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Nasopharyngeal cancer (NPC) is a multifaceted disease characterized by genetic and epigenetic modifications. While Epstein-Barr virus (EBV) infection is a known risk factor, recent studies highlight the significant role of DNA methylation in NPC pathogenesis. Aberrant methylation, particularly at CpG sites, can silence tumour suppressor genes, promoting uncontrolled cell growth. This study aims to analyse the methylation patterns in Indonesian NPC patients through whole-epigenome sequencing. Seven clinical nasopharyngeal cancer samples were collected and confirmed histopathologically. DNA was extracted, sequenced using Oxford Nanopore technology, and aligned to the GRCh38 human reference genome. Methylation analysis was performed using modkit and statistical analysis with R software. Enriched pathways and processes were identified using ClusterProfiler in R, and gene overlap analysis was conducted. The analysis identified both globally hypermethylated and hypomethylated NPC samples. Key tumour suppressor genes, such as were frequently hypermethylated and confirmed to have lower expression in an independent NPC transcriptome cohort, suggesting their role in NPC carcinogenesis. Enriched KEGG pathways included PI3K-Akt signalling, ECM-receptor interaction, and focal adhesion. The presence of EBV DNA was confirmed in all samples, implicating its role in influencing methylation patterns. This study provides comprehensive insights into the epigenetic landscape of NPC, underscoring the role of CpG methylation in tumour suppressor gene silencing. These findings pave the way for targeted therapies and highlight the need for region-specific approaches in NPC management.

Spermatogenic maturation arrest is thought to be caused by epigenetic defects, specifically in chromatin remodeling and histone modification. This study evaluated the status of chromatin remodeling chromodomain helicase DNA binding protein 5 ( ) and histone modifications histone 4 lys-12 acetylation ( ) and histone 3 lys-9 trimethylation ( ) in human testicular biopsies, based on maturation arrest type. The cross-sectional study utilized 18 Bouin-fixed paraffin-embedded (BFPE) specimens prepared from residual tissue from routine laboratory tests of infertile patients. The expression of CHD5, H4K12ac, and H3K9me3 was examined through immunohistochemistry (IHC). The intensity was measured using ImageJ with IHC Profiler and StarDist plugins. Statistical analysis was performed using Python with Scipy.Stats module. The data were tested with Shapiro- Wilk for normality and Levene test for homogeneity. The differences in the intensity of spermatogenic cells were assessed using Kruskal-Wallis and Mann-Whitney tests. A difference was considered statistically significant if P<0.05. We found three types of maturation arrest, including Sertoli cell only (n=5), spermatocyte arrest (n=4), and spermatid arrest (n=9). was positive in spermatogonia and round spermatids but absent in spermatocytes. The mean grey value (MGV) of in spermatogonia was generally weak in spermatocyte arrest (157.4 ± 16.6) and spermatid arrest (155.3 ± 16.8), and there was no significant difference between them [P=0.49, 95% confidence interval (CI): (-4.3, 6), effect size (r): 0.02]. Although there was a significant difference in the expression of and (P<0.001), both histone modifications were found in all observed spermatogenic cells. The expressions of , , and in different spermatogenic cell types produce similar results, indicating that they cannot be used as markers to determine the type of spermatogenic maturation arrest in humans. The significant finding in this research is the expression of in human spermatogonia cells, which requires further study for elaboration.

Hypertension is a multifactorial disease due to a complex interaction among genetic, epigenetic, and environmental factors. Characterized by raised blood pressure (BP), it is responsible for more than 7 million deaths per annum by acting as a leading preventable risk factor for cardiovascular disease. Reports suggest that genetic factors are estimated to be involved in approximately 30 to 50% of BP variation, and epigenetic marks are known to contribute to the initiation of the disease by influencing gene expression. Consequently, elucidating the genetic and epigenetic mediators associated with hypertension is essential for better discernment of its pathophysiology. By deciphering the unprecedented molecular hypertension basis, it could help to unravel an individual’s inclination towards hypertension which eventually could result in an arrangement of potential strategies for prevention and therapy. In the present review, we discuss known genetic and epigenetic drivers that contributed to the hypertension development and summarize the novel variants that have currently been identified. The effect of these molecular alterations on endothelial function was also presented.

