Molecular Biology Research Communications最新文献

{"title":"Observations and points of interest regarding bioinformatics predictions of miRNA targeting syncytin genes in endometriosis and miscarriage.","authors":"Piruz Shadbash, Marzieh Bahari-Babadi","doi":"10.22099/mbrc.2025.55165.2254","DOIUrl":"10.22099/mbrc.2025.55165.2254","url":null,"abstract":"","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":"15 2","pages":"131-132"},"PeriodicalIF":1.4,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13148448/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The possibility of prognostic and functional values of the 8q24 and 20q13 chromosomal bands in colorectal cancer.","authors":"Seyed Ahmadreza Siadat","doi":"10.22099/mbrc.2025.54114.2202","DOIUrl":"10.22099/mbrc.2025.54114.2202","url":null,"abstract":"<p><p>Colorectal cancer (CRC) remains a major global health concern, especially given its increasing incidence among younger individuals. While genome-wide association studies (GWAS) have identified numerous CRC-associated polymorphisms, their spatial distribution and functional implications are not fully understood. This study examined the locations of 1,346 CRC-linked polymorphisms across chromosomal bands. The results revealed significant nonrandom clustering across thirteen chromosomal bands: 1q41, 6p21, 8q24, 9q34, 10p14, 10q25, 11q12, 12p13, 15q13, 18q21, 19q13, 20p12, and 20q13. Functional enrichment analysis of genes within these bands revealed several Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Reciprocal chromosomal enrichment confirmed that many of these terms and pathways were not randomly localized within the same bands, highlighting their potential biological significance. Survival analysis using TCGA data identified three KEGG pathways and 33 GO terms mapped to nine of the thirteen bands that were significantly associated with poor prognosis. Notably, the 8q24 and 20q13 regions were enriched for differentially expressed genes and survival-associated terms yet showed no significant enrichment for genes with high somatic mutation rates. These results imply that 8q24 and 20q13 act as regulatory hotspots rather than mutation-driven regions. Overall, this integrative approach identified functionally and clinically relevant genomic regions that may contribute to inherited CRC risk and progression, providing valuable targets for the development of diagnostic and prognostic biomarkers.</p>","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":"15 1","pages":"3-10"},"PeriodicalIF":1.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12673626/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145677752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Wharton's jelly mesenchymal stem cell-derived conditioned media inhibits colon cancer cells via activating AMPK/mTOR-mediated autophagy.","authors":"Dian Dayer, Zahra Akbari-Jonoush, Roya Mahdavi, Afshin Amari, Amirhesam Keshavarz-Zarjani, Layasadat Khorsandi","doi":"10.22099/mbrc.2025.52891.2133","DOIUrl":"10.22099/mbrc.2025.52891.2133","url":null,"abstract":"<p><p>Prior studies have shown that conditioned media derived from Wharton's jelly mesenchymal stem cells (WJ-CM) have anti-cancer properties. This research investigated the impact of WJ-CM on HT-29 colorectal adenocarcinoma cells by examining autophagy biomarkers and the AMPK/mTOR pathway. The HT-29 cells were subjected to WJ-CM and an AMPK activator (AICAR). Autophagy and levels of AMPK and mTOR proteins were investigated. WJ-CM increased the expression of phosphorylated AMPK while reducing the level of phosphorylated mTOR in HT-29 cells. WJ-CM treatment elevated the LC3B/LC3A ratio and ATG7, ATG5, and Beclin-1 expression. However, there was a parallel drop in p62 expression, which indicates autophagy induction. AICAR increased the influence of WJ-CM on viability, as well as the levels of biomarkers associated with autophagy, phosphorylated  AMPK, and phosphorylated  mTOR in the HT-29 cells. WJ-CM inhibits colorectal cancer cell growth via activating AMPK/mTOR-mediated autophagy.</p>","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":"15 1","pages":"31-38"},"PeriodicalIF":1.