BAT25, ACVR2, and TGFBR2 Mononucleotide STR Markers: A Triplex Panel for Microsatellite Instability Testing in Colorectal Tumors.

Background: Microsatellite instability (MSI) in colorectal cancer (CRC) patients is considered as a diagnostic and prognostic marker. MSI is a consequence of mismatch repair deficiency which is evaluated using the different microsatellite markers on the whole genome. In this pilot study, the diagnostic value of a novel triplex panel including three mononucleotide markers has been evaluated in comparison to the standard Promega kit for MSI testing in CRC patients with Amsterdam II criteria. Materials and Methods: DNA extracted from tumors and normal Formalin-Fixed Paraffin-Embedded (FFPE) tissues of index cases from 37 HNPCC (Hereditary non-polyposis colorectal cancer) families were evaluated for MSI state. Primer design for three markers, including BAT25, ACVR2, and TGFBR2, was performed using 19 nucleotides of the M-13 phage. The instability of each marker was assessed through fragment analysis in comparison with Promega kit markers for all patients. The sensitivity and specificity of each marker have been calculated. Results: The comparative evaluation of MSI in both tumors and normal adjacent FFPE tissues demonstrated a separate sensitivity as 100%, 83.3%, and 76.9% for BAT25, ACVR2, and TGFBR2, respectively, and 100% sensitivity in the form of a triplex. Moreover, the specificity for each of these three markers in MSI testing was estimated as 100%, separately and in the form of the triplex in comparison with the Promega pentaplex standard Kit. Conclusions: A high sensitivity and specificity for the novel triplex panel in MSI-testing were estimated among Iranian patients. More studies are recommended to confirm this panel as a diagnostic kit for MSI testing.

Vitamin D can be effective on the prevention of COVID-19 complications: A narrative review on molecular aspects.

The widespread COVID-19 pandemic has been, currently, converted to a catastrophic human health challenge. Vitamin D (VD) and its metabolites have been used as a palliative treatment for chronic inflammatory and infectious diseases from ancient times. In the current study, some molecular aspects of the potential effects of VD against COVID-19 side-effects have been discussed. An arguable role in autophagy or apoptosis control has been suggested for VD through calcium signaling at the mitochondrial and ER levels. 1,25(OH)2D3 is also an immunomodulator that affects the development of B-cells, T-cells, and NK cells in both innate and acquired immunity. The production of some anti-microbial molecules such as defensins and cathelicidins is also stimulated by VD. The overexpression of glutathione, glutathione peroxidase, and superoxide dismutase, and down-regulation of NADPH oxidase are induced by VD to reduce the oxidative stress. Moreover, the multi-organ failure due to a cytokine storm induced by SARS-CoV2 in COVID-19 may be prevented by the immunomodulatory effects of VD. It can also downregulate the renin-angiotensin system which has a protective role against cardiovascular complications induced by COVID-19. Given the many experimental and molecular evidences due to the potential protective effects of VD on the prevention of the COVID-19-induced morbidities, a VD supplementation is suggested to prevent the lethal side-effects of the infection. It is particularly recommended in VD-deficient patients or those at greater risk of serious or critical effects of COVID-19, including the elderly, and patients with pre-existing chronic diseases, especially those in nursing homes, care facilities, and hospitals.

A Simplified Protocol for Microsatellite Instability Evaluation in Iranian Patients at Risk for Lynch Syndrome.

OBJECTIVE: The most important tumor characteristic of Lynch syndrome (LS) is microsatellite instability (MSI). In the current study, BAT34c4 and BAT26 mononucleotide markers were evaluated as part of efforts to test a cost-effective panel for MSI testing in Iranian patients, comparing it with the Promega kit. METHODS: Amsterdam II clinical criteria were used to identify patients at risk for LS. The MSI status of these patients was determined using BAT34c4 and BAT26 markers, as well as the Promega kit. The results of both methods were compared, and the sensitivity and specificity of new short tandem repeat (STR) markers were estimated using statistical formulas. RESULTS: Of the 37 patients we studied who were at risk for LS, 27% showed MSI-high results, via the Promega kit. The same results were achieved for BAT34c4 and BAT26 separately. CONCLUSIONS: The novel 2-marker kit for MSI testing has similar accuracy as the Promega kit at a lower cost, due to fewer markers and a more economical labeling method.

