Deleterious and ethnic-related BRCA1/2 mutations in tissue and blood of Egyptian colorectal cancer patients and its correlation with human papillomavirus.

This study aimed to identify BRCA1/2 mutational patterns in the tissue and blood of Egyptian colorectal cancer (CRC) patients and to study the possible correlation of this mutational pattern with Human papillomavirus (HPV) infection. Eighty-two colonoscopic biopsies and forty-six blood samples were collected from Egyptian CRC patients, as well as blood samples of age and sex-matched healthy controls (n = 43) were enrolled. The libraries were performed using Qiaseq Human BRCA1 and BRCA2 targeted DNA panel and sequenced via Ion proton sequencer. Also, the CRC tissues were subjected to conventional PCR targeting the HPV Late 1 (L1) region. Our analysis revealed that the BRCA-DNA damage pathway had been altered in more than 65% of the CRC patients. Comparing tissue and blood samples from CRC patients, 25 somatic mutations were found exclusively in tissue, while 41 germline mutations were found exclusively in blood. Additionally, we identified 23 shared BRCA1/2 pathogenic (PVs) mutations in both blood and tissue samples, with a significantly higher frequency in blood samples compared to tissue samples. The most affected exon in BRCA1 was exon 10, while the most affected exons in BRCA2 were 11, 14, 18, 24, and 27 exons. Notably, we revealed an ethnic-related cluster of polymorphism variants in our population closely related to South Asian and African ethnicities. Novel PVs were identified and submitted to the ClinVar database. HPV was found in 23.8% of the CRC tissues, and 54% of HPV-positive cases had somatic BRCA1/2 PVs. The results of this research point to a possible connection between infection with HPV and BRCA1/2 mutations in the occurrence of colorectal cancer in the Egyptian population, which has a mixed ethnic background. Our data also indicate that liquid biopsy (blood samples) may be more representative than tissue samples for detecting BRCA1/2 mutations. These findings may have implications for cancer screening and the development of personalized, targeted therapies, such as PARP inhibitors, which can effectively target BRCA1/2 mutations.

The Landscape of BRCA Mutations among Egyptian Women with Breast Cancer.

BACKGROUND: Deleterious germline mutations in BRCA1 and BRCA2 genes are associated with a high risk of breast and ovarian cancer. In many developing countries, including Egypt, the prevalence of BRCA1/2 mutations among women with breast cancer (BC) is unknown. AIM: We aimed to determine the prevalence of deleterious germline BRCA mutations in Egyptian patients with breast cancer. METHODS: We report the results of a cohort study of 81 Egyptian patients with breast cancer who were tested for germline BRCA1/2 mutations during routine clinical practice, mostly for their young age of presentation, BC subtype, or presence of family history. In addition, we searched five databases to retrieve studies that reported the prevalence of BRCA1/2 mutation status in Egyptian women with BC. A systematic review of the literature was performed, including prospective and retrospective studies. RESULTS: In our patient cohort study, 12 patients (14.8%) were positive for either BRCA1/2 deleterious mutations. Moreover, 13 (16.1%) patients had a variant of unknown significance (VUS) of BRCA1/2 genes. Twelve studies were eligible for the systematic review, including 610 patients. A total of 19 deleterious germline mutations in BRCA1/2 were identified. The pooled prevalence of BRCA1/2 mutations was 40% (95% confidence interval 1-80%). CONCLUSION: The reported prevalence was highly variable among the small-sized published studies that adopted adequate techniques. In our patient cohort, there was a high incidence of VUS in BRCA1/2 genes. Accordingly, there is an actual demand to conduct a prospective well-designed national study to accurately estimate the prevalence of BRCA1/2 mutations among patients with BC in Egypt.

Insight into the role of clathrin-mediated endocytosis inhibitors in SARS-CoV-2 infection.

