Genetic Basis of Breast and Ovarian Cancer: Approaches and Lessons Learnt from Three Decades of Inherited Predisposition Testing

Germline variants occurring in BRCA1 and BRCA2 give rise to hereditary breast and ovarian cancer (HBOC) syndrome, predisposing to breast, ovarian, fallopian tube, and peritoneal cancers marked by elevated incidences of genomic aberrations that correspond to poor prognoses. These genes are in fact involved in genetic integrity, particularly in the process of homologous recombination (HR) DNA repair, a high-fidelity repair system for mending DNA double-strand breaks. In addition to its implication in HBOC pathogenesis, the impairment of HR has become a prime target for therapeutic intervention utilizing poly (ADP-ribose) polymerase (PARP) inhibitors. In the present review, we introduce the molecular roles of HR orchestrated by BRCA1 and BRCA2 within the framework of sensitivity to PARP inhibitors. We examine the genetic architecture underneath breast and ovarian cancer ranging from high- and mid- to low-penetrant predisposing genes and taking into account both germline and somatic variations. Finally, we consider higher levels of complexity of the genomic landscape such as polygenic risk scores and other approaches aiming to optimize therapeutic and preventive strategies for breast and ovarian cancer.

ARPIR: automatic RNA-Seq pipelines with interactive report

BACKGROUND

RNA-Seq is an increasing used methodology to study either coding and non-coding RNA expression. There are many software tools available for each phase of the RNA-Seq analysis and each of them uses different algorithms. Furthermore, the analysis consists of several steps regarding alignment (primary-analysis), quantification, differential analysis (secondary-analysis) and any tertiary-analysis and can therefore be time-consuming to deal with each step separately, in addition to requiring a computer knowledge. For this reason, the development of an automated pipeline that allows the entire analysis to be managed through a single initial command and that is easy to use even for those without computer skills can be useful. Faced with the vast availability of RNA-Seq analysis tools, it is first of all necessary to select a limited number of pipelines to include. For this purpose, we compared eight pipelines obtained by combining the most used tools and for each one we evaluated peak of RAM, time, sensitivity and specificity.

RESULTS

The pipeline with shorter times, lower consumption of RAM and higher sensitivity is the one consisting in HISAT2 for alignment, featureCounts for quantification and edgeR for differential analysis. Here, we developed ARPIR, an automated pipeline that recurs by default to the cited pipeline, but it also allows to choose, between different tools, those of the pipelines having the best performances.

CONCLUSIONS

ARPIR allows the analysis of RNA-Seq data from groups undergoing different treatment allowing multiple comparisons in a single launch and can be used either for paired-end or single-end analysis. All the required prerequisites can be installed via a configuration script and the analysis can be launched via a graphical interface or by a template script. In addition, ARPIR makes a final tertiary-analysis that includes a Gene Ontology and Pathway analysis. The results can be viewed in an interactive Shiny App and exported in a report (pdf, word or html formats). ARPIR is an efficient and easy-to-use tool for RNA-Seq analysis from quality control to Pathway analysis that allows you to choose between different pipelines.

A new MEFV gene mutation in an Iranian patient with familial Mediterranean fever

Familial mediterranean fever (FMF) is an inherited autoinflammatory disorder characterized by recurrent episodes of fever and painful inflammation involving the intra-abdominal organs, the lungs and the joints, which is highly prevalent in specific ethnic groups including the Iranians. We report a 12-year-old boy from Iran, with a clinical history of recurrent fever. Based on the suggestive clinical data, mutational analysis revealed the presence of the novel c.1945C>T heterozygous variant in exon 10, which leads to a leucine to phenylalanine change at position 649 of the protein. The mutation was inherited from the mother. This novel mutation lies in exon 10 of the MEFV gene, which encodes for a domain called B30.2-SPRY, located in the C-terminal region of the pyrin protein and contains the most frequent mutations associated with FMF. The present report expands the spectrum of MEFV gene mutations associated with FMF. The uniqueness of this study, compared with other published case reports, consists in the new mutation found in the MEFV gene. In fact, new mutations in this gene are of high interest, in order to better understand the role of this gene in autoinflammation.

Association of a polymorphism of the Fcγ-receptor 2A (FCGR2A) gene with chronic periaortitis

OBJECTIVES

Chronic periaortitis (CP) is an inflammatory disease associated in 20-60% of the cases with IgG4 related disease. Current evidence supports an autoimmune nature for CP. Fc gamma receptors (FcγRs) are involved in several immune system activities and are associated with autoimmunity in general. We explored the influence of genetic variants within this region on susceptibility to CP.

