

The significance of many BRCA unclassified variants (UVs) has not been evaluated. Classification of these variations as neutral or pathogenic presents a significant challenge and has important implications for breast and ovarian cancer genetic counseling. Here we report a combined molecular and computational approach to classify BRCA UVs missense variations. By using the LOH (Loss of heterozygosity) analysis at the BRCA1/BRCA2 loci, five bioinformatics approaches namely fathmm, PhD-SNP, SNAP, MutationTaster and Human Splicing Finder and the association with the clinico-pathological characteristics related to BRCA tumors, we were able to classify the R2787H (in BRCA2 gene) variant as pathogenic. Then, to investigate the functional role of the R2787H variation in altering BRCA2 structure, the homology model of this variant was constructed using the Rattus norvegicus BRCA2 (PDB ID: 1IYJ) as a template. The predicted model was then assessed for stereochemical quality and side chain environment. Furthermore, docking and binding free energy simulations were performed to investigate the ssDNA-BRCA2 complex interaction. Binding energy value calculation proves that this substitution affects the complex stability. Moreover, this alteration was not found in one hundred healthy controls. These findings suggest that R2787H variant could have potential functional impact. Our approach might be useful for evaluation of BRCA unclassified variants. However additional functional analyzes may provide appropriate assessment to classify such variants.

Li-Fraumeni syndrome in Tunisian carriers with different and rare tumor phenotype: genotype-phenotype correlation.

BACKGROUND: Li-Fraumeni syndrome (LFS) is a rare autosomal hereditary predisposition to multiples cancers, mainly affecting young individuals. It is characterized by a broad tumor spectrum. To our best knowledge, only one Tunisian study with a confirmed LFS was published. METHODS: Our study focused on the clinical, histopathological and genetic results of two patients with rare tumor phenotype and tried to establish genotype-phenotype correlation. The clinical diagnosis was based on Chompret-Bonaiti criteria relative to LFS. Molecular study was assessed using Sanger sequencing of the hotspot germline variants of TP53 gene. RESULTS: We report 2 Tunisian families fulfilling the clinical criteria of Chompret-Bonaiti. The tumor phenotype was bilateral breast cancer (BC) in 27-year-old woman and multiple tumors for the second proband, with an onset age of 14, 35 and 36 yo for osteosarcoma, BC and esophageal cancer respectively. Each of them had a rare histological type of breast cancer associated with LFS, phyllode tumor and intralobular carcinoma. Both patients had cancer family history. The molecular study showed deleterious heterozygous germline TP53 variants in each index case: The first had a well-known hotspot missense variation c.742C>T p.(R248W) with a rare histological association, explaining genotype phenotype correlation. The second case had a nonsense variation c.159G>A p.(W53*), rare worldwide, extending the phenotype spectrum in LFS. Immunohistochemistry study in tumor samples confirmed the lack of p53 protein expression. CONCLUSIONS: Conclusively, germline TP53 testing is primordial in patients with a family history suggestive of LFS for clinical practice avoiding genotoxic treatments and adapting the surveillance. National database in LFS listing clinical and mutational data is important to set, particularly for variants rarely reported worldwide. Experience from different countries must be integrated to harmonize global protocols for cancer surveillance in LFS.

Prevalence of BRCA1 and BRCA2 large genomic rearrangements in Tunisian high risk breast/ovarian cancer families: Implications for genetic testing.

Germline mutations in the BRCA tumor suppressor genes account for a substantial proportion of hereditary breast/ovarian cancer. However, this contribution is lower than expected. This underestimation can partly be explained by the BRCA alterations missed by using Sanger sequencing methods. Thus, large genomic rearrangements (LGRs) in BRCA1 and BRCA2 are responsible for 4-28% of all inherited BRCA mutations. In this study, Multiplex ligation-dependent probe amplification (MLPA) assay was used for detection of large rearrangements of BRCA1 and BRCA2 genes in 36 unrelated high-risk breast/ovarian cancer patients negative for BRCA1/2 point mutations. MLPA assay for all exons of both genes and for 1100delC variant of CHEK2 gene were performed. Positive MLPA results were confirmed by real-time quantitative PCR (qPCR). Two different rearrangements in the BRCA1 gene were identified consisting of exon 5 deletion and exon 20 duplication. MLPA analysis did not reveal any large genomic rearrangements in BRCA2 gene. Overall BRCA1/2 LGRs prevalence among high-risk Tunisian patients was 5.5%. Quantitative real-time PCR confirmed MPLA findings. Our results suggest the usefulness of screening for LGRs in BRCA genes in the Tunisian population. To avoid false-negative results, we suggest that MLPA should be used in genetic testing programs. These results are important for guidance counseling and clinical management of Tunisian high-risk patients.