Nasopharyngeal carcinoma (NPC) is prevalent in Southeast Asia, particularly in Indonesia. Despite advances in treatment, patients with advanced NPC face poor outcomes. Examining the NPC mutational landscape is crucial for understanding its biology and enable potential new therapeutic strategy. To characterize the landscape of single nucleotide variants (SNVs), structural variants (SVs), copy number variations (CNVs), and short tandem repeats (STRs) in locally advanced to advanced NPC within an Indonesian cohort using long-read sequencing. Six fresh-frozen nasopharyngeal biopsy samples were collected from the NPC biobank. DNA was extracted and sequenced using Oxford Nanopore’s Promethion 2 Solo long-read sequencer. Structural and small variants were identified and annotated. The SNVs, SVs, and CNVs were categorized based on predicted effects, and key findings were validated using external RNA-seq data. Copy number loss genes were checked against the Tumour Suppressor Gene database (TSGene v2.0). Genetic findings were correlated with patient clinical histories. Approximately 4.4 to 5.1 million SNVs were identified per sample, with 0.023% categorized as high consequence. Notable tumour suppressor genes, such as LIMD1 and CNDP2 , were frequently mutated. Around 30,000 to 41,599 SVs were detected per sample. High-consequence tumour suppressor gene SVs were identified in EPHA3 , CASP8 , DMBT1 , ZFHX3 , and IRF5 gene. Common copy number tumour suppressor gene loss observed in RNH1 , H19 , CDKN1C , and others, suggesting their role in NPC carcinogenesis. Copy number gains were found in potential oncogenes such as Y RNA , LTO1 , and FADD . Pathogenic short tandem repeats (STRs) in PABPN1 and RFC1 were identified in three samples, presenting a novel association with NPC. NPC sample which exhibited significant genomic instability had the shortest survival, potentially linked to multiple defective DNA repair genes. This study utilized long-read sequencing to identify a complex spectrum of genetic alterations, including numerous SVs and potentially pathogenic STRs, in Indonesian NPC. Extensive DNA repair gene defects, primarily complex SVs detectable by long reads, were observed and highly possibly associated with poor survival. These findings underscore the potential of long-read sequencing for uncovering clinically relevant mutations in NPC.

Alteration of molecular pathways triggering apoptosis gives raise to various pathological tissue processes, such as tumorigenesis. The mitochondrial pathway is regulated by both the genes of the Bcl-2 family and the genes encoding mitochondrial transport molecules. Those proteins allow a release of cyctochrome c through the outer mitochondrial membrane. This release activates the caspase cascade resulting in death of cells. There are at least two main transport systems associated with the family of Bcl-2 proteins that are involved in transport of molecules through the outer mitochondrial membrane, i.e., the voltage dependent anion channels (VDACs) and translocases of the outer mitochondrial membrane proteins (TOMs). We investigated the expression of genes of the Bcl-2 family, i.e., pro-apoptotic Bak and Bid, and anti-apoptotic Bcl-2; VDAC gene, i.e., VDAC1, VDAC2 and VDAC3; and TOMM genes, i.e., TOMM20, TOMM22 and TOMM40. This study was performed at the mRNA and the protein level. Fourteen paraffin embedded prostate cancer tissues and five normal prostate tissues were analyzed by the quantitative PCR array and immunohistochemistry. We found a significant increase in both mRNA expression of the anti-apoptotic Bcl-2 gene and VDAC1 gene in prostate cancer tissue in comparison with their normal counterparts. Translation of the anti-apoptotic Bcl-2 and VDAC1 genes in prostate cancer tissue was slightly increased. We observed no significant differences in the mRNA expression of the pro-apoptotic Bak and Bid genes, VDAC2 or VDAC3 genes or the three TOMM genes in these tissues. The pro-apoptotic Bax protein was downtranslated significantly in secretory cells of prostate cancer as compared to normal prostate. We suggest that this protein is a good candidate as biomarker for prostate cancer.