METHODS

Genotyping of 4 candidate single nucleotide polymorphisms (SNPs) of the FCGR region was performed in CP patients and controls.

RESULTS

One hundred and eighty-three cases and 181 controls were included. An association between the SNP rs1801274 of the FCGR2A and CP was detected (OR 1.6, 95%CI 1.18-2.16;corrected p-value, pcorr=0.0085). After stratification of the population according to clinical characteristics, the association was restricted to cases of idiopathic retroperitoneal fibrosis (OR 1.66, 95%CI 1.21-2.29;pcorr=0.028), without involvement of the thoracic aorta (OR 1.77, 95%CI 1.21-2.57;pcorr=0.043), with deep vein thrombosis at onset (OR 3.96, 95%CI 1.81-8.66;pcorr=0.0021) and with normal IgG4 levels (OR 2.67, 95%CI 1.39-5.12;pcorr=0.031).

CONCLUSIONS

In the largest candidate gene approach study performed so far in CP, we demonstrated an association for CP with a gene hallmark of autoimmunity. The association appears restricted to typical cases of CP without increase of IgG4 levels.

Discrimination of FCGR2B polymorphism without coamplification of FCGR2A and FCGR2C genes

The FCGR locus is characterized by high polymorphism and sequence homology. In particular, the Ile232Thr polymorphism in the FCGR2B gene results in inaccurate genotyping in most published papers. The purpose of the study was to develop an accurate genotyping assay able to discriminate this polymorphism.

FCGR2A single nucleotide polymorphism confers susceptibility to childhood-onset idiopathic nephrotic syndrome

Childhood-onset idiopathic nephrotic syndrome affects 1.15-3.4 children/100,000 children/year in Western Countries. Immune-mediated mechanisms, particularly T cell-mediated, are thought to play a key pathogenic role. The genetic basis of the disease is still poorly understood. We tested the association between single nucleotide polymorphisms (SNPs) of four genes encoding Fc gamma receptors (FCGR2A, FCGR2B, FCGR3A, FCGR3B) and idiopathic nephrotic syndrome in a case-control study of paediatric patients. Children with idiopathic nephrotic syndrome (aged 1-16 years) were included. FCGR2A rs1801274 and FCGR3A rs396991 SNPs were genotyped using real-time PCR with the TaqMan method, while FCGR2B rs1050501 and FCGR3B NA1/NA2 were genotyped using Sanger sequencing. Fisher's exact test was used to explore genetic association. We enrolled 103 idiopathic nephrotic syndrome patients and 181 healthy controls. A significant association was found between idiopathic nephrotic syndrome and FCGR2A rs1801274 SNP (both with the T allele and the TT genotype, p value=0.0009, OR 1.81, 95% CI 1.27-2.59 and p value=0.0007, OR 2.39, 95% CI 1.44-3.99, respectively). No associations were found for the remaining SNPs. Fc gamma receptors might modulate response to rituximab; since 60 of the enrolled patients were treated with rituximab, we also tested the association between the studied SNPs and rituximab efficacy in this patient subgroup, but found only a weak association with FCGR2A CC genotype (p value=0.03). The FCGR2A rs1801274 SNP in the gene encoding the activating receptor CD32A confers susceptibility to idiopathic nephrotic syndrome.

Patterns of Novel Alleles and Genotype/Phenotype Correlations Resulting from the Analysis of 108 Previously Undetected Mutations in Patients Affected by Neurofibromatosis Type I

Neurofibromatosis type I, a genetic disorder due to mutations in the NF1 gene, is characterized by a high mutation rate (about 50% of the cases are de novo) but, with the exception of whole gene deletions associated with a more severe phenotype, no specific hotspots and few solid genotype/phenotype correlations. After retrospectively re-evaluating all NF1 gene variants found in the diagnostic activity, we studied 108 patients affected by neurofibromatosis type I who harbored mutations that had not been previously reported in the international databases, with the aim of analyzing their type and distribution along the gene and of correlating them with the phenotypic features of the affected patients. Out of the 108 previously unreported variants, 14 were inherited by one of the affected parents and 94 were de novo. Twenty-nine (26.9%) mutations were of uncertain significance, whereas 79 (73.2%) were predicted as pathogenic or probably pathogenic. No differential distribution in the exons or in the protein domains was observed and no statistically significant genotype/phenotype correlation was found, confirming previous evidences.

