Whole Exome Sequencing in BRCA1-2 Candidate Families: The Contribution of Other Cancer Susceptibility Genes

Polymorphisms and Pharmacogenomics of NQO2: The Past and the Future

The flavoenzyme N-ribosyldihydronicotinamide (NRH):quinone oxidoreductase 2 (NQO2) catalyzes two-electron reductions of quinones. NQO2 contributes to the metabolism of biogenic and xenobiotic quinones, including a wide range of antitumor drugs, with both toxifying and detoxifying functions. Moreover, NQO2 activity can be inhibited by several compounds, including drugs and phytochemicals such as flavonoids. NQO2 may play important roles that go beyond quinone metabolism and include the regulation of oxidative stress, inflammation, and autophagy, with implications in carcinogenesis and neurodegeneration. NQO2 is a highly polymorphic gene with several allelic variants, including insertions (I), deletions (D) and single-nucleotide (SNP) polymorphisms located mainly in the promoter, but also in other regulatory regions and exons. This is the first systematic review of the literature reporting on NQO2 gene variants as risk factors in degenerative diseases or drug adverse effects. In particular, hypomorphic 29 bp I alleles have been linked to breast and other solid cancer susceptibility as well as to interindividual variability in response to chemotherapy. On the other hand, hypermorphic polymorphisms were associated with Parkinson's and Alzheimer's disease. The I and D promoter variants and other NQO2 polymorphisms may impact cognitive decline, alcoholism and toxicity of several nervous system drugs. Future studies are required to fill several gaps in NQO2 research.

Diagnostics and treatment of ovarian cancer in the era of precision medicine - opportunities and challenges

Due to predictions of increasing incidences and deaths from ovarian cancer, this neoplasm is a challenge for modern health care. The advent of NGS technology has made it possible to understand the molecular characteristics of many cancers, including ovarian cancer. The data obtained in research became the basis for the development of molecularly targeted therapies thus leading to the entry of NGS analysis into the diagnostic process of oncological patients. This review presents targeted therapies currently in preclinical or clinical trials, whose promising results offer hope for their use in clinical practice in the future. As more therapeutic options emerge, it will be necessary to modify molecular diagnostic regimens to select the best treatment for a given patient. New biomarkers are needed to predict the success of planned therapy. An important aspect of public health is molecular testing in women with a familial predisposition to ovarian cancer enabling patients to be included in prevention programs. NGS technology, despite its high throughput, poses many challenges, from the quality of the diagnostic material used for testing to the interpretation of results and classification of sequence variants. The article highlights the role of molecular testing in ongoing research and also its role in the diagnostic and therapeutic process in the era of personalized medicine. The spread of genetic testing in high-risk groups, the introduction of more targeted therapies and also the possibility of agnostic therapies could significantly improve the health situation for many women worldwide.

Genetic analyses of DNA repair pathway associated genes implicate new candidate cancer predisposing genes in ancestrally defined ovarian cancer cases

Not all familial ovarian cancer (OC) cases are explained by pathogenic germline variants in known risk genes. A candidate gene approach involving DNA repair pathway genes was applied to identify rare recurring pathogenic variants in familial OC cases not associated with known OC risk genes from a population exhibiting genetic drift. Whole exome sequencing (WES) data of 15 OC cases from 13 families tested negative for pathogenic variants in known OC risk genes were investigated for candidate variants in 468 DNA repair pathway genes. Filtering and prioritization criteria were applied to WES data to select top candidates for further analyses. Candidates were genotyped in ancestry defined study groups of 214 familial and 998 sporadic OC or breast cancer (BC) cases and 1025 population-matched controls and screened for additional carriers in 605 population-matched OC cases. The candidate genes were also analyzed in WES data from 937 familial or sporadic OC cases of diverse ancestries. Top candidate variants in ERCC5, EXO1, FANCC, NEIL1 and NTHL1 were identified in 5/13 (39%) OC families. Collectively, candidate variants were identified in 7/435 (1.6%) sporadic OC cases and 1/566 (0.2%) sporadic BC cases versus 1/1025 (0.1%) controls. Additional carriers were identified in 6/605 (0.9%) OC cases. Tumour DNA from ERCC5, NEIL1 and NTHL1 variant carriers exhibited loss of the wild-type allele. Carriers of various candidate variants in these genes were identified in 31/937 (3.3%) OC cases of diverse ancestries versus 0-0.004% in cancer-free controls. The strategy of applying a candidate gene approach in a population exhibiting genetic drift identified new candidate OC predisposition variants in DNA repair pathway genes.

