The Structural Annotations of The Mir-122 Non-Coding RNA from The Tilapia Fish (Oreochromis niloticus)

Tilapia (Oreochromis niloticus) is an important fisheries commodity. Scientific efforts have been done to increase its quality. One of them is staging a premium diet such as a fat-enriched diet. The transcriptomics approach is able to provide the signatures of the diet outcomes by observing the micro(mi)RNA signature in transcriptional regulation. Hence, it was found that the availability of mir-122 is essential in the regulation of a high-fat diet in tilapia. However, this transcriptomics signature is lacking structural annotations and the complete interaction annotations with its silencing(si)RNA. RNAcentral website was navigated for the latest annotation of mir-122 from tilapia and other species as a comparison. MEGA X was employed to comprehend the miRNA evolutionary repertoire. The RNA secondary structure prediction tools from the Vienna RNA package and the RNA tertiary structure prediction tools from simRNA and modeRNA are secured with default parameters. The HNADOCK tools were leveraged to observe the interaction between mir-122 and its siRNA. The post-processing was conducted with the Chimera visualization tool. The secondary and tertiary structure of the mir-122 and its siRNA could be elucidated, docked, and visualized. In this end, further effort to develop a comprehensive molecular breeding tool could be secured with the structural annotation information

BIOMARKER POTENTIAL OF IQ-DOMAIN GTPASE-ACTIVATING PROTEINS FAMILY PROTEIN IN PANCREATIC CANCER: A MINI REVIEW

Objectives: Our present study was done to understand molecular regulatory mechanisms of IQGAP proteins and their potentials as biomarker in pancreatic cancer.Methods: In this review, relevant studies were obtained by assessing the PubMed database using the combination of words that included IQGAP†and pancreatic cancerâ€.Results: There is an increasing evidence showing that the expression of IQGAP1 and IQGAP3 is positively correlated with tumorigenesis; however, IQGAP2 might play a role to suppress tumor progression.Conclusion: IQGAP proteins might have potentials as predictive and prognostic biomarker for human pancreatic cancer

PENERAPAN PENDEKATAN MACHINE LEARNING PADA PENGEMBANGAN BASIS DATA HERBAL SEBAGAI SUMBER INFORMASI KANDIDAT OBAT KANKER

Cancer is still an epidemiological disease in Indonesia. Drug development against cancer still relies to pharmacological laboratories and natural chemicals, which could have side effects. Cancer drug development has entered the stage of molecular biology, where the interaction of ligand chemical structure with receptor protein can be studied with high accuracy. Various chemical compounds, ranging from synthetic, semi-synthetic, to natural materials, developed for the purpose to fight one of the most dangerous diseases. In the context of the development of herbal-based drugs, there has been found heaps of natural compounds, curated and annotated, in various databases belonging to China, Taiwan, Indonesia, Japan, and several other countries. However, problems arise when choosing the best bioactive compounds to develop against cancer. Complexity arises because the metabolic pathway of cancer is very diverse, depending on the type and phase of cancer. Therefore, in this systematic review, we developed a machine learning approach to screen for these bioactive compounds, then took the best candidates for molecular simulation operations that would be tested for validity in wet experiments. Thus, the automation of the candidate drug development process for cancer could be achieved with great significance. It is known that the most effective and efficient machine learning method was Naïve Bayes, but the best in processing large amounts of compound data was classfier SVM. The future of complex bioactive compounds data could be secured by employing deep learning method. Keywords: machine learning, drug development, natural material compounds, metabolic pathways, cancer

IN SILICO STUDY OF MIRNA-REGULATED IQ MOTIF-CONTAINING GTPASE-ACTIVATING PROTEIN FAMILY IN LIVER CANCER

Objective: The aim of this paper is to identify the list of microRNA (miRNA) which can regulate the aberrant expression of IQGAP in liver cancer formation. The aberrant expression of IQ motif-containing GTPase-activating protein (IQGAP) family which consists of IQGAP1, IQGAP2, and IQGAP3 has been linked to carcinogenesis in human cancers. The reciprocal expression of IQGAP family in human cancer has been studied to act as oncogenes or tumor suppressor genes. A growing number of studies suggest that upregulated or downregulated expression of IQGAP family triggers cancer development.Methods: A correlation study was performed to construct a pathway to inhibit or activate IQGAP family between miRNAs and IQGAPs. A pre-processing step was conducted to download, filter and process the dataset from TCGA. It yields miRNA and IQGAP gene expression matrix. Then, correlation computation was computed using MATLAB. Moreover, this study linked the results to the MiRTarBase to validate the prediction result with the wet lab experimental result.Results: This study identified significantly inversely correlation in 51 miRNAs-IQGAP1, 169 miRNAs-IQGAP2, and 33 miRNAs-IQGAP3, respectively, which may potentially play a role in a liver cancer formation. Some of the results also can be found in miRTarBase. It supports the precision of those miRNA and IQGAP interaction between dry lab and wet lab study. IQGAP1 and IQGAP2 mostly has been identified as an oncogene in cancer but IQGAP2 has been discovered as tumor suppressor gene. The list of miRNA in the result of this study can become a potential therapy to target the aberrant expression of IQGAP family.Conclusion: miRNA function is known as an oncogene or tumor suppressor gene in cancer development. Therefore, it can be one of the important molecular biology which may target the aberrant expression of IQGAP in liver cancer

