The challenges in the interpretation of genetic variants detected by genomics techniques in patients with congenital anomalies.

BACKGROUND: Despite the efforts that have been made to standardize the interpretation of variants, in some cases, their pathogenicity remains vague and confusing, and sometimes their interpretation does not help clinicians to establish clinical correlation using genetic test results. This study aims to shed more lights on these challenging variants. METHODS: In a clinical setting, the variants found from 81 array CGH and 79 whole exome sequencing (WES) in patients with congenital anomalies were interpreted based on American College of Medical Genetics and Genomics guidelines. RESULTS: In this study, the interpretation of the disease-causing variants and the variants with uncertain clinical significance detected by WES was far more challenging than the variants detected by array CGH. The presence of unreported clinical symptoms, incomplete penetrance, variable expressivity, parents' reluctance to analyze segregation in the family, and the limitations of prenatal tests, were among the challenging factors in the interpretation of variants in this study. CONCLUSION: A careful study of the pedigree and disease mode of inheritance, as well as a careful clinical examination of the carrier parents in diseases with autosomal dominant inheritance, are among the primary strategies for determining the clinical significance of the variants. Continued efforts to mitigate these challenges are needed to improve the interpretation of variants.

Overexpression of miR-490-5p/miR-490-3p Potentially Induces IL-17-Producing T Cells in Patients With Breast Cancer.

Objective: Breast cancer (BC) is the most prevalent female cancer globally and this is also true in Iranian women. Alteration in circulating microRNAs affects the fate of immune cells, affecting immunological response to neoplasia. Materials and Methods: We investigated the expression of miR-490-5p and miR-490-3p in peripheral blood mononuclear cells (PBMCs) and plasma of patients with BC. Moreover, the correlation of these microRNAs with the expression levels of CD3d, interleukin 2 (IL-2), IL-2 receptor chain alpha (IL-2RA), forkhead box O1 (FOXO1) and nuclear factor of activated T cells 5 (NFAT5) were investigated. Results: Two groups, including 42 patients with BC, aged 22-75 years with stage I, II, III disease without administration of immunosuppressive chemotherapy regimens/radiotherapy and 40 healthy controls aged 27-70 years, participated. Overexpression and higher circulation levels of miR-490-5p and miR-490-3p were found in the patients with consequent down-regulation of all targets investigated in PBMCs. Furthermore, there was a significant negative correlation between the overexpression of these microRNAs and a reduction in levels of CD3d, IL-2, and IL-2RA in patients with BC. Conclusion: These results suggest that down-regulation of the target genes by miR-490 may predispose and facilitate the production of Th17 lymphocytes and IL-17-producing Tregs. The variation in miR-490-5p/-3p and the investigated targets in the PBMCs of BC patients may be used as non-invasive diagnostic markers.

Concomitant overexpression of mir-182-5p and mir-182-3p raises the possibility of IL-17-producing Treg formation in breast cancer by targeting CD3d, ITK, FOXO1, and NFATs: A meta-analysis and experimental study.

T cells are polarized toward regulatory T cells (Tregs) in tumor microenvironment by the shuttling of microRNAs that target T cell-activating signaling pathways. We evaluated the expression of the miR-182 cluster (miR-96, 182, and 183) in peripheral blood mononuclear cells (PBMCs) of patients with breast cancer (BC), and T cell polarization by the expression of FOXO1, NFATs, ITK, TCR/CD3 complex, and IL-2/IL-2RA. Twenty-six microRNAs overexpressed in tumor tissues and sera of these patients were extracted by a meta-analysis. Then, the expression of the miR-182 cluster was investigated in PBMCs and sera of these patients and correlated with their targets in PBMCs. Finally, miR-182 was cloned into Jurkat cells to evaluate its effects on T cell polarization. FOXO1, CD3d, ITK, NFATc3, NFATc4, and IL-2RA were targeted by miR-182, due to which their expression decreased in PBMCs of patients. Although IL-6, IL-17, and TGF-ß increased after miR-182 transduction, IL-2 dramatically decreased. We revealed CD4+ FOXP3+ T cell differentiation in the miR-182-transduced group. Although miR-182 has inhibitory effects on T cells by the inhibition of FOXO1, TCR/CD3 complex, NFATs, and IL-2/IL-2RA signaling pathways, it increases FOXP3, TGF-ß, and IL-17 expression to possibly drive T cell deviation toward the transitional state of IL-17-producing Tregs and Treg formation in the end.

Evaluation of serotonin receptors (5HTR2A and 5HTR3A) mRNA expression changes in tumor of breast cancer patients.

