Asmarinah Asmarinah

Context: Pediatric diarrhea is often associated with dysbiosis and pathogenic microorganisms, necessitating further molecular investigation. Differential gene expression (DEG) analysis offers potential insights into biomarkers for the molecular pathogenic mechanisms of diarrhea and antibiotic resistance in children. Aims: To identify differentially expressed genes (DEGs) associated with pathogenicity and antimicrobial resistance by analyzing publicly available transcriptomic two datasets (GSE69529 and GSE54070) in children with diarrhea. Methods: DEG analysis was performed using GEO2R on GSE69529 and GSE54070 datasets. Multiple machine learning models (SVM, RF, NN, LR, XGBoost) were applied via Orange 3.10.2 for cross-validation. Cytoscape and databases such as STRINGdb, IntAct, and CTD were utilized for protein interaction and upstream regulatory analysis. To confirm ARGs, five fecal cohort samples were collected from the primary public health in Jakarta, Indonesia, and analysed using the Vitek-2 compact system. Results: Key DEGs included RYK, CREBL2, and ST14, associated with intestinal integrity, inflammation, and immune regulation. Seven resistance genes were commonly identified in different age groups. Pathogen mapping revealed Escherichia coli, Pseudomonas aeruginosa, Salmonella enterica, Staphylococcus aureus, and Salmonella typhimurium as dominant. Resistance-related genes such as mexA/acrA, arnA, tolC, and mexB/acrB were implicated in β-lactam and CAMP resistance pathways. Resistance genes common to different age groups included tetO, tetQ, and SUL2. To validate those findings, Support Vector Machines and Neural Networks exhibited the best classification performance for machine learning models. Conclusions: Several genes identified among DEGs related to pathogenicity and antimicrobial resistance markers may serve as potential biomarkers for developing diagnostic and therapeutic targets for pediatric diarrhea.

Menstrual blood flow is reversed through the fallopian tubes during the menstrual process and implants outside the uterus, which is the theory of pathogenesis in endometriosis sufferers. This study aims to analyze the level of DNA methylation and mRNA expression of the Nerve Growth Factor (NGF) gene in menstrual blood in endometriosis patients and analyze the correlation. The study was conducted among 20 women in each group with and without Endometriosis (controls) of reproductive age. Filter paper pads were used to collect the menstrual blood sample, while the eutopic endometrium was collected by biopsy. Following that, NGF DNA methylation analysis of menstrual blood was performed using Methylation-Specific PCR (MS-PCR) and Pyrosequencing. Additionally, the study of NGF mRNA expression was conducted by RT-qPCR. Data analysis using independent T-test or Mann-Whitney, SPSS 22, and p<0.05 was considered statistically significant. We found that the DNA of NGF in the menstrual blood of endometriosis patients was hypomethylated; conversely, its mRNA expression was increased compared to that of women without Endometriosis. There was a statistically significant difference in the level of NGF DNA methylation and the relative mRNA expression level of the NGF gene in the menstrual blood of endometriosis patients compared to women without Endometriosis (p0,05). Furthermore, the increased expression of NGF mRNA in the menstrual blood of women with Endometriosis is not driven by a decrease in DNA methylation. However, hypomethylation and an increase in mRNA expression of the NGF gene in menstrual blood have the potential to be a biomarker for the early diagnosis of non-invasive Endometriosis.

Introduction: 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. Methods: 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. Results: The analysis identified both globally hypermethylated and hypomethylated NPC samples. Key tumour suppressor genes, such as PRKCB, PLCB3, ITGB3, EPHA2, PLCE1, PRKCD, CDKN2A, CDKN2B, RPS6KA2, ERBB4, LRRC4, AKT1, PPP2R5C, and STK11 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. Discussion: 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.

