مهدی مغنی باشی

Colorectal cancer (CRC) ranks fourth and second among all types of cancer in terms of incidence and mortality rates, respectively. Although colorectal cancer screening has been effective in improving the prevention and treatment of this disease, many obstacles, including colorectal cancer metastasis, have severely hampered the prognosis of this disease. Long non-coding RNAs are a type of RNAi molecule that is classified into several functional groups and participates in some important cellular pathways. LncRNA-RNA interactions control mRNA translation and degradation or act as microRNA (miRNA) silencing sponges. LncRNA-protein interaction regulates protein activity in transcriptional activation and silencing. LncRNA guide, decoy, and scaffold transcriptional regulators regulate the enhancer or repressor region of coding genes to alter expression. Non-coding RNAs have attracted increasing attention from researchers due to their key role in regulating gene expression and potential effects on cell signaling pathways. These RNAs, as biomarkers, play an important role in the diagnosis, progression, and prognosis of colorectal cancer. This study investigated the change in the expression level of non-coding RNA LINC01139 in colorectal cancer compared to healthy tissue.

In this study, the expression change of the LncRNA LINC01139 gene from two databases, UALCAN and Gepia2, was investigated in colon adenocarcinoma tumor tissues compared to healthy tissue. Then, total RNA was extracted from 41 colorectal cancer tumor tissue samples and 41 healthy tissue samples adjacent to the tumor, and after qualitative and quantitative analysis of the extracted RNA, cDNA synthesis was performed using the kit. Then, by designing and synthesizing a specific primer, the expression level of LINC01139 non-coding RNA was measured in two tumor and healthy tissues using the Real-time RT-PCR technique. In the end, considering the Gapdh gene as a housekeeping gene, the resulting data were analyzed by Graph pad prism software.

Data analysis of this study based on bioinformatics analysis showed that the expression of non-coding RNA LINC01139 is decreased in colorectal tumors. This is even though the expression of this gene increases significantly in tumor tissues (both metastatic and non-metastatic) compared to the adjacent normal tissue, regardless of gender(P<0.0001). However, It was also shown that increased expression of LINC01139 non-coding RNA in tumor tissues can serve as a biomarker in identifying tumor tissues from healthy colorectal tissues(AUC=0.81, P<0.0001). as no significant expression difference between non-metastatic and metastatic samples (P>0.05).

Considering the known role of LINC01139 lncRNA in the HIF1α signaling pathway as a scaffold, the oncogenic function of LINC01139 lncRNA in liver cancer through the miR-30/MYBL2 axis and the strong Linc01139-PIP3 LncRNA interaction and the effect on the PIP3-AKT pathway. It seems that increased expression of cytoplasmic lncRNA LINC01139 and its function as an oncogene may be involved in colorectal carcinogenesis through signaling pathways.

Multiple sclerosis (MS) is a chronic autoimmune disease in which the myelin sheaths of nerve cells in the brain and spinal cord are damaged. The prevalence of disease is higher in women and it seems that sex hormones, which usually exert their effects through receptors, are involved in susceptibility to MS. Considering the functional role of Alu insertion 306 bp polymorphism of progesterone receptor in expression level of progesterone receptor, in this study, the association of Alu insertion polymorphism in intron 7 of progesterone receptor with the risk of MS was investigated.

In a case-control study, genomic DNA was extracted from the blood samples of 200 patients (180 women and 20 men) with relapsing remitting MS (RRMS) and 226 healthy individuals (186 women and 40 men) as a control group. In order to determine the polymorphic genotype of Alu insertion, PCR technique was used and the PCR product was electrophoresed on 2% agarose gel. Data were analyzed in SPSS V21 using logistic regression test.

Findings showed that WI (P= 0.003) and II (P= 0.001) genotypes increase the risk of MS compared to WW genotype, and allele I acts as a risk allele (P<0.001).

According to this study, it seems that allele I of Alu insertion polymorphism may play a dominant role in susceptibility to MS by decreasing PGR gene expression.

In clinical practice, distinguishing invasive lung tumors from primary tumors remains a challenge. With recent advances in understanding biological alterations of tumorigenesis and molecular analytic technologies, using these molecular alterations can be sensitive and tumor-specific as biomarker for the stratification of patients. In this study, the molecular network of miRNA-mRNA contributing to primary lung cancer has been assessed by bioinformatics approaches.