Emergence of SARS-CoV-2 variants warrants sustainable efforts to upgrade both the diagnostic and therapeutic protocols. Understanding the details of cellular and molecular basis of the virus-host cell interaction is essential for developing variant-independent therapeutic options. The internalization of SARS-CoV-2, into lung epithelial cells, is mediated by endocytosis, especially clathrin-mediated endocytosis (CME). Although vaccination is the gold standard strategy against viral infection, selective inhibition of endocytic proteins, complexes, and associated adaptor proteins may present a variant-independent therapeutic strategy. Although clathrin and/or dynamins are the most important proteins involved in CME, other endocytic mechanisms are clathrin and/or dynamin independent and rely on other proteins. Moreover, endocytosis implicates some subcellular structures, like plasma membrane, actin and lysosomes. Also, physiological conditions, such as pH and ion concentrations, represent an additional factor that mediates these events. Accordingly, endocytosis related proteins are potential targets for small molecules that inhibit endocytosis-mediated viral entry. This review summarizes the potential of using small molecules, targeting key proteins, participating in clathrin-dependent and -independent endocytosis, as variant-independent antiviral drugs against SARS-CoV-2 infection. The review takes two approaches. The first outlines the potential role of endocytic inhibitors in preventing endocytosis-mediated viral entry and its mechanism of action, whereas in the second computational analysis was implemented to investigate the selectivity of common inhibitors against endocytic proteins in SARS-CoV-2 endocytosis. The analysis revealed that remdesivir, methyl-ß-cyclodextrin, rottlerin, and Bis-T can effectively inhibit clathrin, HMG-CoA reductase, actin, and dynamin I GTPase and are more potent in inhibiting SARS-CoV-2 than chloroquine. CME inhibitors for SARS-CoV-2 infection remain understudied.

Antiviral activity of chitosan nanoparticles encapsulating silymarin (Sil-CNPs) against SARS-CoV-2 (in silico and in vitro study).

To develop a specific treatment against COVID-19, we investigated silymarin-chitosan nanoparticles (Sil-CNPs) as an antiviral agent against SARS-CoV-2 using in silico and in vitro approaches. Docking of Sil and CNPs was carried out against SARS-CoV-2 spike protein using AutoDock Vina. CNPs and Sil-CNPs were prepared by the ionic gelation method and characterized by TEM, FT-IR, zeta analysis, and the membrane diffusion method to determine the drug release profile. Cytotoxicity was tested on both Vero and Vero E6 cell lines using the MTT assay. Minimum binding energies with spike protein and ACE2 were -6.6, and -8.0 kcal mol-1 for CNPs, and -8.9, and -9.7 kcal mol-1 for Sil, respectively, compared to -6.6 and -8.4 kcal mol-1 respectively for remdesivir (RMV). CNPs and Sil-CNPs were prepared at sizes of 29 nm and 82 nm. The CC50 was 135, 35, and 110 µg mL-1 for CNPs, Sil, and Sil-CNPs, respectively, on Vero E6. The IC50 was determined at concentrations of 0.9, 12 and 0.8 µg mL-1 in virucidal/replication assays for CNPs, Sil, and Sil-CNPs respectively using crystal violet. These results indicate antiviral activity of Sil-CNPs against SARS-CoV-2.

In-house protocol: spin-based viral RNA purification.

A worldwide shortage of molecular biology consumables is in surge. This includes filter tips, nucleic acid purification kits, polymerases, reverse-transcriptase, and different types of reagents which are included in viral diagnostic kits. In developing countries, the problem is even worse, since there is few capital enterprise to adopt this kind of industry. So, our aim is to develop a suitable, functional, comparable to commercial ones, and affordable in-house protocol to purify viral RNA. We sought some published and commercial RNA purification solutions to set-up an in-house protocol for viral RNA extraction. Solution was prepared accordingly. Also, LPA (linearized polyacrylamide) carrier was evaluated. The whole setting of in-house solutions with addition of LPA carrier was compared to QIAamp viral RNA minikit solutions. Our results showed that linearized polyacrylamide (LPA) carrier in homemade solutions is comparable to poly A carrier which is used in the most commercial kit. In addition, the whole setting of RNA purification solutions did achieve the purpose of viral RNA purification. Also, the result was confirmed using sputum of a Sars-Cov2 infected patient. Our experiments did end up with an affordable homemade solutions for viral RNA purification.

