Shiraz University Press Molecular Biology Research Communications 2322-181X 15 1 2026 03 01 Artificial intelligence and genomic data privacy: Balancing innovation with security 1 2 8294 10.22099/mbrc.2025.54335.2217 EN Leila Kohan Department of Biology, Ars.C., Islamic Azad University, Arsanjan, Iran 0000-0001-7124-2849 Journal Article 2025 09 20 No abstract

https://mbrc.shirazu.ac.ir/article_8294_5e10d544ba10cd65e68aa85377c19655.pdf

Shiraz University Press Molecular Biology Research Communications 2322-181X 15 1 2026 03 01 The possibility of prognostic and functional values of the 8q24 and 20q13 chromosomal bands in colorectal cancer 3 10 8296 10.22099/mbrc.2025.54114.2202 EN Seyed Ahmadreza Siadat Department of Biology, School of Science, Shiraz University, Shiraz, Iran Journal Article 2025 08 28 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.

https://mbrc.shirazu.ac.ir/article_8296_3e311499954b7347abe29e657b77b848.pdf

Shiraz University Press Molecular Biology Research Communications 2322-181X 15 1 2026 03 01 CPUK02 sensitizes U87 glioblastoma cell lines to TMZ treatment via autophagy flux inhibition 11 20 8298 10.22099/mbrc.2025.52011.2079 EN Hooman Rezaie Department of Clinical Biochemistry, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran Sanaz Dastghaib Endocrinology and Metabolism Research Center, Shiraz University of Medical Science, Shiraz, Iran Morvarid Siri Autophagy Research center, Shiraz University of Medical Sciences, Shiraz, Iran Pooneh Mokarram Autophagy Research Center, Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran Mina Hemmati Department of Clinical Biochemistry, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran Journal Article 2024 12 25 Adjuvant chemotherapy with TMZ (Temozolomide) does not improve the survival of patients suffering from GBM (Glioblastoma). Given the importance of autophagy and UPR (Unfolding Protein Response) in chemotherapy resistance, as well as the role of Beclin-1, LC3IIβ, and P62 in the regulation of autophagy, we evaluated the effect of TMZ along with CPUK02 on U87 cells as a model of Glioblastoma cancer in this study. To achieve this goal, we treated the U87 cells with different doses of TMZ (50, 100, 200, 400, and 800 μM) and CPUK02 (1, 0.5, 0.25, 0.125, 0.06, 0.03, 0.01, and 0.007 μM); then, cell viability was assessed by MTT assay. The gene expression of Beclin1, P62, LC3IIβ, and XBP-1s was analyzed using quantitative real-time polymerase chain reaction. The comparison of the control group with the groups treated with the TMZ drug showed that, in 48 and 72 hours, doses of TMZ more than IC50 (100 μM) (p<0.001) significantly led to cell death. CPUK02 doses more than 0.125 (p<0.0001) significantly led to cell death. TMZ and CPUK02 combination therapy (100 and 0.03 μM, respectively) increased the expression of Beclin-1, LC3IIβ, and P62 and activated the IRE-1 arm of UPR by increasing the expression of XBP-1s. TMZ and CPUK02 treatment inhibits the autophagic flux (p62, LC3IIβ). Increased XBP-1s expression might contribute to the enhanced TMZ sensitivity. This combination therapy is promising for TMZ-resistant cancers, but it needs further investigation.

https://mbrc.shirazu.ac.ir/article_8298_e13a2880fa3023f4a8b56d436d46d270.pdf

Shiraz University Press Molecular Biology Research Communications 2322-181X 15 1 2026 03 01 Analysis of amino acid residues affecting the transcriptional activity of nuclear factor Ya 21 29 8301 10.22099/mbrc.2025.54185.2206 EN Duhan Tao Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Tochigi 329-0498, Japan Nutrigenomics Research Group, Institute of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan Yoshinori Takeuchi Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Tochigi 329-0498, Japan Samia Karkoutly Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Tochigi 329-0498, Japan Zahra Mehrazad Saber Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Tochigi 329-0498, Japan Ye Chen Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Tochigi 329-0498, Japan Nutrigenomics Research Group, Institute of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan Tsolmon Mendsaikhan Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Tochigi 329-0498, Japan Rika Saikawa Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Tochigi 329-0498, Japan Yuichi Aita Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Tochigi 329-0498, Japan Nutrigenomics Research Group, Institute of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan Yuki Murayama Nutrigenomics Research Group, Institute of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan Akito Shikama Nutrigenomics Research Group, Institute of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan Yukari Masuda Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Tochigi 329-0498, Japan Naoya Yahagi Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Tochigi 329-0498, Japan Nutrigenomics Research Group, Institute of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan 0000-0002-1823-1865 Journal Article 2025 09 05 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 Fasn 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.

https://mbrc.shirazu.ac.ir/article_8301_0a82367c32b78aa446c7bc9953906735.pdf

Shiraz University Press Molecular Biology Research Communications 2322-181X 15 1 2026 03 01 Wharton's jelly mesenchymal stem cell-derived conditioned media inhibits colon cancer cells via activating AMPK/mTOR-mediated autophagy 31 38 8302 10.22099/mbrc.2025.52891.2133 EN Dian Dayer Cellular and Molecular Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Zahra Akbari-Jonoush Cellular and Molecular Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Department of Immunology, School of Medicine Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Roya Mahdavi Department of Immunology, School of Medicine Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran Afshin Amari Cellular and Molecular Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Department of Immunology, School of Medicine Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Amirhesam Keshavarz-Zarjani Cellular and Molecular Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Department of Anatomical Sciences, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Layasadat Khorsandi Cellular and Molecular Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Department of Anatomical Sciences, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Journal Article 2025 04 09 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.

