Mutational pattern of PIK3CA exon 20 in circulating DNA in breast cancer.

Breast cancer (BC) is one of the most common cancers with diverse mutations, etiology and causes. Mutational signature of the driver genes could allow for better understanding disease etiology and progression. This study aims to assess PIK3CA Exon 20 somatic mutational signature in relation to potential underlying etiology. Circulating DNA of 71 Egyptian BC patients was isolated, amplified for PIK3CA Exon 20, and sequenced. Mutational signature was determined according to COSMIC v2 signature. Public BC dataset was analysed to assess PIK3CA mutations effect on the transcriptomic profile. Somatic mutations of PIK3CA exon 20 were found in 66.2% of the study cohort. Nucleotide substitution patterns were similar to general nucleotide substitution patterns in BC. Signature 3 and 9 were the most common signatures in the studied BC patients. Signature of Aristolochic acid exposure was found in some cases. The most common nucleotide substitution was T > A transversion, but substitutions T > G and T > C were correlated to each other and to the total mutation number. PIK3CA mutations were found to disrupt several pathways including RAC1, PDGF, Wnt, and integrin signalling. PIK3CA exon 20 mutational signatures in Egyptian BC patients could suggest a disease etiology involving homologous recombination deficiency (HRD) and polymerase eta (Pol η). Nucleotide substitution patterns could indicate the role of exposure to oxidative stress and some carcinogens such as 4-aminobiphenyl and Aristolochic acid.

The potential role of miR-27a and miR-320a in metabolic syndrome in obese Egyptian females.

BACKGROUND: Metabolic syndrome (MetS) is a combination of many health complications, such as obesity, high blood pressure, hyperlipidemia, hyperglycemia, and insulin resistance, with an increasing threat of type 2 diabetes mellitus (T2DM) and cardiovascular diseases. As the MetS develops, an alteration in the expression of some genes regulated by circulating microRNAs may also develop as a consequence. TaqMan microRNA primers specific for both miR-27a and miR-320a were used to estimate their expression levels in plasma samples collected from two groups: obese females with metabolic syndrome (n = 49) and lean healthy female volunteers (n = 23), to detect if their expression levels were deregulated with MetS. RESULTS: The study results revealed that miR-27a was upregulated in the plasma of MetS group compared to the healthy controls, while miR-320a was downregulated (p ≤ 0.005). There was a highly significantly positive correlation between miR-27a expression and body mass index (BMI), waist circumference (WC), fasting blood glucose (FBG), insulin resistance (represented as HOMA-IR), and triglycerides (TG), while it showed significantly negative correlation only with HDL-cholesterol (p ≤ 0.0001). miR-320a showed significantly negative correlation with BMI, WC, waist-hip ratio (WHR), FBG, HOMA-IR, and TG. The expression value of miR-320a was positively correlated with HDL-cholesterol. Area under the curves (AUC) was equal to 1.000 for both microRNAs. CONCLUSION: Our study added more evidence that monitoring changes in expression levels of both miR-27a and miR-320a in MetS patients could help in the evaluation of disease progression, risk, and susceptibility.

SUMO pathway, blood coagulation and oxidative stress in SARS-CoV-2 infection.

Severe Acute Respiratory Syndrome Corona Virus 2 (SARS CoV-2) is currently an international pandemic causing coronavirus disease 19 (COVID-19). Viral entry requires ACE2 and transmembrane protease serine 2 (TMPRSS2) for membrane fusion or through endosomal pathway. This Study aims to assess transcriptomic changes and differentially expressed genes (DFGs) in COVID-19. METHODS: Transcriptomic data of the publicly available dataset (GSE147507) was quantile normalized and analysed for DFGs, network analysis and pathway analysis. RESULTS: DFG sets showed that 8 genes (SAE1, AEBP2, ATP1A1, DKK3, MAFF, NUDC, TRAP1, and VAV1) were significantly dysregulated in all studied groups. Functional analysis revealed that negative regulation of glucocorticoid biosynthesis, protein SUMOylation (SAE1), blood coagulation (VAV1) and cellular response to stress were affected by SARS CoV-2 infection. Cell line transduction with ACE2 vector didn't show significant changes in the dysregulated pathways. Also, no significant change was observed in expression levels of ACE2 or TMPRSS2 in response to SARS CoV-2 infection. Further analysis showed dysregulation of several genes in the SUMOylation pathway and blood coagulation process in human and cell lines transcriptome. Also, several Cathepsins proteases were significantly dysregulated in case of SARS CoV-2 infection. Genes related to cellular response to stress such as TRAP-1 and NOX were dysregulated in cases of SARS CoV-2 infection. CONCLUSION: Dysregulation in genes of protein SUMOylation, blood coagulation and response to oxidative stress pathways in SARS CoV-2 infection could be critical for disease progression. Drugs acting on SUMO pathway, VAV1, NOX genes could be studied for potential benefit to COVID-19 patients.