Zinc Oxide Nanoparticle-Loaded Electrospun Polyvinylidene Fluoride Nanofibers as a Potential Face Protector against Respiratory Viral Infections.

ZnO-NPs loaded polyvinylidene fluoride (PVDF) composite nanofibers were fabricated by electrospinning and optimized using different concentrations (0, 2, and 5 wt %) of ZnO-NPs. Characterization techniques, for example, FTIR, SEM, XRD, and tensile strength analysis were performed to analyze the composite nanofibers. Molecular docking calculations were performed to evaluate the binding affinity of PVDF and ZnO@PVDF against the hexon protein of adenovirus (PDB ID: 6CGV). The cytotoxicity of tested materials was evaluated using MTT assay, and nontoxic doses subjected to antiviral evaluation against human adenovirus type-5 as a human respiratory model were analyzed using quantitative polymerase chain reaction assay. IC50 values were obtained at concentrations of 0, 2, and 5% of ZnO-loaded PVDF; however, no cytotoxic effect was detected for the nanofibers. In 5% ZnO-loaded PVDF nanofibers, both the viral entry and its replication were inhibited in both the adsorption and virucidal antiviral mechanisms, making it a potent antiviral filter/mask. Therefore, ZnO-loaded PVDF nanofiber is a potentially prototyped filter embedded in a commercial face mask for use as an antiviral mask with a pronounced potential to reduce the spreading of infectious respiratory diseases, for example, COVID-19 and its analogues.

Presence of HPV, EBV and HMTV Viruses Among Egyptian Breast Cancer Women: Molecular Detection and Clinical Relevance.

BACKGROUND: Oncogenic viruses, their possible association with breast cancer (BC) and effect on its clinical course are interesting issue. The present study evaluates the presence of human papillomavirus (HPV), EpsteinBarr virus (EBV), and human mammary tumor virus (HMTV) in BC and their relation with clinico-pathological characteristics. PATIENTS AND METHODS: This study was conducted on 80 Egyptian women with BC and 30 control women without known oncological disease. Forty formalin-fixed paraffin-embedded (FFPE) tissues, forty fresh tissue samples, and white blood cells (WBCs) of BC patients and WBCs of controls were subjected to a qualitative polymerase chain reaction (PCR). Quantitative real-time PCR was used to measure viral loads in fresh tissues of BC. The result was correlated with clinico-pathological characteristics of BC. RESULTS: HPV was detected in 33 (41.25%), EBV in 30 (37.5%) and HMTV in 33 (41.25%) BC patients. None of the control women was positive for HPV or EBV while HMTV was detected in 7 (23.3%). Among 40 BC WBCs specimens, HPV/HMTV were found together in 25%, followed by EBV/HMTV in 2.5% and EBV/HPV in 2.5%. However, the three viruses (HPV/EBV/HMTV) were found together in only 5%. In the 40 fresh BC tissues, the three viruses were found together in 12 (30%), EBV/HMTV in 7 (17.5%), HPV/HMTV in 4 (10%), and HPV/EBV in 4 (10%). EBV, HMTV, or multiple viral infections were associated with younger age of BC women. HPV, EBV, and HMTV median loads in fresh tissues were 4.8×103 copies/µL, 6.3×103 copies/µL, and 97 copies/µL, respectively. CONCLUSION: WBCs could be a more suitable specimen instead of fresh tissue for HMTV detection in BC patients to avoid invasive procedures. The presence of HPV, EBV, and HMTV together in Egyptian women with BC was significantly associated with younger age.