In this analytical-observational study gene expression profiles of patients with primary lung cancer were collected from the RNASeq data of the Cancer Genome Atlas (TCGA) database by TCGAbiolinks package. With edgeR and limma packages in R, non-specific expression genes were filtered and the significant differentially expressed mRNAs and miRNAs between tumor tissues and normal tissues were saved and their targets were predicted by 2 databases; miRWalk, and Targetscan. Subsequently, the interaction regulatory network of miRNA-mRNA was visualized using Cytoscape software.

By miRNA-mRNA network analysis revealed that, 7 miRNAs included; hsa-miR-373-3p, hsa-let-7a-5p, hsa-miR-23b-3p, hsa-miR-152-3p, hsa-miR -216a-3p, hsa-miR-106-5p, hsa-let-7i-5p and 6 miRNAs including; has-miR-107, has-miR-17-5p, has-185-5p, has-miR-34a- 5p, has-miR-130a-5p and has-96-5p, mediated regulation of up-regulated and down-regulated mRNAs in primary lung cancer patients, respectively.

This bioinformatics study proposes a miRNA–mRNA network associated with primary lung cancer, which may help to screening and new therapeutic targets for primary lung cancer as prognostic marker.

Over the past 15 years, significant insights have been gained into the roles of miRNAs in cancer. In various cancers, miRNAs can act as oncogenes, tumor suppressors, or control the metastasis process by modulating the expression of numerous target genes. The aim of the present study was to identify molecular network of miRNA-mRNA regulating lung cancer invasion, by bioinformatics approaches.

In this experimental study that was done in 2022, gene expression profiles of patients with lung cancer were collected from the RNASeq data of Cancer Genome Atlas (TCGA), by TCGAbiolinks package. Differentially expressed miRNAs and mRNAs were identified using “limma” and “edgeR” R packages and their targets were predicted by 2 databases; miRWalk, and Targetscan. Subsequently, the interaction regulatory network of miRNA-mRNA visualized using Cytoscape software. Data analysis was performed using Testing Multiple Hypotheses and False Discovery Rate.

The results of bioinformatics analysis of the lung cancer invasion specific miRNA-mRNA regulatory network, showed that six hub miRNAs including; hsa-let-7c-5p, hsa-let-7b-5p, hsa-let-7e-5p, hsa-miR-6838-5p, hsa-miR-320b and hsa-miR-4458, are regulator of the lung cancer invasion up-regulated genes and four hub miRNAs are regulator of this situation down-regulated gene including; hsa-miR-92a-3p, hsa-miR-204-5p ,hsa-miR-24-3p and hsa-miR-506-3P.

The results in our study suggest that a specific miRNA-mRNA network is associated with the lung cancer invasion which this new insight into the molecular mechanism of lung cancer invasion result in the identification of molecular biomarkers and therapeutic targets for this malignancy.

One of the genes that has been proven to play a role in colorectal cancer is IL1RL1 (Interleukin 1 receptor like 1). This gene encodes a receptor for interleukin 33 that has been shown with its ligand, to be involved in colorectal cancer. Several single nucleotide polymorphisms are involved in regulating the expression of IL1RL1 gene, so that this study investigated the association between genotypes of rs6543115 polymorphism in the promoter of IL1RL1 gene and colon cancer.

In this descriptive study, genomic DNA was extracted from blood samples of 100 patients with colon cancer and 100 healthy individuals. The region containing the desired polymorphic site was amplified using appropriate primers and PCR technique, and then was sequenced, and all samples were genotyped. Finally, logistic regression analysis and chi-square test were used to assess the association between rs6543115 genotypes in IL1RL1 gene and colon cancer.

The results showed that genotype GC (OR= 0.273, 95%CI: 0.090-0.827, p= 0.022) and CC (OR= 0.086, 95%CI: 0.032-0.232, p<0.001) as a risk factor in comparison to genotype GG, significantly decreased the susceptibility of colon cancer. Also, the results showed that the allele C, in comparison to allele G, significantly reduced the risk of colon cancer (OR= 0.119, 95%CI: 0.066-0.232, p< 0.001).

