Research Output
Articles
Publication Date: 2025
Scientific Reports (20452322)15(1)
Papillary thyroid carcinoma (PTC) is a malignancy with an ambiguous etiology. The competitive endogenous RNA (ceRNA) hypothesis provides a framework for clarifying the molecular mechanisms that drive carcinogenesis. In this study, we constructed a novel ceRNA network to identify reliable diagnostic and prognostic indicators applicable across all stages of PTC. Transcriptome analysis was performed to identify stage-specific hub genes using the MCC, IVI, and MCODE algorithms. A novel five-layer ceRNA network and its associated regulatory network (DE-TF) were constructed. Receiver operating characteristic curves were used to evaluate the diagnostic performance of elements within both networks. A risk assessment model was developed by identifying key genes from the ceRNA and DE-TF components through univariable Cox regression and LASSO regression analyses. RNA-seq findings were validated by RT-qPCR. The correlations between gene expression levels and blood calcium levels were examined. The ceRNA and DE-TF networks contained 33 and 21 components, respectively. Logistic regression analysis identified PKMYT1, E2F1, NFATC1, STAT6, E2F3, LINC02910, GAS5, and TK1 as reliable diagnostic markers for PTC, achieving an AUC of 96.9%. Among these, PKMYT1 and GAS5 were stage-specific markers, showing significant upregulation in highly aggressive PTC tumors compared to less aggressive ones. Both genes demonstrated strong diagnostic value in differentiating high- from low-aggressive tumors, with AUCs of 0.81 and 0.87, respectively. circMET, which was overexpressed in both low- and high-aggressive tumors, showed diagnostic potential in distinguishing low-aggressive tumors from normal adjacent tissues (AUC = 0.81). GAS5 expression demonstrated an association with blood calcium levels. The SERN prognostic model, including STAT6, E2F1, RMI2, and NR4A1, illustrates the importance of these four genes as reliable prognostic markers for overall survival in PTC. Three components of the ceRNA network—PKMYT1, GAS5, and circMET—were significantly associated with PTC aggressiveness. PKMYT1 and GAS5 demonstrated strong diagnostic value in distinguishing high-aggressive from low-aggressive tumors, while circMET showed notable diagnostic efficacy in differentiating low-aggressive PTC tumors from adjacent normal tissues. Furthermore, GAS5 expression levels were correlated with blood calcium levels. © The Author(s) 2025.
Mahdavi, S.B.,
Javadirad, S.M.,
Rafieian, M.,
Poursafa, P.,
Zavareh, V.A.,
Daniali, S.S.,
Heidari-beni, M.,
Goodarzi-khoigani, M.,
Vahdatpour, B.,
Mirhendi, H. Publication Date: 2025
Bioimpacts (22285652)15
Introduction: It is believed that DNA methylation can modify disease susceptibility in response to environmental factors as early as the perinatal period. In this study, we aimed to present a streamlined DNA methylation analysis procedure for osteoporosis-related gene promoters in the umbilical cord blood. Methods: The Prospective Epidemiological Research Studies in Iran (PERSIAN) birth cohort was established in 2016. In this study, a total of 300 umbilical cord blood samples were collected at the time of delivery. For all samples, DNA was extracted and converted using sodium bisulfite. Multiple primer sets were designed for Wnt1, Wnt10b, β-catenin, OPG, and RANKL gene promoters in the online MethPrimer platform. Next, bisulfite sequencing PCR (BSP), as the gold standard method for exploring methylated and unmethylated cytosines, was performed in a gradient-controlled setting. The PCR products were then purified and directly sequenced. Subsequently, the chromatograms were interpreted. Results: For Wnt10b, β-catenin, and OPG genes, the converted DNA could be successfully amplified. The frequency of acceptable chromatograms for analysis was 195 for Wnt10b (195/300, 0.65%), 198 for β-catenin (198/300, 0.66%), and 50 for OPG (50/50, 100%). Conclusion: BSP can be efficiently used to investigate the methylation of target gene promoters in umbilical cord blood DNA. © 2025 The Author(s).
Publication Date: 2025
Scientific Reports (20452322)15(1)
Adrenocortical carcinoma (ACC), with poor prognosis, is one of the most aggressive endocrine cancers. Surgery is the mainstay of treatment; nevertheless, chemotherapy is usually needed. Mitotane, the medication licenced for ACC, has had mixed results. Drug repositioning based on gene coexpression networks has proven to be an effective method of discovering potential cancer treatments. A total of 139 human specimens were examined, comprising 106 metastatic ACCs, 14 benign adrenocortical adenomas (ACAs), and 19 normal adrenal cortex tissues. Hub genes were identified using weighted correlation network analysis (WGCNA), and their differential expression was confirmed by microarrays and RNA sequencing. Hub genes were analyzed in more depth for enrichment, coexpression, and protein–protein interaction. Two phases of survival analysis were conducted considering sex. Hub gene expression was associated with TP53 mutations and cancer stage. Hub genes were evaluated using regression analysis. Hub genes were associated with immune cell infiltration. Network analysis identified transcription factors that regulate hub genes. Drug-gene interaction network analyses were performed to reposition existing drugs. WGCNA-PPI analysis revealed 31 hub genes, 11 of which were overexpressed by more than fourfold, as well as HMMR and UBE2T, which were novel genes. All hubs showed significant correlations with survival, tumor staging, and TP53 mutation status in ACC tissues. Women overexpressing CDK1, UBE2C, PCLAF, and CCNB1 were more likely to suffer catastrophic deaths than men. In terms of ACC diagnostic capacity, all hub genes had AUCs greater than 0.90, with TOP2A, CDK1, and CCNB1 having the highest values. All hub genes, except for THYMS and RACGAP1, were negatively correlated with M2 macrophages and CD8 + T cells infiltration. Hub genes were co-expressed and regulated by 21 DE-TFs expressed differently between ACC and normal tissues. Novel pharmaceuticals are represented by fifteen out of thirty-four medications directed at hub genes and DE-TFs. Paclitaxel and cisplatin were the central nodes within the drug-gene network. Multiple drugs target TYMS and TOP2A, making them both promising targets for ACC. Fluorouracil and epirubicin target HMMR novel hub gene. HMMR as a novel ACC hub gene targets by fluorouracil and epirubicin, but fluorouracil has advantageous. The reason for this is that M2 macrophages promote fluorouracil resistance, whereas tumors overexpressing the HMMR gene demonstrate a negative infiltration of macrophages. Hub genes, associated with ACC development and progression, have negative impacts on survival rates, particularly in women. Network analysis shows fluorouracil and epirubicin target the ACC novel hub gene, HMMR. Fluorouracil was more effective due to its impact on M2 macrophage infiltration. © The Author(s) 2025.