Background: 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 ( CHD5 ) and histone modifications histone 4 lys-12 acetylation ( H4K12ac ) and histone 3 lys-9 trimethylation ( H3K9me3 ) in human testicular biopsies, based on maturation arrest type. Materials and Methods: 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. Results: We found three types of maturation arrest, including Sertoli cell only (n=5), spermatocyte arrest (n=4), and spermatid arrest (n=9). CHD5 was positive in spermatogonia and round spermatids but absent in spermatocytes. The mean grey value (MGV) of CHD5 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 H3K9me3 and H4K12ac (P<0.001), both histone modifications were found in all observed spermatogenic cells. Conclusion: The expressions of CHD5 , H3K9me3 , and H4K12ac 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 CHD5 in human spermatogonia cells, which requires further study for elaboration.

PCOS's origin and mechanism are still unknown. Epigenetics has been linked to PCOS in an increasing number of studies in recent years. The most extensively researched epigenetic alteration is DNA methylation. During organismal development, DNA methylation can control gene expression by altering transcription factor binding. The alterations in DNA methylation are directly associated with follicular development in PCOS. Studies show that increased levels of pregnenolone and estrogen in the follicular fluid may affect follicle formation in PCOS patients; the process is largely associated with the expression of HSD17B1. There is evidence to suggest that these levels may have an impact on follicle development in PCOS patients. The mechanism for this effect is partially linked to HSD17B1 expression, which catalyzes the final step in estrogen biosynthesis, 17β-estradiol (E2). We speculated that defects in DNA methylation increase gene dysregulation, resulting in decreased mRNA expression of HSD17B1, which eventually generates insufficient E2 in PCOS patients. The objective of this study is to investigate DNA methylation, mRNA expression, and E2 level in PCOS patients and healthy women groups; the correlation between DNA methylation and mRNA expression in PCOS patients; and the correlation between mRNA expression and E2 serum level in PCOS patients. We provided informed consent to participants; we studied 60 female patients, 30 PCOS patients and 30 healthy women served as the control group, we used the Methyl-Specific PCR (MSP) method and quantitative PCR (qPCR) for DNA methylation and mRNA expression analyses, respectively; and we examined E2 serum levels and hormonal levels. The methylation of the HSD17B1 gene in PCOS women was 42.64% and a healthy group showed 53.80% (p = 0.160). The two groups' differences were not statistically significant. The relative expression value of the HSD17B1 gene was 0.70-fold lower compared with the healthy women (p = 0.003) group. Significant variances were between the two groups. The average E2 serum level in the PCOS group is 25.78 pg/mL and in the healthy women group, it is 36.74 pg/mL. Compared to the group of healthy women, the PCOS group had a decreased E2 serum level. The correlation of DNA methylation level versus mRNA expression in PCOS patients is not significant. (p = 0.076). A significant negative association has been seen between the mRNA. There is a significant negative correlation between the mRNA expression of the HSD17B1 gene and serum E2 levels. (p = 0.020). "The more down-regulated mRNA expression of the HSD17B1 gene, the lower serum E2 levels." The integrated analysis in this study was hypomethylated DNA and down-regulated mRNA expression of HSD17B1 genes. The hypomethylated DNA was not involved in down-regulating mRNA expression. Therefore, down-regulated mRNA expression of the HSD17B1 gene in PCOS patients can cause lower E2 levels in PCOS, preventing cell growth and potentially contributing to the cause of PCOS pathogenesis.

Studies show Human Milk Oligosaccharides (HMOs) influence on infant growth were conflicted. This study aims to determine the relationship between HMO profiles and weight growth indicators of infants ages 0-4 months in Indonesia. A prospective longitudinal study was conducted among 120 mother-infant pairs aged 0 – 4 months from the hospital and Public Health Center in Jakarta between August 2021 – May 2022. The gene analysis for the Secretor and Lewis status of the mother were performed by using targeted Next Generation Sequencing (NGS) and Sanger at baseline. The HMO profiles (2'FL, LNFP I, LNT, LNnT, 3'SL, and 6'SL), breast milk calories, and fat were examined at 0, 2, and 4 months. Weight for age z-score, weight for length z-score, infection episode, and mother's body mass index were examined every month. Data were analyzed using Pearson or Spearman correlation test (correlation coefficient), general linear model for repeated measures ANOVA test and Friedman test (mean difference between and within groups, respectively) and logistic regression unadjusted OR (association between dependent and independent variables), with a p-value <0.05 considered statistically significant. Infants' weight velocities were higher among high LNT and 3'SL levels in the second month, and in high 2'FL and LNFP I mothers in the fourth month. HMO profile (2’FL, LNFP I, and LNT) of lactating mothers have a positive relationship with weight growth indicators, and innovative interventions to enhance HMO concentration among mothers should be considered as one of the ways to improve infant growth.