The Frontal Behavioural Inventory (Italian version) differentiates frontotemporal lobar degeneration variants from Alzheimer's disease

The objective was to evaluate the construct validity of the Italian version of the Frontal Behavioural Inventory (FBI) and its usefulness in the differential diagnosis of dementias. Standard criteria were used in the clinical diagnosis of dementias in 83 patients and 33 agematched healthy volunteers. The FBI scale was translated from English into Italian language and back-translated. Cronbach's alpha, inter-rater and test-retest reliability, FBI convergent validity and discriminant analysis were calculated. FBI profile was compared between patients affected by frontotemporal lobar degeneration (FTLD) and Alzheimer's disease (AD). The FBI showed a high internal consistency and inter-rater reliability and it distinguished normal behavioural conditions from those presented in FTLD or AD. An 86.8% diagnostic accuracy was calculated by the discriminant analysis, selecting only age at disease onset and FBI, and particularly distinguishing behavioural variants within the FTLD spectrum. FTLD patients showed a characteristic behavioural profile. The FBI might be a reliable and useful diagnostic tool for dementias in clinical practice.

[Complications in stomach cancer surgery. A review of cases]

The improvement in surgical and anesthesiological techniques have allowed a reduction in oncological surgical morbidity and mortality. The objective of this retrospective study is to evaluate the morbidity and the mortality in oncological gastric surgery up to date. Between 1979 and 1994 we evaluated 281 patients for gastric cancer, of whom 249 underwent surgery. The patients ranged in age from 34 to 88 years, with a mean age of 67.8 years, and included 158 males and 91 females. An oncological radical excision was performed in 184 patients (122 gastroresections and 62 gastrectomies). The other 65 patients underwent exploratory or palliative surgery: 26 explorative laparotomies, 26 gastroenteroanastomoses, 9 gastroresections, 3 digiunostomies and one gastrostomy. The overall post-operative morbidity has been 40.1%, 27.3% was generic and 12.8% was surgical morbidity. The overall mortality has been 9.6%, of whom about one third following surgical complications. In our experience the factors related with morbidity and mortality have been: age, preoperative nutritional state and stage of the disease.

[Neoplasms and kidney transplantation. Case contribution]

BACKGROUND

The incidence of malignancies after transplantation is higher when compared with expected cancer in control patients, particularly skin and female genital cancer, non-Hodgkin's disease and Kaposi's sarcoma. The aim of this study is to evaluate the frequency and the efficacy of the treatment of cancer following renal transplantation.

METHODS

A retrospective analysis of 404 recipients was performed and it showed the onset of 15 cancers (8 skin cancers, 3 Kaposi's sarcomas, 2 renal carcinomas, 1 urotelioma and 1 colon cancer) in 11 patients (3.7%). At the time of diagnosis, the mean period of immunosuppressive therapy (7 cases of double therapy, 4 cases of triple therapy) was 44.8 months. Skin cancer (53.3%) and Kaposi's sarcoma (20%) were the most frequent in personal experience as reported in literature. Neither lymphomas, nor female genital cancers were detected.

RESULTS

All the cases were surgically treated, except patients with Kaposi's sarcoma, whose immunosuppressive therapy was reduced without alteration of renal function. Death-rate was 0.25% (1 case), the remaining patients show no signs of local recurrence or metastasis with preserved renal function except for the patient with renal carcinoma of the transplanted kidney, who underwent nephrectomy and returned in replacement therapy.

CONCLUSIONS

The conclusion is drawn that the research of relationship between type of immunosuppressive therapy and cancer incidence and careful clinical and instrumental examination of transplant patients may contribute to reduce the onset of neoplastic degenerations and lead to an early diagnosis.

[Ileocolic invagination caused by ileal lipoma simulating cancer of the cecum. Description of a clinical case]

The authors describe the diagnostic difficulties that occurred during the study of a patient affected by a small bowel lipoma with ileo-colic intussusception, and operated for suspicion of colic neoplasm. The report suggests some evaluations about the reliability diagnostic techniques in the study of the small bowel.

[Criteria for a rational choice of treatment in biliary ileus. The authors' personal experience]

Treatment of biliary ileus is still controversial in respect of surgical strategy. While some surgeons have agreed enterolithotomy as a simple and safe operation, others prefer to perform enterolithotomy, cholecystectomy and repair bilio-enteric fistula at the same time. The authors examine their experience and discuss various modalities of treatment to identify the rational method of therapy in these patients.

Abdominal aortic aneurysms: some controversial points

A retrospective review of the surgical treatment of 51 abdominal aortic aneurysms is reported. Thirty-five (69%) patients were operated on electively, and 16 (31%) had emergency surgery. Fissurated aneurysms were included in the elective surgery group. The operative death rate was respectively 2.7% and 50%. Controversial points about diagnosis, treatment of associated diseases, surgical technique, and selection of the patients for surgery are presented and discussed.