Background: Several studies have proven the pattern of neurotransmitters, especially serotonin, in carcinogenesis and tumor development. Several studies have also shown that changes in serotonin receptors, especially 5HTR2A and 5HTR3A, can play an important role in incidence of cancers. This study was conducted to investigate changes in mRNA expression of 5HTR2A and 5HTR3A receptors in the breast tumor tissue compared to their marginal zone. Methods: In this study, tissue samples were obtained from 40 female patients with breast cancer. Entire RNA was obtained from the tissues and cDNA synthesis was performed. Finally, real ime PCR technique was performed to investigate the gene expression variation of both 5HTR2A and 5HTR3A. To analyze the results of real time PCR, both ΔΔCt and 2-ΔΔCt equations were used. All statistical analyses were performed using the SPSS 18 software and R-Studio 1.0.136. P values less than 0.05 (p<0.05) and 0.001 (p<0.001) were considered statistically significant. Results: The results showed increased expression of 5HTR2A and 5HTR3A genes in tumoral tissues of patients with breast cancer compared to their marginal tissues, where the 5HTR2A and 5HTR3A genes expression in tumor tissue was 3.12 and 3.24 times more than that of the marginal zone, respectively. Conclusion: The results indicated an increase in the mRNA expression of serotonin receptors (5HTR2A and 5HTR3A) in the tumor tissue compared to the marginal zone, which due to the mitogenic nature of these receptors, is likely to induce more proliferation of cancer cells.

Variable Clinical Manifestations of COVID-19: Viral and Human Genomes Talk.

The new coronavirus, known as "SARS-CoV-2"; is the cause of one of the most prevalent infectious viral diseases that was recently announced pandemic by the world health organization. Ongoing research in the fields of prevention, management, and therapy establishes a functional scaffold for clinics during the time of crisis. To obtain this goal, it is necessary that all pathophysiologic aspects of COVID-19 from infection to predisposing backgrounds of infection be identified, so that all the ambiguities of researchers regarding transmission mechanisms, variable clinical manifestation, and therapeutic response can be solved. Here, we firstly discuss about the homology screening between nCoV-2019 and beta-coronavirus family using phylogenetic analyses. Secondly, we analyzed the viral motifs to show that viral entry into the host cells requires a primary activation step performed by FURIN and FURIN-like-mediated enzymatic cleavage on the structural glycoprotein. The cleavage increases viral performance by 1000 folds. We then present a comprehensive view on host cells and the significance of gene variants affecting activation enzymes, supportive entry, and spread mechanisms in humans including renin-angiotensin-aldosterone system (RAAS) a pathway results in certain phenotypes or exacerbate infection-related phenotypes in different organs, hence causes variable clinical manifestations. This is followed by discussing about the importance of personalized medicine in nCoV-2019 exposure. Moreover, chemical drugs prescribed for individuals affected with COVID-19, as well as genes involved in drug transport and metabolisms are reviewed as a prelude to drug response. Finally, we suggest some therapeutic approaches developed based on new methods and technology such as anti-sense therapy and antibodies.

Preventive effects of oxytocin and oxytocin receptor in breast cancer pathogenesis.

AIM: Modifications of oxytocin (OT) concentration and OT receptor (OXTR) expression level have different effects on breast cancer-derived cells. This study was conducted to evaluate OT variation in breast cancer patients and to evaluate OXTR expression changes in breast cancer tissues. METHODS: The plasma concentrations of OT in both breast cancer patients and healthy individuals' samples were assessed. OXTR variations were then assessed in both cancerous and noncancerous breast tissues. RESULTS: OT had an increase in breast cancer patients and expression of OXTR in contralateral breast was more than cancerous tissues. CONCLUSION: Despite the high levels of OT concentration in breast cancer patients, it seems that a lower expression of OXTR in cancerous tissues can be effective in the breast cancer progression.

The diversity in the expression profile of caveolin II transcripts, considering its new transcript in breast cancer.

Most studies have revealed the effects of caveolins in cancer inhibition. However, due to a lack of reports about their new transcripts, their presence and their effects on different cancers are unclear. This study was conducted to evaluate the cavolin-2 (cav-2) transcripts expression changes in tumoral and corresponding tissues and in contralateral breast, to investigate their variation associated with the variation of caveolin-1 (cav-1) expression in breast cancer. There were 40 breast-derived tumoral, corresponding, and contralateral tissues obtained from the patients with breast cancer. The RNA and proteins were extracted from these samples. So, cav-1 and cav-2 transcripts' variation were assessed in whole tumoral, corresponding, and contralateral breast. Also, their expression modifications were evaluated via the Western blotting technique. The results derived from this study verified the presence of transcript III of cav-2 for the first time, which was reported only in the gene bank, but we could not detect and validate any protein associated with these transcripts. Also, the decreasing trend of cav-1 and the cav-2 (transcripts I and II) were observed in tumoral tissues compared to unaffected tissues especially in stages I and II. It seems that the descending expression levels of cav-1 and cav-2 (transcript I, II) besides the lasting expression of cav-2 (transcript III) are associated with the incidence and promotion of breast cancer, especially in the initial stages of breast cancer. So, this may show a potential in determining the patients who can undergo the prophylactic mastectomy. Moreover, the results of the study demonstrated that transcript III may be a candidate as a non-coding RNA.