https://mbrc.shirazu.ac.ir/article_8302_06f34c393af3b61c8b4db69745e97dca.pdf

Shiraz University Press Molecular Biology Research Communications 2322-181X 15 1 2026 03 01 Molecular dynamics simulation of thermal activation of human TRPV1 39 48 8332 10.22099/mbrc.2025.53301.2171 EN Juan David Bermudes-Contreras Sección de Estudios de Posgrado e Investigación, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, México Luis Manuel Arratia-Cortés Sección de Estudios de Posgrado e Investigación, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, México María Esther Ramírez-Moreno Sección de Estudios de Posgrado e Investigación, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, México Beatriz Zamora-López Departamento de Psiquiatría y Salud Mental, Facultad de Medicina, UNAM, Ciudad de México, México César López-Camarillo Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México Laurence Annie Marchat Sección de Estudios de Posgrado e Investigación, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, México Absalom Zamorano-Carrillo Sección de Estudios de Posgrado e Investigación, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, México Journal Article 2025 06 03 TRPV1 (Transient Receptor Potential Vanilloid 1) is a non-selective ion channel that responds to various thermal, chemical, mechanical, and ligand stimuli. It is expressed in various tissues, mainly in nociceptive neurons, adipocytes, and other cell types. This channel is involved in pain and temperature transition processes, although it has recently been implicated in adipocyte browning processes. That is why the study of this receptor has increased in recent years to understand the process of activation and inactivation by various stimuli. In this work, we focus on modeling a complete channel of human TRPV1 (hTRPV1), the structural changes, and especially the behavior of the pore when this protein is subjected to high temperatures (400 K). We report that when molecular dynamics simulate hTRPV1 at 400 K, it suffers an increase in the diameter of the two gates reported elsewhere in the pore, suggesting the opening of the channel. In this work, we describe the structural changes in the entire protein, concomitant to those in the pore, favoring this process, which might be associated with its biological activity.

https://mbrc.shirazu.ac.ir/article_8332_22c6dada8fab333e167ea93f13389fca.pdf

Shiraz University Press Molecular Biology Research Communications 2322-181X 15 1 2026 03 01 Integrative computational approach to farnesyltransferase inhibition toward anti-liver cancer drug candidate from Syzygium cumini essential oils 49 61 8333 10.22099/mbrc.2025.54110.2201 EN Wira Eka Putra Biotechnology Study Program, Department of Applied Sciences, Faculty of Mathematics and Natural Sciences, Universitas Negeri Malang, East Java, 65145, Indonesia Arief Hidayatullah Democratic Governance and Poverty Reduction Unit, United Nations Development Programme, Eijkman-RSCM Building, Jakarta, 10430, Indonesia Diana Widiastuti Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Pakuan, West Java, 16129, Indonesia Hary Isnanto Department of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand Muhammad Fikri Heikal Tropical Medicine Graduate Program, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand S Sustiprijatno Research Center for Applied Botany, National Research and Innovation Agency, West Java, 16911, Indonesia Journal Article 2025 08 28 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 Syzygium cumini 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 S. cumini. 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 S. cumini exhibit favorable drug-like properties, high predicted safety margins, and a lack of organ-specific toxicity, underscoring their suitability for further drug development.

https://mbrc.shirazu.ac.ir/article_8333_12243f79b6cd9661ccab4c82f546f015.pdf

Shiraz University Press Molecular Biology Research Communications 2322-181X 15 1 2026 03 01 Prediction of microRNAs affecting the syncytin-1 (HERV-W) and syncytin-2 (HERV-FRD) genes regulation in endometriosis and miscarriage 63 70 8370 10.22099/mbrc.2025.54457.2225 EN Mehdi Gholami-Barzoki Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran Somayeh Shatizadeh-Malekshahi Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran Mohammad Shayestehpour Department of Bacteriology and Virology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran Haleh Soltanghoraee Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran Journal Article 2025 10 04 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.

https://mbrc.shirazu.ac.ir/article_8370_de6a03e3adcdaad82227b8cea15fe256.pdf

Shiraz University Press Molecular Biology Research Communications 2322-181X 15 1 2026 03 01 Genetic polymorphisms of GSTM1 and GSTT1 genes: effects on susceptibility to formaldehyde-induced hematotoxicity 71 79 8371 10.22099/mbrc.2025.54313.2213 EN Reza Pourbabaki Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran Department of Occupational Health and Safety Engineering, Shiraz University of Medical Sciences, Shiraz, Iran Seyed Ahmadreza Siadat Department of Biology, School of Science, Shiraz University, Shiraz, Iran Saeed Yousefinejad Department of Occupational Health and Safety Engineering, Shiraz University of Medical Sciences, Shiraz, Iran Esmaeel Soleimani Department of Occupational Health and Safety Engineering, Shiraz University of Medical Sciences, Shiraz, Iran Journal Article 2025 09 19 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 GSTM1 and GSTT1 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, GSTM1/GSTT1 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 GSTM1 or GSTT1 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 GSTM1/GSTT1 polymorphisms do not influence the workers’ susceptibility to FA-related blood effects.

https://mbrc.shirazu.ac.ir/article_8371_ff9c9212102b1c74058aa44d38312d69.pdf