Epigenetic analysis by integrating DNA methylation, miRNA and microarray data in glioblastoma, ovarian and non-small cell lung cancer

[[abstract]]Epigenetic regulation has been linked to the initiation and progression of cancer. Aberrant expression of microRNAs (miRNAs) is one such mechanism that can activate or silence oncogenes (OCG) and tumor suppressor genes (TSG) in cells. A growing number of studies suggest that miRNA expression can be regulated by methylation modification, thus triggering cancer development. However, there is no comprehensive in silico study concerning miRNA regulation by direct DNA methylation in cancer. This dissertation consists of three publications which constructed epigenetically regulated miRNA pathways. In the first study, this research integrated gene expression and methylation sites expression in glioblastoma (GBM) and ovarian cancer (OSC) with microRNA (miRNA), CpG island, target gene and cancer gene to establish epigenetic-regulated pathways in cancer formation. Next, the database “MethmiRbase”, a database of DNA methylation and miRNA expression in human cancer were set up. For a preliminary study, Non-small cell lung cancer (NSCLC) and ovarian cancer were selected. MethmiRbase made use of the meta-analysis (MA) method by using the Spearman correlation coefficient to identify significant anti-correlate DNA methylation and miRNA expression events (hypermethylation status with low expression miRNA or hypomethylation status with high expression miRNA) to construct epigenetic-mediated miRNA target gene pathways. Furthermore, our study proposed a systematic strategy to construct highly confident epigenetic-regulated miRNA pathways for OSC. The Spearman rank correlation coefficient (SRCC) was used to quantify the correlation between the CpG DNA methylation level and miRNA expression level. Meta-analysis was performed to reduce the effects of biological heterogeneity among different batches. miRNA-target interactions were also inferred by computing SRCC and meta-analysis to assess the correlation between miRNA expression and cancer-associated gene expression and the interactions were further validated by a query against the miRTarBase database. In the first publication, this study constructed several epigenetic-regulated miRNAs events which may potentially cause GBM and OSC. A web-based interface has been set up for the query at http://ppi.bioinfo.asia.edu.tw/ER_microRNA. In the second publication, this study presented MethmiRbase, a database that made use of meta-analysis to identify potential epigenetic-regulated miRNAs for three human cancers, i.e. lung adenocarcinoma, lung squamous carcinoma and ovarian cancers. This research also included experimentally verified cancer-associated miRNA target genes in MethmiRbase (http://ppi.bioinfo.asia.edu.tw/MethmiRbase). In the third publication, a total of 26 potential epigenetic-regulated miRNA genes that can target OCGs or TSGs in OSC were found to show biological relevance between DNA methylation and miRNA gene expression. The inclusion of direct DNA methylated miRNA events may offer another layer of explanation that along with genetics can give a better understanding of the carcinogenesis process. Keywords: Epigenetic, microRNA, DNA methylation, CpG islands, Ovarian cancer, Meta-analysis

The Association of NSAIDs Statin Use And The Development of Urinary Tract Cancers: A Population-Based Case-Control Study In Taiwan

[[abstract]]The association between analgesics drugs and cancer is a topic that still need many contribution since many results gave a different effect of Analgesics toward cancer in worldwide. This research try to explore the association between Non Steroidal Anti inflammatory Drugs (NSAIDs), Statin with Urinary tract cancer by conducting case control study population in Taiwan. Based on data in National Health Insurance Reimbursement Database (NHIRD) in Taiwan. We created relational database to see the association of using NSAIDs and Statin with development of urinary tract cancer by using SAS? (statistical software version 9.2), and then calculate odd ratio and 95% confidence interval. The study confirmed the Association between having history of using NSAIDs and Statin in regular time can significantly influence the development of urinary tract cancers. Beside drugs impact, urinary tract cancer also had a significant association with being male, older age and having history of comorbidities diseases, e.g. hypertension, diabetic, uremia, spinal cord injury, and rheumatoid arthritis

Immunoinformatics Analysis of SARS-CoV-2 ORF1ab Polyproteins to Identify Promiscuous and Highly Conserved T-Cell Epitopes to Formulate Vaccine for Indonesia and the World Population

SARS-CoV-2 and its variants caused the COVID-19 pandemic. Vaccines that target conserved regions of SARS-CoV-2 and stimulate protective T-cell responses are important for reducing symptoms and limiting the infection. Seven cytotoxic (CTL) and five helper T-cells (HTL) epitopes from ORF1ab were identified using NetCTLpan and NetMHCIIpan algorithms, respectively. These epitopes were generated from ORF1ab regions that are evolutionary stable as reflected by zero Shannon’s entropy and are presented by 56 human leukocyte antigen (HLA) Class I and 22 HLA Class II, ensuring good coverage for the Indonesian and world population. Having fulfilled other criteria such as immunogenicity, IFNγ inducing ability, and non-homology to human and microbiome peptides, the epitopes were assembled into a vaccine construct (VC) together with β-defensin as adjuvant and appropriate linkers. The VC was shown to have good physicochemical characteristics and capability of inducing CTL as well as HTL responses, which stem from the engagement of the vaccine with toll-like receptor 4 (TLR4) as revealed by docking simulations. The most promiscuous peptide 899WSMATYYLF907 was shown via docking simulation to interact well with HLA-A*24:07, the most predominant allele in Indonesia. The data presented here will contribute to the in vitro study of T-cell epitope mapping and vaccine design in Indonesia