Family history predictors of BRCA1/BRCA2 mutation status among Tunisian breast/ovarian cancer families.

BACKGROUND: With the increasing request for BRCA1/BRCA2 mutation tests, several risk models have been developed to predict the presence of mutation in these genes; in this study, we have developed an efficient BRCA genetic testing strategy. METHOD: As first step, to identify predictor variables associated with BRCA status, we have undertaken a cumulative mutation analysis including data from three Tunisian studies. Then, we have developed a logistic regression model for predicting the likelihood of harboring a BRCA mutation. Using receiver operating characteristic curves (ROC), an effective evaluation was performed. A total of 92 Tunisian families were included. Overall, 27 women were positive for BRCA1/BRCA2 deleterious mutations. RESULTS: Tow recurrent mutations (c.211dupA and c.5266dupC) explained 76 % of BRCA1-related families and three recurrent mutations (c.1310_1313del, c.1542_1547delAAGA and c.7887_7888insA) explained 90 % of BRCA2-related families. Early age at diagnosis of breast cancer, ovarian cancer, bilateral breast cancer were associated with BRCA1, whereas male breast cancer and four or more breast cancer cases in the family were associated with BRCA2. The area under the receiver operating characteristic curve of the risk score was 0.802 (95 % confidence interval = 0.0699-0. 905). CONCLUSION: Logistic regression reported particular profiles related to BRCA germline mutation carriers in our population, as well as an efficient prediction model that may be a useful tool for increasing the cost-effectiveness of genetic testing strategy.

Dissimilarity between sporadic, non-BRCA1/2 families and hereditary breast cancer, linked to BRCA genes, in the Tunisian population.

BACKGROUND: Most breast cancers (90 %) are sporadic. Only 5-10 % of all cancer cases can be attributed to genetic defects. BRCA genes are strongly incriminated in the hereditary predisposition to the disease. The purpose of our study was to provide more efficient approach to identify pathogenic BRCA mutation carriers and to determine subgroups within the non-BRCA tumor class. METHODS: Different clinicopathological features, reproductive factors, as well as psychosocial ones were compared in women carrying mutations in the BRCA1/BRCA2 genes (12 cases) with non-BRCA1/2 family tumors (36 cases) and age-matched sporadic cases, unselected for family history (44 cases). RESULTS: A BRCA-related class was yielded based on age at diagnosis (age ≤ 35 years; p = 0.1), molecular subtypes(the triple-negative subtype was predominant: 43 % of cases; p = 0.025) and age at menarche (p = 0.04). Furthermore, a "probably sporadic" class was distinguished using hormonal contraceptive use (through 30-40 years of age; p = 0.039), the number of full-term pregnancies (age ≥40 years; p = 0.01), age at menopause(age > 50 years; p = 0.04) and psychosocial factors (age ≥ 40 years; p = 0.01). However, analysis of non-BRCA1/2 family tumors indicated that they constitute a heterogeneous class, showing few perceptible differences with sporadic group, but distinct from BRCA1/2 tumors. CONCLUSIONS: In Tunisian population, breast cancer can be classified with a high level of accuracy as sporadic or related to BRCA germline mutations by combining different clinicopathological features and reproductive factors. This can be clinically useful in genetic counseling and decision making for BRCA genetic test.

High-resolution melting (HRM) assay for the detection of recurrent BRCA1/BRCA2 germline mutations in Tunisian breast/ovarian cancer families.

Germline deleterious mutations in the BRCA1/BRCA2 genes are associated with an increased risk for the development of breast and ovarian cancer. Given the large size of these genes the detection of such mutations represents a considerable technical challenge. Therefore, the development of cost-effective and rapid methods to identify these mutations became a necessity. High resolution melting analysis (HRM) is a rapid and efficient technique extensively employed as high-throughput mutation scanning method. The purpose of our study was to assess the specificity and sensitivity of HRM for BRCA1 and BRCA2 genes scanning. As a first step we estimate the ability of HRM for detection mutations in a set of 21 heterozygous samples harboring 8 different known BRCA1/BRCA2 variations, all samples had been preliminarily investigated by direct sequencing, and then we performed a blinded analysis by HRM in a set of 68 further sporadic samples of unknown genotype. All tested heterozygous BRCA1/BRCA2 variants were easily identified. However the HRM assay revealed further alteration that we initially had not searched (one unclassified variant). Furthermore, sequencing confirmed all the HRM detected mutations in the set of unknown samples, including homozygous changes, indicating that in this cohort, with the optimized assays, the mutations detections sensitivity and specificity were 100 %. HRM is a simple, rapid and efficient scanning method for known and unknown BRCA1/BRCA2 germline mutations. Consequently the method will allow for the economical screening of recurrent mutations in Tunisian population.