Whole-Exome Sequencing Identifies a Recurrent Small In-Frame Deletion in MYO15A Causing Autosomal Recessive Nonsyndromic Hearing Loss in 3 Iranian Pedigrees.

BACKGROUND: Hearing loss (HL) is the most prevalent and genetically heterogeneous sensory disabilities in humans throughout the world. METHODS: In this study, we used whole-exome sequencing (WES) to determine the variant causing autosomal recessive nonsyndromic hearing loss (ARNSHL) segregating in 3 separate Iranian consanguineous families (with 3 different ethnicities: Azeri, Persian, and Lur), followed by cosegregation analysis, computational analysis, and structural modeling using the I-TASSER (Iterative Threading ASSEmbly Refinement) server. Also, we used speech-perception tests to measure cochlear implant (CI) performance in patients. RESULTS: One small in-frame deletion variant (MYO15A c.8309_8311del (p.Glu2770del)), resulting in deletion of a single amino-acid residue was identified. We found it to be cosegregating with the disease in the studied families. We provide some evidence suggesting the pathogenesis of this variant in HL based on the American College of Medical Genetics (ACMG) and Genomics guidelines. Evaluation of auditory and speech performance indicated favorable outcome after cochlear implantation in our patients. CONCLUSIONS: The findings of this study demonstrate the utility of WES in genetic diagnostics of HL.

WRN Germline Mutation Is the Likely Inherited Etiology of Various Cancer Types in One Iranian Family.

BACKGROUND: Familial cancers comprise a considerable distribution of colorectal cancers (CRCs), of which only about 5% occurs through well-established hereditary syndromes. It has been demonstrated that deleterious variants at the newly identified cancer-predisposing genes could describe the etiology of undefined familial cancers. METHODS: The present study aimed to identify the genetic etiology in a 32-year-old man with early onset familial CRC employing several molecular diagnostic techniques. DNA was extracted from tumoral and normal formalin-fixed-paraffin-embedded (FFPE) blocks, and microsatellite instability (MSI) was evaluated. Immunohistochemistry staining of MMR proteins was performed on tumoral FFPE blocks. Next-generation sequencing (NGS), multiplex ligation-dependent amplification (MLPA) assay, and Sanger sequencing were applied on the genomic DNA extracted from peripheral blood. Data analysis was performed using bioinformatics tools. Genetic variants interpretation was based on ACMG. RESULTS: MSI analysis indicated MSI-H phenotype, and IHC staining proved no expressions of MSH2 and MSH6 proteins. MLPA and NGS data showed no pathogenic variants in MMR genes. Further analysis of NGS data revealed a candidate WRN frameshift variant (p.R389Efs*3), which was validated with Sanger sequencing. The variant was interpreted as pathogenic since it met the criteria based on the ACMG guideline including very strong (PVS1), strong (PS3), and moderate (PM2). CONCLUSION: WRN is a DNA helicase participating in DNA repair pathways to sustain genomic stability. WRN deficient function may contribute to CRC development that is valuable for further investigation as a candidate gene in hereditary cancer syndrome diagnosis.

Nervous System Involvement in COVID-19: a Review of the Current Knowledge.

The current pandemic of the new human coronavirus (CoV), i.e., severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has created an urgent global condition. The disease, termed coronavirus disease 2019 (COVID-19), is primarily known as a respiratory tract infection. Although SARS-CoV-2 directly invades the lungs, COVID-19 is a complex multi-system disease with varying degrees of severity and affects several human systems including the cardiovascular, respiratory, gastrointestinal, neurological, hematopoietic, and immune systems. From the existing data, most COVID-19 cases develop a mild disease typically presented with fever and respiratory illness. However, in some patients, clinical evidence suggests that COVID-19 might progress to acute respiratory distress syndrome (ARDS), multi-organ dysfunction, and septic shock resulting in a critical condition. Likewise, specific organ dysfunction seems to be related to the disease complication, worsens the condition, and increases the lethality of COVID-19. The neurological manifestations in association with disease severity and mortality have been reported in COVID-19 patients. Despite the continuously increasing reports of the neurological symptoms of SARS-CoV-2, our knowledge about the possible routes of nervous system involvement associated with COVID-19 is limited. Herein, we will primarily describe the critical aspects and clinical features of SARS-CoV-2 related to nervous system impairment and then discuss possible routes of SARS-CoV-2 nervous system involvement based on the current evidence.