Mitochondrial DNA in Fresh versus Frozen Embryo Culture Media of Polycystic Ovarian Syndrome Patients Undergoing Invitro Fertilization: A Possible Predictive Marker of a Successful Pregnancy.

PURPOSE: Frozen embryos transfer (ET) may improve the live-birth and reduce rates of ovarian hyperstimulation in polycystic ovary syndrome (PCOS) patients. Morphological criteria are the classical way for embryo selection, yet recently, many biochemical and genetic markers have been developed. This study aimed to compare fresh and frozen ET using the mtDNA/gDNA ratio of embryo secretome and the possibility of using this ratio as a predictive marker of PCOS pregnancy rate. SUBJECTS AND METHODS: One hundred PCOS patients undergoing IVF were chosen according to Rotterdam criteria and divided into two groups. Group I (50 with fresh ET), group II (50 with frozen ET), and otherwise 33 apparently healthy women as a control group with fresh ET. We then carried out absolute quantification of embryo culture media mtDNA and gDNA by real-time PCR. RESULTS: mtDNA/gDNA ratio was significantly low in PCOS embryo culture media in comparison with control. Additionally, while the mtDNA/gDNA ratio was significantly high in pregnant PCOS embryo culture media, it was high, though not statistically significant, in the fresh ET than frozen ET group. mtDNA/gDNA ratio sensitivity and specificity in PCOS embryo culture media as a predictive value of pregnancy rate were (86% and 96%, respectively). CONCLUSION: mtDNA/gDNA ratio measurement in PCOS embryo culture media is a novel marker that can be clinically applied as a predictive value of the quality of the morphologically good embryo.

Polymorphism of XRCC3 in Egyptian Breast Cancer Patients.

PURPOSE: Polymorphisms of DNA repair genes may contribute to variations in DNA repair capacity and subsequent genetic susceptibility to different cancers. In Egypt, breast cancer is the most common cancer among women, representing 18.9% of the total cancer cases. The present study assesses the correlation between X-ray repair cross-complementing group 3 (XRCC3) polymorphism with breast cancer and treatment response in Egyptian female breast cancer patients. PATIENTS AND METHODS: This pilot case-control study was conducted on 66 female breast cancer patients and 20 apparently healthy females as a control group. Tumor grading, immunohistostaining of hormone (progesterone and estrogen) receptors and human epidermal growth factor receptor 2 (HER2), and RFLP-PCR for XRCC3 (rs861539) polymorphism were performed. All breast cancer patients received a treatment protocol (after surgery) which was either chemotherapy (anthracyclines followed by paclitaxel or anthracyclines + fluorouracil) or radiotherapy, or both. Disease-free survival (DFS) and overall survival (OS) were recorded. RESULTS: The number of patients with a heterozygous allele (GA) was significantly higher in cases of tumor size >20 mm. The A allele was correlated with younger age at diagnosis in both chemotherapy and radiotherapy groups. Poor treatment response and higher mortality rates were significantly associated with AA and GA compared with GG alleles (normal allele). In the chemotherapy group, out of eight patients with the A allele, six showed a poor response to treatment containing fluorouracil. CONCLUSION: XRCC3 rs861539 polymorphism could be associated with lower DFS and OS and poor treatment response. So, we recommend carrying out XRCC3 genotyping before starting treatment to choose the most effective treatment strategy according to XRCC3 polymorphism.

Circulating DNA in Egyptian Women with Breast Cancer.

The commonest cancer in Egyptian females occurs in the breast cfDNA is a non-invasive marker for tumor detetion and prognostic assessment in many types of cancer including breast cancer. This study aimed to assess the role of cfDNA and its fragmentation pattern in breast cancer prognosis and treatment response. Forty female patients with malignant breast tumors and a comparable group of healthy blood donors were enrolled prospectively. cfDNA levels and fragmentation patterns were investigated after cfDNA extraction, gel electrophoresis and gel analysis. The percentage of breast cancer patients positive for cfDNA (92.5%) was significantly higher than that of controls (55%). Also, mean concentration of cfDNA was significantly higher than in the control group (<0.05). Most Her-2 positive patients had long cfDNA fragments, this being significant as compared to Her-2 negative patients (<0.05). Metastasis was also positively linked to significantly higher cfDNA (<0.05) and the mean cfDNA integrity index was significantly higher in non-responders compared to treatment responders (<0.05). In conclusion, both qualitative and quantitative aspects of cfDNA and its different fragments in breast cancer patients could be related to prognosis, metastasis and treatment response. Long cfDNA fragments could be particularly useful for prediction purposes.