The rs6543115 polymorphism in the IL1RL1 gene appears to be associated with the risk of colon cancer.

Several studies have reported the lack or down regulation of sirtuin-3 gene expression in various tumors, including breast cancer. A variable number tandem repeat polymorphism has recently been observed in the intron 5 of sirtuin-3 gene, which influences its transcriptional activity. We investigated the association of this polymorphism with the risk of breast cancer.
After extracting DNA from venous blood of 207 patients with breast cancer and 195 healthy individuals, the samples were genotyped using PCR method by primer pairs flanking the 72 bp repeat region in intron 5 of sirtuin-3 gene. The association of genotypes with risk of breast cancer was analyzed in SPSS 21 using logistic regression test.
The allele and genotype frequencies were separately calculated in the patients and controls. Among the patients and controls, the most frequent allele pertained to one repeat alleles. Statistical analysis indicated that 5- and 6- repeat alleles decrease the risk of breast cancer (P Results of the present study indicate that 72-bp variable number tandem repeat polymorphism in the intron 5 of sirtuin-3 gene may be a significant risk factor for susceptibility to breast cancer.

MU5AC gene plays a key role in the maintenance of gastric mucosa against harmful factors in the stomach through encoding a main mucin of mucus lining gastric mucosa and its expression is reduced in the gastric cancer. In this study, due to the effect of genetic polymorphisms in the promoter region on the gene expression, the association between single nucleotide polymorphism of MU5AC gene promoter and the risk of gastric cancer was assessed.
in this case-control study, a fragment of MUC5AC gene promoter was amplified by PCR technique in 50 individuals and rs17859812 single nucleotide polymorphism was selected by sequencing, and other subjects were genotyped using PCR-RFLP method. Finally, logistic regression and chi-square tests were used for data analysis.
Following sequencing and PCR-RFLP, the findings showed that allele C in the -221 of the promoter increased the risk of gastric cancer (OR= 1.66, CI= 3.09-5.18, p = 0.008) and CC genotype increased the risk of gastric cancer (OR= 4.66, CI= 2.09-10.38, p The results of this study showed that allele C in the rs17859812 polymorphism of the MUC5AC gene is associated with the risk of gastric cancer. As this polymorphism is located in the vicinity of the glucocorticoid receptor binding site, it may affect the MUC5AC gene expression and may result in gastric cancer susceptibility.

Background and Gastric cancer is the most common cancer associated with high mortality worldwide. One of the genes that is down-regulated in gastric cancer, is the SIRT3 that encodes the histone deacetylase enzyme. There is a variable number tandem repeat (VNTR) polymorphism in the intron 5 of SIRT3 gene and evidence shows that expression of SIRT3 gene increases by increase in the number of repeats. According to the deregulation of SIRT3 gene expression in gastric cancer and the effect of intron 5 VNTR polymorphism in the transcription, we investigated the association between intron 5 VNTR polymorphism of SIRT3 gene and the risk of developing gastric cancer.
A case-control study was performed in 116 patients with gastric cancer (attending Isfahan Omid Hospital, Iran) and healthy controls (n= 116). After DNA extraction, all samples were genotyped using PCR and electrophoresis techniques and the results were analyzed applying logistic regression and Chi-square tests.
In addition to the alleles that have been reported so far, alleles with 8 and 9 repeats were observed too, in this study. The results showed that genotype 4-1 increases significantly the risk of gastric cancer (P=0.028, OR= 13.00).
Some variants of intron 5 VNTR polymorphism SIRT3 gene is associated with risk of developing gastric cancer.