Polycystic ovary syndrome (PCOS) is the most common endocrine disorder affecting 5–20% of reproductive-age women. However, the treatment of PCOS is mainly based on symptoms and not on its pathophysiology. Neuroendocrine disturbance, as shown by an elevated LH/FSH ratio in PCOS patients, was thought to be the central mechanism of the syndrome, especially in lean PCOS. LH and FSH secretion are influenced by GnRH pulsatility of GnRH neurons in the hypothalamus. Kisspeptin is the main regulator of GnRH secretion, whereas neurokinin B (NKB) and dynorphin regulate kisspeptin secretion in KNDy neurons. This study aims to deepen the understanding of the neuroendocrine disorder in lean PCOS patients and its potential pathophysiology-based therapy. A cross-sectional study was performed at Dr. Cipto Mangunkusumo Kencana Hospital and the IMERI UI HRIFP cluster with 110 lean PCOS patients as subjects. LH, FSH, LH/FSH ratio, kisspeptin, NKB, dynorphin, leptin, adiponectin, AMH, fasting blood glucose, fasting insulin, HOMA-IR, testosterone, and SHBG were measured. Bivariate and path analyses were performed to determine the relationship between variables. There was a negative association between dynorphin and kisspeptin, while NKB levels were not associated with kisspeptin. There was no direct association between kisspeptin and the LH/FSH ratio; interestingly, dynorphin was positively associated with the LH/FSH ratio in both bivariate and pathway analyses. AMH was positively correlated with the LH/FSH ratio in both analyses. Path analysis showed an association between dynorphin and kisspeptin levels in lean PCOS, while NKB was not correlated with kisspeptin. Furthermore, there was a correlation between AMH and the LH/FSH ratio, but kisspeptin levels did not show a direct significant relationship with the LH/FSH ratio. HOMA-IR was negatively associated with adiponectin levels and positively associated with leptin and FAI levels. In conclusion, AMH positively correlates with FAI levels and is directly associated with the LH/FSH ratio, showing its important role in neuroendocrinology in lean PCOS. From the path analysis, AMH was also an intermediary variable between HOMA-IR and FAI with the LH/FSH ratio. Interestingly, this study found a direct positive correlation between dynorphin and the LH/FSH ratio, while no association between kisspeptin and the LH/FSH ratio was found. Further research is needed to investigate AMH and dynorphin as potential therapeutic targets in the management of lean PCOS patients.

Implantation failure has long been identified as a common problem underlying low success rate of IVF. Currently, endometrial receptivity has gained expert attention as it is demonstrated to contribute to successful embryo implantation. MicroRNAs (miRNAs) is known to affect endometrial receptivity through post-transcriptional gene expression regulation. This study aimed to evaluate the expression of miRNA 135b and HOXA-10 during the implantation window in endometrial tissue of infertile women. A total of 14 patients diagnosed with infertility in the gynaecology clinic of Cipto Mangunkusumo and Daya Medika hospitals Jakart, Indonesia were selected as the observed group, and 9 fertile patients were enrolled in the control group. Total RNA was isolated from endometrial tissues collected at the secretory phase of the menstrual cycle. The miRNA 135b and HOXA-10 mRNA expression were measured using quantitative real-time PCR (qPCR). The correlation between these variables was then determined using Pearson's correlation coefficient. The expression of miRNA 135b in the infertile group was significantly higher by 1.81-fold compared to the control group (p<0.01), whereas, expression of HOXA-10 mRNA was significantly lower in the infertile group compared to the controls (p=0.047). Significant negative correlation was observed between the expression of miRNA 135b and HOXA-10 mRNA in infertile women (p=0.021; r=-0.607). Taken together, this study provides that alteration of miRNA expression is involved in regulating the implantation process partly via modulation of the expression of gene required for implantation.

Introduction Colorectal cancer has emerged as a concerning health problem, ranking the third most common form of cancer in both men and women. The phosphatase and tensin homologue (PTEN) protein is widely known for its role as an inhibitor of the phosphatidylinositol 3-kinase/protein kinase-B/mammalian target of rapamycin (PI3K/Akt/mTOR) pathway, playing a major role inhibiting tumor development. Previous studies investigated the role of this protein in the PI3K pathway and how it affected colorectal cancer. However, a standardized cut-off value for PTEN expression has not been established. Methods Immunohistochemistry was used in examining PTEN. The staining grade ranging from 0 to 3 was then multiplied by the number of 100 cancer cells counted, with total score between 0 and 300. In this study, receiver operating characteristic (ROC) curve was employed to determine the expression cut-off value for PTEN in colorectal cancer. Results This study showed statistically significant results (P < 0.001) in either tumor or non-tumor tissues by using the ROC curve with a cut-off value of 199.0. This study also revealed significant correlation between nodal status with PTEN (P = 0.008) and stage with PTEN (P = 0.019) with sensitivity 0.753 and specificity 0.728. Conclusion Semiquantitative assessment with cell counting multiplied by color intensity is a good method in determining PTEN expression. The use of immunohistochemical staining intensity and cell scoring with ROC cut-off is effective to elaborate the effects of PTEN in colorectal cancer (PTEN value > 199.0 was classified as strong and ≤ 199.0 as weak).