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12673627/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145677920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of amino acid residues affecting the transcriptional activity of nuclear factor Ya.","authors":"Duhan Tao, Yoshinori Takeuchi, Samia Karkoutly, Zahra Mehrazad Saber, Ye Chen, Tsolmon Mendsaikhan, Rika Saikawa, Yuichi Aita, Yuki Murayama, Akito Shikama, Yukari Masuda, Naoya Yahagi","doi":"10.22099/mbrc.2025.54185.2206","DOIUrl":"10.22099/mbrc.2025.54185.2206","url":null,"abstract":"<p><p>Nuclear factor Y (NF-Y) is a heterotrimeric transcription factor essential for regulating genes involved in lipid metabolism, including fatty acid synthase (Fasn). Although NF-Y activity is known to be dynamically regulated during adipocyte differentiation, the amino acid residues responsible for its transcriptional function remain unclear. In this study, we examined the contribution of nuclear factor Ya (NF-Ya) to DNA-binding activity and transcriptional regulation in 3T3-L1 adipocytes. Using deletion constructs and adenoviral expression systems, we identified a region spanning amino acid residues 184-347 of NF-Ya as critical for acquiring DNA-binding ability during differentiation. Electrophoretic mobility shift assays revealed that NF-Ya undergoes modification within this region, conferring stage-specific DNA-binding activity to the <i>Fasn</i> promoter. These findings suggest that post-translational modification of NF-Ya is a key mechanism regulating NF-Y function in adipogenesis. Our work provides novel insights into transcriptional control of lipogenic genes and their relevance to metabolic regulation.</p>","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":"15 1","pages":"21-29"},"PeriodicalIF":1.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12673625/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145678313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prediction of microRNAs affecting the syncytin-1 (HERV-W) and syncytin-2 (HERV-FRD) genes regulation in endometriosis and miscarriage.","authors":"Mehdi Gholami-Barzoki, Somayeh Shatizadeh-Malekshahi, Mohammad Shayestehpour, Haleh Soltanghoraee","doi":"10.22099/mbrc.2025.54457.2225","DOIUrl":"10.22099/mbrc.2025.54457.2225","url":null,"abstract":"<p><p>Abnormal expression levels of microRNAs are associated with numerous diseases in the female reproductive tract. A small subset of human endogenous retroviruses (HERVs) genes have retained open reading frames (ORFs) that serve beneficial functions for the host. Syncytin-1 (HERV-W) and Syncytin-2 (HERV-FRD) play crucial roles in mammalian development and are expressed in placental trophoblasts. The miRNAs associated with HERV-W and HERV-FRD in spontaneous abortion and endometriosis have not been elucidated. The present study aimed to identify potential miRNAs that affect the regulation of Syncytin-1 and Syncytin-2 in endometriosis and miscarriage using bioinformatics tools. Complete CDS of Syncytin-1 (ERVW-1) and Syncytin-2 (ERVFRD-1) genes were collected from the gene bank database. Several target prediction algorithms were utilized, such as TargetScan, DIANA, miRDB, and miRWalk. Complete CDS of Syncytin-1 (ERVW-1) and Syncytin-2 (ERVFRD-1) genes were collected from the gene bank database. By integrating data from these diverse bioinformatics databases, miR-509-3p and miR-625-5p were consistent across multiple platforms, ensuring robust selection criteria. These tools facilitate the identification of differentially expressed miRNAs, understanding their roles in cellular processes, and potentially utilizing them as biomarkers for disease diagnosis and prognosis. Validation of the identified miRNAs in experimental models or clinical samples is needed to confirm their roles in endometriosis and miscarriage.</p>","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":"15 1","pages":"63-70"},"PeriodicalIF":1.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12673623/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145677740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic polymorphisms of <i>GSTM1</i> and <i>GSTT1</i> genes: effects on susceptibility to formaldehyde-induced hematotoxicity.","authors":"Reza Pourbabaki, Seyed Ahmadreza Siadat, Saeed Yousefinejad, Esmaeel Soleimani","doi":"10.22099/mbrc.2025.54313.2213","DOIUrl":"10.22099/mbrc.2025.54313.2213","url":null,"abstract":"<p><p>Formaldehyde (FA) is a known human carcinogen for the upper respiratory tract. However, its hematotoxicity remains unclear. This study was performed to assess probable effects of FA on blood parameters and to determine the common polymorphisms in the detoxification enzymes <i>GSTM1</i> and <i>GSTT1</i> as biomarkers of susceptibility. Sixty-four workers with high occupational FA exposure and 57 non-exposed controls were studied. Complete blood count was performed. Also, <i>GSTM1</i>/<i>GSTT1</i> genotypes were determined. After adjusting for potential confounding variables, FA exposure was only associated with the levels of hemoglobin, mean corpuscular hemoglobin concentration, and reticulocytes. Notably, workers with homozygous deletions of <i>GSTM1</i> or <i>GSTT1</i> had hematological parameters similar to those with active genes. In conclusion, very high FA exposure resulted in only slight alterations in MCHC and no overt hematotoxicity was observed. These findings suggest that even at high exposure levels, FA may not reach the bone marrow in sufficient amounts to cause hematotoxicity. Also, it seems that <i>GSTM1</i>/<i>GSTT1</i> polymorphisms do not influence the workers' susceptibility to FA-related blood effects.