The incidence of gastric cancer is different in two sexes with ratio 2 to 1 that it is more common in men. The most important biologically reason is sexual hormones between two sexes that lead to sexual dimorphism and in turn can cause a sex bias in incidence of disease between two sexes. Recently, studies have shown that microRNA is involved in sexual dimorphism in gene expression. Given the sexual dimorphism in the incidence of gastric cancer and sex hormones response elements in the regulatory regions of miR-146a and miR-148a genes, in this study, the expression of these two genes in the stomach of healthy men and women at different age groups were compared.
Using endoscopy, gastric antrum tissues of 35 healthy women and 35 healthy men were collected. After RNA extraction and synthesis of cDNA, the expression of miR-146a and miR-148a genes were compared between sexes by Real time RT-PCR and data were analyzed using independent sample t and ANOVA tests.
There was no difference between men and women in genes expression of miR-146a and miR-148a. However, expression of miR-146a gene was significantly more in men under 45 years than men over 45 years (p= 0.017, df= 14, t= 1.47). Also, expression of miR-148a gene was significantly more in men over 45 years than men under 45 years (p=0.001, df= 12, t= 1.28). But the expression of both genes had no significant difference between women under 45 years and women over 45 years.
Expression of miR-146a and miR-148a genes in the stomach is increased and decreased with aging in men, respectively.

Breast cancer is the most common cancer among women and the second most common cause of death from cancer. In Iran, of 10 to 15 women, one woman has the risk of breast cancers. The RHOB gene is one of the genes that is associated with cancer and the coding of the protein with GTPase functional and studies have shown that expression of this gene increases in breast cancer. The human-RHOB-gene promoter harbors a VNTR polymorphism which is located 820 bp upstream of the transcriptional start site which carries 34 bp tandem repeat.
In this study, blood samples were taken from 138 controls and 136 patients with breast cancer. After DNA extraction, PCR and electrophoresis were done and the collected data were analyzed with χ2 and regression logestic tests.
In this study, 10 different alleles in promoter VNTR of RHOB gene were found that most of them were alleles with 9 and 10 repeat. The number of sick people who have repeat allele 9 were significantly higher than the healthy controls.
The results showed that alleles with 9 repeat increases risk of developing breast cancer. [OR₌0.515(95%CI=0.317-0.836), P=0.007 ]

In recent years, it is found that a large number of genes are differentially expressed in two sexes; this can be referred to sexual dimorphism in gene expression. One of the main reasons for the differences in gene expression between male and female is assigned to sex hormones. Regarding to the presence of estrogen and androgen response elements in the regulatory region of Foxa1 and Foxa2 genes and sexual dimorphism in the incidence of gastric cancer, in this study, we compared the expression of these genes in the stomach of healthy men and women.

Sampling was done from 20 healthy men and 21 healthy women using endoscopy from the gastric antrum. Following RNA extraction and complementary DNA (cDNA) synthesis, expression of Foxa1 and Foxa2 genes was compared between the men and women using semi-quantitative technique of reverse transcription polymerase chain reaction (RT-PCR). Then, the data were analyzed using statistical t and ANOVA tests.

The expression of Foxa1 was significantly higher in women than men (P = 0.041, df = 36, t = 2.12). In addition, the expression of this gene was significantly higher in people under the age of 45 years than people above it (P = 0.010, df = 36, t = 2.71). But about Foxa2 gene, no significantly results were seen.

Foxa1 gene expression in women’s stomach is higher than men’s; besides, the expression of this gene in the stomach is decreased by age.

Hearing loss is the most common sensory neural defect in humans, affecting 1 in 1000 neonates, with over half of these cases predicted to be hereditary in nature. Most hereditary hearing loss is inherited in a recessive fashion, accounting for approximately 80 % of non-syndromic hearing loss (NSHL). Mutations in GJB2 gene are major cause of inherited deafness in the European and American populations. To date, more than 90 mutations have been reported in this gene. Although most of these mutations are rare but 35delG mutation is the most common deafness causing allelic variant of GJB2 in most parts of the world.

In this project, 120 probands from 120 families with ARNSHL in Yazd Province were studied. Mutations Screening of GJB2 was performed by Amplification Refractory Mutation System (ARMS)-PCR for detection of 35delG and then all samples excluding 35delG homozygote were analyzed by DHPLC and Direct Sequencing.

GJB2-related deafness was present in 7.5% of this population. We identified 4 mutations (35delG, 312del14, 314del14 and 167delT) and 4 polymorphisms (V153I, V27I, E114G and R127H) in this study.

Prevalence of GJB2 mutations in this population was lower than American and European populations, and also other provinces of Iran. Interestingly, 312del14 rather than 35delG was the most common mutation found in the population under study. 56.25 % of GJB2 mutant alleles carried 312del14 mutation. To date, this frequency has not been reported in any of the world populations.