Introduction: BRAFV600E and RAS mutations are the most common gene mutations in papillary thyroid carcinoma (PTC) that may be correlated with its biological behavior. There are still limited data about BRAFV600E and RAS mutations in Indonesia. This study aims to determine the prevalence of BRAFV600E and RAS mutations, and their association with clinicopathologic characteristics. Methods: Patients who had total thyroidectomy from 2019 to 2021 and those who met our study criteria underwent PCR and DNA sequencing analysis for BRAFV600E, BRAFK601E, exon 2 and 3 of NRAS, HRAS, and KRAS. Analyses were performed to determine the associations of BRAFV600E and RAS mutations with clinicopathologic characteristics. Results: Of 172 PTC patients, BRAFV600E mutation was observed in 37.8% of the patients and RAS mutations were found in 21.5%. One patient harbored BRAFK601E mutation. There was a significant association of BRAFV600E with a high-stage (p = 0.033, OR: 3.279; 95% CI: 1.048-10.259), tall-cell variants (p <0.001, OR: 41.143; 95% CI: 11.979- 141.308), non-encapsulated (p = 0.001, OR: 4.176; 95% CI: 2.008-8.685), lymphovascular invasion (p = 0.043, OR: 1.912; 95% CI: 1.018- 3.592), extrathyroidal extension (p = <0.001, OR: 3.983; 95% CI: 1.970-8.054), and lymph node metastasis (p = 0.009, OR: 2.301; 95% CI: 1.224-4.326). Follicular variant (p = 0.001, OR: 7.011; 95% CI: 2.690-18.268), encapsulated (p = 0.017, OR: 2.433; 95% CI: 1.161-5.100), and absent of extrathyroidal extension (p = 0.033, OR: 2.890; 95% CI: 1.052-7.940) were associated with RAS mutations. Conclusion: A significant association between BRAFV600E mutation and high clinical stage, tall-cell variants, non- encapsulated morphology, lymphovascular invasion, extrathyroidal extension, and lymph node metastasis in PTC was observed. RAS mutations were associated with the follicular variant, encapsulated tumor, and no extrathyroidal extension. HRAS-mutated PTC frequently exhibited tumor multifocality. Keywords: papillary thyroid carcinoma, BRAFV600E, BRAFK601E, RAS, clinicopathological characteristics

Endometriosis is a common, benign, oestrogen-dependent, chronic gynaecological disorder associated with pelvic pain and infertility. Increasing of P2X3 receptors induced sensitization of pain in endometriosis patients. Epigenetic mechanism such as DNA methylation could lead to alteration of gene expression. The aim of this study was to analyse DNA methylation of P2X3 receptor gene promoter in peritoneal endometriotic tissue from 9 patients compared to endometrial tissue from 9 without endometriosis women as control. The DNA from samples was isolated and with sodium bisulfite converted. We used Methyl Specific PCR (MSP) method to amplify the DNA and then running MSP product in gel electrophoresis. The band intensity of samples were measured by ImageJ software. Statistical analysis was significant correlation between pain and endometriosis (p=0.000). DNA methylation of P2X3 receptor gene promoter among peritoneal endometriotic tissue in women endometriosis and endometrial tissue woman without endometriosis were 100% unmethylated and there was no significant differences (p=0.287), although density of band unmethylated peritoneum endometriosis group was higher than control group. This study was suggesting that DNA methylation of P2X3 receptor gene promoter might be a potential biomarker to early diagnostic of endometriosis without invasive procedure in endometriosis patienst especially with pain symptoms.