Intestinal and extraintestinal neoplasms in patients with NTHL1 tumor syndrome: a systematic review

Germline biallelic pathogenic variants (PVs) in NTHL1 have since 2015 been associated with the autosomal recessive tumor predisposition syndrome: NTHL1 tumor syndrome or NTHL1-associated polyposis. In this systematic review, we aim to systematically investigate the phenotypic and genotypic spectrum of the condition including occurrence of both benign and malignant tumors. The databases PubMed, EMBASE, and Scopus were searched. The search was conducted the 25th of august 2021. We included patients with germline PVs, both heterozygous and homo-/compound heterozygous carriers. Twenty-one papers were selected including 47 patients with biallelic PVs in NTHL1 in 32 families. Twenty-three out of 47 patients (49%) were diagnosed with colorectal cancer (CRC) (mean age: 55, range: 31-73) and 12 out of 22 female patients (55%) were diagnosed with breast cancer (mean age: 49, range: 36-63). Apart from three, all patients who underwent a colonoscopy, had colonic adenomas (93%), and three patients (6%) had duodenal adenomatosis. We also identified 158 heterozygous carriers of germline PVs in NTHL1. Twenty-six out of 68 (38%) heterozygous carriers, who underwent colonoscopy, had colonic polyps or adenomas. Twenty-nine heterozygous carriers (18%) were diagnosed with CRC and 59 (49%) with breast cancer. We observed a high frequency of early onset CRC and breast cancer in patients with NTHL1 tumor syndrome. Subsequently, colorectal, breast, and endometrial cancer screening programs are recommended for NTHL1 biallelic carriers. Trial registry PROSPERO: CRD42021275159.

Multi-gene panel testing increases germline predisposing mutations’ detection in a cohort of breast/ovarian cancer patients from Southern Italy

Breast cancer is the most common neoplasia in females worldwide, about 10% being hereditary/familial and due to DNA variants in cancer-predisposing genes, such as the highly penetrant BRCA1/BRCA2 genes. However, their variants explain up to 25% of the suspected hereditary/familial cases. The availability of NGS methodologies has prompted research in this field. With the aim to improve the diagnostic sensitivity of molecular testing, a custom designed panel of 44 genes, including also non-coding regions and 5’ and 3’ UTR regions, was set up. Here, are reported the results obtained in a cohort of 64 patients, including also few males, from Southern Italy. All patients had a positive personal and/or familial history for breast and other cancers, but tested negative to routine BRCA analysis. After obtaining their written informed consent, a genomic DNA sample/patient was used to obtain an enriched DNA library, then analyzed by NGS. Sequencing data analysis allowed the identification of pathogenic variants in 12 of tested patients (19%). Interestingly, MUTYH was the most frequently altered gene, followed by RNASEL, ATM, MSH6, MRE11A, and PALB2 genes. The reported resultsreinforce the need for enlarged molecular testing beyond BRCA genes, at least in patients with a personal and familial history, strongly suggestive for a hereditary/familial form. This gives also a hint to pursue more specific precision oncology therapy.

Effect of Rho GTPase activating protein 9 combined with preoperative ratio of platelet distribution width to platelet count on prognosis of patients with serous ovarian cancer

Background

This study aimed to investigate the relationship between Rho GTPase activating protein 9 (ARHGAP9) combined with preoperative ratio of platelet distribution width to platelet count (PDW/PLT) and patients prognosis with serous ovarian cancer.

Methods

The clinical data of 80 patients with serous ovarian cancer treated in Jiangsu Cancer Hospital from May 2011 to May 2016 were analyzed retrospectively. We verified ARHGAP9 expression in The Cancer Genome Atlas (TCGA) database, then detected messenger RNA (mRNA) expression encoding ARHGAP9 in ovarian cancer tissue samples using reverse transcription quantitative polymerase chain reaction (RT-qPCR). These patients were divided into an ARHGAP9 low-expression group and an ARHGAP9 high-expression group. The optimal critical value of PDW/PLT was determined by receiver operating characteristic (ROC) curve. The patients were divided into low PDW/PLT group and high PDW/PLT group. Kaplan-Meier method and log-rank test were used for univariate survival analysis, Cox regression method was used for multivariate analysis, and then a nomogram was constructed for internal verification.

Results

The ARHGAP9 protein was highly expressed both in TCGA serous ovarian cancer database and the serous ovarian cancer tumor tissues. There were significant differences in menstrual status, the International Federation of Gynecology and Obstetrics (FIGO) stage and grade between the ARHGAP9 low expression group and ARHGAP9 high expression group (all P<0.05). There were significant differences in FIGO stage, lymph node metastasis, and ascites between the low PDW/PLT group and high PDW/PLT group (all P<0.05). Finally, 80 patients were included, with a mortality rate of 45.0% and a survival rate of 55.0%; the median progression-free survival (PFS) was 19 months, and the median overall survival (OS) was 62.5 months. Cox multivariate analysis showed that PDW/PLT and ARHGAP9 were independent risk factors for tumor progression (P=0.026 and P=0.028, respectively). In the internal validation, the C-index of the nomogram was 0.6518 [95% confidence interval (CI): 0.5685 to 0.7352], and the prediction model had certain accuracy.

Conclusions

ARHGAP9 and PDW/PLT Decrease can significantly prolong OS and PFS in serous ovarian cancer patients. Therefore, ARHGAP9 can be used as a new predictive biomarker and may be related to the immune infiltration of serous ovarian cancer.