Association of the gene expression variation of tumor necrosis factor-α and expressions changes of dopamine receptor genes in progression of diabetic severe foot ulcers.

OBJECTIVES: Regulation of pro-inflammatory factors such as TNF-α which are secreted by the immune cells through induction of their several receptors including dopamine receptors (especially DRD2 and DRD3) is one of the noticeable problems in diabetic severe foot ulcer healing. This study was conducted to evaluate the alteration of TNF-αin plasma as well as DRD2 and DRD3 changes in PBMCs of diabetics with severe foot ulcers. MATERIALS AND METHODS: Peripheral blood samples were collected from 31 subjects with ulcers, 29 without ulcers, and 25 healthy individuals. Total mRNA was extracted from PBMCs for the study of DRD2, DRD3, and TNF-α gene expression variations. Expression patterns of these genes were evaluated by real-time PCR. Consequently, concentration of TNF-α was investigated in plasma. RESULTS: Significant decrease in gene expression and plasma concentration of TNF-α in PBMCs was observed in both patient groups at P<0.05. These diminutions are correlated to the decrease in the expression of both DRD2 and DRD3 in PBMCs of both patient groups. Also, the same relationship is present between expressions of two new DRD3 transcripts with TNF-α downturn. CONCLUSION: We concluded that DRD2 and DRD3 expression alteration and presence of new DRD3 transcripts can be effective in reduction of TNF-α expression as a pro-inflammatory factor. Performing complementary studies, may explain that variations in DRD2 and DRD3 are prognostic and effective markers attributed to the development of diabetes severe foot ulcers.

T-helper Cell Type-1 Transcription Factor T-Bet Is Down-regulated in Type 1 Diabetes.

T cells have been identified as key players in the pathogenesis of type 1 diabetes. However, the exact role of T-cell subpopulations in this pathway is presently unknown. The purpose of this study was to assess the expression pattern of two lineage-specifying transcription factors GATA-3 and T-bet, which are important in T helper type 1 (Th1) and Th2 cell development, respectively. Gene expression analysis of peripheral blood mononuclear cells (PBMCs) was performed using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Plasma levels of IFN-γ and IL-4 were also determined by ELISA. T-bet and IFN-γ gene expression was significantly lower in patients group compared with healthy controls (p<0.05). The expression of GATA-3 was relatively similar in patients and controls; however, IL-4 mRNAs were significantly increased in the PBMCs from patients as compared with normal controls (p<0.05). In addition, a marked increase in plasma IL-4 levels were observed in patient group compared with controls (p<0.001). To the contrary, IFN-γ protein levels were decreased in patients in comparison with controls (p<0.001). These data suggest additional implications of the role of Th1/Th2 imbalance for the immunopathogenesis of type 1 diabetes.

Th1/Th2 cytokines in Type 1 diabetes: Relation to duration of disease and gender.

BACKGROUND: T-cells are important in the pathogenesis of Type 1 diabetes (T1D). However, the exact role of T-cell subpopulations in this pathway remains unknown. The purpose of this study was to assess the expression pattern of T helper 1 (Th1) interferon-gamma (IFN-γ) and Th2 interleukin-4 (IL-4) cytokines and their relationship with sex and disease duration in T1D patients. MATERIALS AND METHODS: This study was conducted on 21 T1D patients and 22 healthy subjects. Gene expression analysis of peripheral blood mononuclear cells (PBMCs) was performed using real-time reverse transcriptase polymerase chain reaction. RESULTS: IFN-γ gene expression was significantly lower in T1D patients compared with controls (P < 0.05). Conversely, IL-4 mRNAs were significantly increased in the PBMCs from patients as compared to controls (P < 0.05). There was no significant difference in the expression of IL-4 and IFN-γ between men and women with T1D (P > 0.05) while IL-4 mRNA expression in male patients was about 1.9 folds higher than female patients. Moreover, IFN-γ mRNA expression in female patients was about 1.8 folds lower than male patients. Patients were divided into two groups regarding their disease duration: <10 years and >10 years. A significant increase in the IL-4 expression was observed between two groups of patients compared to controls (P < 0.0001). Conversely, there was a significant difference in the expression of IFN-γ only between patients with more than 10 years of disease duration (P = 0.02). CONCLUSION: These data propose supplementary implications for the role of Th1/Th2 imbalance in T1D immunopathogenesis. Moreover, factors such as sex and disease duration may have some influence on cytokine mRNA expression.