</p>","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":"15 1","pages":"71-91"},"PeriodicalIF":1.4,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12673629/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145678454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative computational approach to farnesyltransferase inhibition toward anti-liver cancer drug candidate from <i>Syzygium cumini</i> essential oils.","authors":"Wira Eka Putra, Arief Hidayatullah, Diana Widiastuti, Hary Isnanto, Muhammad Fikri Heikal, Sustiprijatno","doi":"10.22099/mbrc.2025.54110.2201","DOIUrl":"10.22099/mbrc.2025.54110.2201","url":null,"abstract":"<p><p>Farnesyltransferase plays a critical role in the post-translational modification of mammalian proteins, including the Ras oncogene, which is strongly associated with cancer development. Essential oils from <i>Syzygium cumini</i> have demonstrated promising therapeutic effects, particularly in cancer treatment, potentially through the inhibition of farnesyltransferase activity. This study employed integrative computational approaches to investigate the anticancer potential of essential oils derived from <i>S. cumini</i>. Various compounds were screened for toxicity, biological activities, membrane permeability, gene expression profiles, and survival correlations were conducted to investigate cancer-associated properties. Molecular docking and molecular dynamics (MD) simulations were performed to evaluate the binding interactions and stability of ligand-protein complexes involving farnesyltransferase. α-Humulene epoxide II exhibited antineoplastic activity, functioned as an apoptosis agonist, and inhibited cancer-related targets such as HIF1A and MMP9. Bornyl acetate showed potential as a JAK2 inhibitor. Both compounds demonstrated favorable membrane permeability, indicating high bioavailability and effective cellular uptake. Analysis of the farnesyltransferase (FNTB) gene revealed significantly higher expression in cancerous tissues and a positive correlation with pro-tumor immune cell infiltration. Molecular docking identified Tipifarnib as the strongest binder, serving as a positive control, while α-humulene epoxide II and bornyl acetate showed moderate to weaker binding affinities. However, MD simulations confirmed that both essential oil compounds exhibit binding stability comparable to that of Tipifarnib. Finally, α-humulene epoxide II and bornyl acetate from <i>S. cumini</i> exhibit favorable drug-like properties, high predicted safety margins, and a lack of organ-specific toxicity, underscoring their suitability for further drug development.</p>","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":"15 1","pages":"49-61"},"PeriodicalIF":1.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12673631/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145678399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Linking <i>SIRT1</i> gene variation and protein levels to the pathophysiology of type 2 diabetes.","authors":"Hayder Hasan-Idan, Leila Kohan","doi":"10.22099/mbrc.2026.55659.2277","DOIUrl":"10.22099/mbrc.2026.55659.2277","url":null,"abstract":"<p><p>Sirtuin 1 (<i>SIRT1</i>), an NAD⁺-dependent deacetylase, is involved in glucose homeostasis, insulin signaling, and inflammatory regulation, making it a potential molecular target in type 2 diabetes mellitus (T2DM). This case-control study investigated the association between serum SIRT1 levels, the <i>SIRT1</i> promoter polymorphism rs7895833, and metabolic parameters in 150 patients with T2DM and 150 age- and sex-matched healthy controls. Serum SIRT1 concentrations were measured by ELISA, and rs7895833 genotyping was performed using allele-specific PCR. Clinical and biochemical variables were also assessed. Serum SIRT1 levels were significantly lower in patients with T2DM than in controls (<i>p</i> < 0.001) and showed significant inverse correlations with fasting plasma glucose (<i>p</i> = 0.001) and HbA1c (<i>p</i> < 0.001). Genotypic analysis revealed a significant difference in the distribution of the rs7895833 AG genotype between the two groups (<i>p</i> = 0.03), and under the overdominant model (AG vs. AA + GG), the heterozygous AG genotype was significantly associated with T2DM risk (OR = 1.81, <i>p</i> = 0.011), whereas no significant association was found between <i>SIRT1</i> genotypes and circulating SIRT1 levels. These findings suggest that reduced SIRT1 is associated with hyperglycemia and poor glycemic control in T2DM. Overall, SIRT1 may serve as a potential biomarker and molecular mediator in T2DM pathogenesis. This study provides original data from a Middle Eastern population and may help inform future mechanistic and comparative studies.