The Cancer Genome Atlas (TCGA) has classified papillary thyroid carcinoma (PTC) into indolent RAS-like and aggressive BRAF-like based on its distinct driver gene mutations. This retrospective study aimed to assess clinicopathology and pERK1/2 expression variations between BRAF-like and RAS-like PTCs and establish predictive models for BRAFV600E and RAS-mutated PTCs. A total of 222 PTCs underwent immunohistochemistry staining to assess pERK1/2 expression and Sanger sequencing to analyze the BRAF and RAS genes. Multivariate logistic regression was employed to develop prediction models. Independent predictors of the BRAFV600E mutation include a nuclear score of 3, the absence of capsules, an aggressive histology subtype, and pERK1/2 levels exceeding 10% (X² = 0.128, p > 0.05, AUC = 0.734, p < 0.001). The RAS mutation predictive model includes follicular histology subtype and pERK1/2 expression > 10% (X² = 0.174, p > 0.05, AUC = 0.8, p < 0.001). We propose using the prediction model concurrently with four potential combination group outcomes. PTC cases included in a combination of the low-BRAFV600E-scoring group and high-RAS-scoring group are categorized as RAS-like (adjOR = 4.857, p = 0.01, 95% CI = 1.470–16.049). PTCs included in a combination of the high-BRAFV600E-scoring group and low-RAS-scoring group are categorized as BRAF-like PTCs (adjOR = 3.091, p = 0.001, 95% CI = 1.594–5.995). The different prediction models indicate variations in biological behavior between BRAF-like and RAS-like PTCs.

The Cancer Genome Atlas (TCGA) has classified papillary thyroid carcinoma (PTC) into indolent RAS-like and aggressive BRAF-like based on its distinct driver gene mutations. This study aimed to assess clinicopathology and pERK1/2 expression variations between BRAF-like and RAS-like PTCs and establish predictive models for BRAFV600E and RAS-mutated PTCs. A total of 222 PTCs underwent immunohistochemistry staining to assess pERK1/2 expression and Sanger sequencing to analyze the BRAF and RAS genes. Multivariate logistic regression was employed to develop prediction model. Independent predictors for the BRAFV600E mutation include a nuclear score of 3, the absence of capsules, an aggressive histology variant, and pERK1/2 levels exceeding 10% (X2=0.128, P>0.05, AUC=0.734, P10% (X2=0.174, P>0.05, AUC=0.8, P<0.001). We proposed using the prediction model concurrently with four potential combination group outcomes. PTC cases included in combination of low BRAFV600E-scoring group and high RAS-scoring group are categorized as RAS-like (adjOR=4.857, P=0.01, 95% CI=1.470-16.049). PTCs included in combination of high BRAFV600E-scoring group and low RAS-scoring group are categorized as BRAF-like PTCs (adjOR=3.091, P=0.001, 95% CI=1.594-5.995). The different prediction models indicate variations in biological behaviour between BRAF-like and RAS-like PTCs, necessitating adjustments in treatment approaches.

Endometriosis is gynecology disease that still needs advance knowledge to develop best treatment for enhancing the best quality of patient life. It is characterized by forming the endometrium tissue outside the uterus and happened approximately in 5-10% of reproductive women. Endometriosis with poor prognosis can be a high risk of endometrium cancer, ovarian cancer and results in infertility. A deep attempt to reach the knowledge of clear molecular etiology of endometriosis is needed. Here, there are three molecular mechanism dysfunction that occurs on endometriosis; (1) immune system dysfunction, (2) disturbance in apoptosis signal, (3) and oxidative stress elevation. Therefore, the determination of molecular pathogenesis of endometriosis will be useful in developing of diagnostic and therapeutic methods.

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.