Background/Aim: Recent studies imply the significance of promoter CpG methylation as a biomarker for various cancer types in different genes. ALX3 is one of the candidate genes with prominent promoter methylation status change. In this study, the methylation status of ALX3 gene promoter and its expression was analyzed in lung cancer cell lines and clinical samples from The Cancer Genome Atlas Program (TCGA) program. Materials and Methods: Methylation status was screened using the COBRA Assay, and gene expression in two cancer (A549 & H1299) and one normal (Beas 2B) lung cell lines was determined using RT-PCR. Results: ALX3 gene promoter was found to be hypermethylated in both lung cancer cell lines compared to normal cells. However, no difference in the expression of this gene was observed. In addition to our in vitro findings, DNA Methylation and RNA-seq data of 413 adenocarcinoma samples from TCGA-LUAD dataset were analyzed. ALX3 gene was found to be hypermethylated in tumor compared to normal samples. Interestingly, the expression level of ALX3 gene in tumors was found to be higher than that in normal samples. Conclusion: ALX3 gene promoter hypermethylation could serve as a biomarker in lung cancer.

Introduction:: Hereditary angioedema (HAE) is a rare, potentially life-threatening genetic condition characterized by recurrent episodes of localized tissue swelling, often affecting the skin, upper respiratory tract, and gastrointestinal system. HAE-FXII, also known as HAE with normal C1 inhibitor ( C1INH ), has been associated with mutations in only one of several genes, including FXII encoding coagulation factor XII (FXII). The aim of the study was to investigate the pathogenicity and functional consequences of the c.1681-7G>A intronic variant in the FXII gene according to ACMG guidelines in familial cases of HAE-FXII. Materials and Methods:: Genetic analysis was performed using Sanger sequencing on affected individuals. To assess whether the variant affects splicing, in silico analysis and Messenger RNA (mRNA) studies were conducted on patient-derived samples. Results:: The c.1681-7G>A variant was identified in multiple individuals from affected families. However, splicing analysis revealed that this intronic variant did not cause any alteration in mRNA processing. No aberrant transcripts were detected, and expression levels were comparable to controls, indicating that the variant does not have an effect on splicing or gene function. Discussion:: The c.1681-7G>A variant in the FXII gene is unlikely to be a pathogenic alteration in HAE type III. Contribution to the Literature:: These findings support its classification as a benign variant, emphasizing the importance of functional validation when interpreting intronic changes in genetic diagnostics.

Transmembrane and Coiled-Coil Domains 1 (TMCO1) protein is encoded by TMCO1 gene consists of 7 exons. Previous studies have identified multiple TMCO1 variants in patients with cerebro-facio-thoracic dysplasia (CFTD) and TMCO1 locus was also shown to be associated with primary open angle glaucoma (POAG). However, there are limited number of research exist reporting associations of the TMCO1 gene sequence variants and majority of the findings affirm the pathogenicity of the nonsense and frameshift TMCO1 variants and their associations with clinical phenotypes. Thus functional properties of the single nucleotide variants causing amino acid changes in the TMCO1 are yet to be comprehensively elucidated. In this study, we evaluated the effects of amino acid substitutions on protein structure, identified their putative roles in post-translational modifications (PTM) and in regulatory mechanism for TMCO1 protein. We classified 41 missense variants as pathogenic based on combined scores of common in silico tools (SIFT, MutationTaster2, Polyphen2). Of these 41 variants, four (p.K211Q, p.K105E, p.S235F, p.K237R) were identified to be located in PTMs and regulatory protein binding sites; thus they were proposed to be putative functional variants. Moreover, rs1387528611 (p.Lys128Gln) had also strong evidence (RegulomeDB score=2b) for its possible regulatory function. The results of our in silico analyses highlight the functional importance of the missense TMCO1 variants that may contribute to the TMCO1-associated disease phenotypes and further in vivo evaluation yet to be needed to uncover their role in human diseases.