</p>","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":"15 3","pages":"165-173"},"PeriodicalIF":1.4,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13370758/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148456344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Steroids from <i>Talaromyces stipitatus</i> as potential hepatocellular carcinoma inhibitors: A computational study.","authors":"Hung Duc Nguyen","doi":"10.22099/mbrc.2026.55232.2260","DOIUrl":"10.22099/mbrc.2026.55232.2260","url":null,"abstract":"<p><p>Hepatocellular carcinoma frequently exhibits evasion of apoptosis, rendering the anti-apoptotic Bcl-2 protein a pertinent therapeutic target. Steroids from <i>Talaromyces stipitatus</i> were evaluated as Bcl-2 inhibitors using molecular docking, molecular dynamics simulation, MMGBSA free-energy estimation, ADMET prediction, and DFT descriptors. Docking prioritized CPD2 over Paclitaxel. It also indicated accommodation within a conserved pocket supported by hydrogen-bond and hydrophobic interactions. Molecular dynamics suggested sustained stability and compactness for the CPD2-Bcl-2 complex. In contrast, the reference complex exhibited comparatively larger conformational excursions. MMGBSA favored CPD2, with improved net association attributable primarily to a reduced solvation penalty. ADMET profiling indicated limited aqueous solubility and a shared hERG II liability, while predicting no hepatotoxicity alert for CPD2. DFT descriptors were consistent with higher electronic responsiveness for CPD2 relative to the reference. These findings suggest that CPD2 may serve as a promising scaffold for developing Bcl-2-targeted therapeutic strategies against HCC. Future in vitro and in vivo studies are required to validate these computational predictions and guide lead optimization.</p>","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":"15 3","pages":"145-158"},"PeriodicalIF":1.4,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13370759/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148456347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>SH3D21</i> rs34416442 genetic variation is associated with pancreatic cancer patients' overall survival and their response to gemcitabine.","authors":"Mohammad Masoudi, Negin Ahangarian, Hossein Ammarlou","doi":"10.22099/mbrc.2026.55565.2273","DOIUrl":"10.22099/mbrc.2026.55565.2273","url":null,"abstract":"<p><p>Pancreatic cancer remains one of the most lethal malignancies worldwide due to late diagnosis and limited therapeutic response. Gemcitabine is widely used as a first-line chemotherapeutic agent, and <i>SH3D21</i> has been identified as a gemcitabine sensitizer in pancreatic cancer cells. Here, we investigated whether rs34416442 polymorphism of <i>SH3D21</i> is associated with overall survival in a cohort of Iranian patients with pancreatic cancer. Peripheral blood samples were collected from 26 patients, and genotyping was performed. Patients were followed and survival outcomes were analyzed using Kaplan-Meier curves and the log-rank test. Three genotypes-TTT/TTT, TTT/T, and T/T-were identified with frequencies of 38%, 54%, and 8%, respectively. Significant differences in survival were observed among genotypes (<i>p</i> = 0.004). Patients carrying the <i>T/T</i> genotype exhibited markedly shorter mean overall survival (135 days) compared with those harboring at least one TTT allele (395 and 450 days). A recessive model further confirmed the reduced survival associated with the homozygous T/T genotype (<i>p</i> = 0.001). Stratified analyses showed that this association persisted in both gemcitabine-received (<i>p</i> = 0.006) and not-received (<i>p</i> = 0.016) subgroups. While different genotype-based survival patterns were observed among patients of the two groups. The TTT/T genotype showed the best survival in patients receiving gemcitabine, while TTT/TTT genotype did so in patients not receiving gemcitabine. These findings suggest <i>SH3D21</i> rs34416442 as a potential predictive biomarker for pancreatic cancer.</p>","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":"15 3","pages":"159-164"},"PeriodicalIF":1.4,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13370760/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148456384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}