miRNA-21 as High Potential Prostate Cancer Biomarker in Prostate Cancer Patients in Indonesia.

OBJECTIVE: This study aimed to explore the diagnostic performance of miRNA-21 to differentiate between Prostate Cancer (PCa) and Benign Prostatic Hyperplasia (BPH) patients in Indonesia. METHODS: Urine samples were collected from each PCa and BPH patient. miRNA-21 relative expression against the reference gene was analyzed and compared between the two. miRNA expression was then analyzed using the comparative quantification method to find the fold change. miR-21 validity in identifying PCa patients was performed by quantifying the sensitivity and specificity using samples in this study. RESULT: The results of this study indicated that miRNA-21 relative expression against miRNA-16 in PCa and BPH showed 12.95 differences in fold change. Moreover, using prostate biopsy as the gold standard to differentiate PCa and BPH, miRNA-21 Cq expression has 100% sensitivity and 75% specificity in differentiating the two. CONCLUSION: miRNA-21 relative expression can be used to discriminate PCa from BPH by using a urine sample. Furthermore, the expression of miR-21 has higher sensitivity than PSA; therefore, miR-21 has a high potential to be analyzed and developed further for clinical diagnosis of prostate cancer.

Corrigendum to "The potential of miRNA-based therapeutics in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: A review" [J. Pharma. Anal. 11 (2021) 265-271].

[This corrects the article DOI: 10.1016/j.jpha.2021.03.003.].

Circulation microRNA expression profiles in patients with complete responses to chemoradiotherapy in nasopharyngeal carcinoma.

Background: Nasopharyngeal carcinoma (NPC) is endemic cancer in Southeast Asia with a relatively poor prognosis. Chemoradiotherapy is a primary treatment that advantages certain patients, particularly in the early stages. New predictive and prognostic biomarkers are required to guide and select the best treatment. Aims: To evaluate the circulation expression profile of microRNAs (miRNAs) associated with responses to chemoradiotherapy in nasopharyngeal carcinoma. Methods: Peripheral blood from 17 patients was collected before and after chemotherapy and radiotherapy. Differential expression circulating miRNAs were analyzed using microRNA Cancer Panels and were compared among patients with complete responses. Differential expression analysis using GenEx 7 Multid, statistic represented by GraphPad Prism 9. Alterations mechanism signaling pathways and biological function using IPA (Ingenuity Pathways Analysis). Results: Using microRNAs Cancer Plate consisting of 116 miRNAs, we identified ten circulating miRNAs that were differentially expressed in NPC patients after chemoradiotherapy. Unsupervised clustering and confirmation using qRT-PCR showed that miR-483-5p, miR-584-5p, miR-122-5p, miR-7-5p, miR-150-5p were overexpressed and miRNA are miR-421, miR-133a-3p, miR-18a-5p, miR-106b-3p, miR-339-5p were significantly downregulated after chemoradiotherapy (p < 0.0001). In addition, ROC analysis through AUC (Area Under Curve) with 99% confidence interval (CI) p value < 0.0001. Gene enrichment analysis of microRNAs and the targeted proteins revealed that the main involved pathways for chemoradiotherapy in NPC were cell death and survival signaling pathways. Conclusion: qPCR profiling in circulating blood compared before and after chemoradiotherapy in nasopharyngeal carcinoma can identify pathways involved in treatment responses. miR-483-5p, miR-584-5p, miR-122-5p, miR-7-5p, miR-150-5p, miR-421, miR-133a-3p, miR-18a-5p, miR-106b-3p, miR-339-5p are differentially regulated after chemoradiotherapy in NPC.

Designing multi-epitope based peptide vaccine candidates against SARS-CoV-2 using immunoinformatics approach.

Introduction: The current incidence of the novel coronavirus disease has shown only small reductions of cases and has become a major public health challenge. Development of effective vaccines against the virus is still being encouraged such as multi-epitope vaccines designed from the components of SARS-CoV-2 including its spike, nucleocapsid and ORF1a proteins. Since the addition of adjuvants including HABA protein and L7/L12 ribosomal are considered helpful to increase the effectiveness of the designed vaccine, we proposed to design multiepitope vaccines by two different adjuvants. Methods: We used the IEDB server to predict BCL and TCL epitopes that were characterized using online tools including VaxiJen, AllPred and IL-10 Prediction. The selected epitopes were further constructed into multiepitope vaccines. We also added two different adjuvants to the vaccine components in order to increase the effectiveness of the vaccines. The 3D-structured vaccines were built using trRosetta. They were further docked with different Toll-like-receptors (TLR 3, 4 and 8) and the entry receptor of SARS-CoV-2, ACE2 using ClusPro, PatchDock and refined by FireDock. All structures were visualized by USCF Chimera and PyMOL. Results: In this study, we succeeded in designing two different candidate vaccines by the addition of HABA protein and L7/L12 ribosomal as adjuvants. The two vaccines were almost equally good in terms of their physicochemical properties and characteristics. Likewise, their strong interactions with TLR3 4, 8 and ACE2 show the lowest energy level of both was estimated at more than -1,000. Interactions of vaccines with ACE2 and TLRs are essential for activation of immune responses and production of antibodies. Conclusion: The two designed and constructed multiepitope vaccine have good characteristics and may have the potential to activate humoral and cellular immune responses against SARS-CoV-2. Further research is worth considering to confirm the findings of this study.

Chitosan nanoparticle-mediated effect of antimiRNA-324-5p on decreasing the ovarian cancer cell proliferation by regulation of GLI1 expression.

Introduction: MicroRNAs (miRNAs) are short-sequence RNAs that regulate gene expression by targeting messenger RNAs (mRNAs). Recent studies reveal that miRNA-324-5p plays an important role in worsening the ovarian cancer prognosis when the expression is very high. This study aimed to develop a miRNA targeted therapy by targeting the miRNA-324-5p function as a miRNA-324-5p inhibitor. Methods: Chitosan nanoparticles were used for antimiRNA-324-5p delivery into SKOV3 cell lines formulated by ionic gelation method. Antiproliferative effect of CS-NPs-antimiRNA was assessed by the MTT Assay. A mechanism study assessed the anticancer effect of the formula. In silico analysis used miRTar.Human and StarmiRDB combined with Genecard to predict the target genes of antimiR. Hawkdock web server was used to analyze protein-protein interactions that were further validated by quantitative polymerase chain reaction (qPCR). Results: The results of qPCR analysis showed endogenous miRNA-324-5p decreased after 24-hour transfection of antagonist miRNA. Furthermore, the MTT assay results showed that antimiRNA was able to inhibit SKOV3 cell proliferation (80 nM 68.13%, P < 0.05). In silico analysis found miRNA-324-5p can regulate MEN1 and indirectly repress Gli1 mRNA. Validation results confirmed antimiR can decrease GLI1 mRNA expression. Conclusion: Our results showed antimiRNA-324-5p can act as a microRNA-based therapy to inhibit ovarian cancer proliferation by the reduction of GLI1 expression.

Human Papillomavirus Type 16 L2 Gene Sequence Variation Analysis in Indonesian Cervical Cancer Specimens.

BACKGROUND: Human papillomavirus type 16 (HPV16) is the most prevalent etiology of cervical cancer in Indonesian women. The L2 minor capsid protein has considerable potential as a broad-protective antigen target of the cervical cancer vaccine strategies, yet the data on L2 gene variation is still minimal. In this research, we determined the variations of the HPV16 L2 gene sequences in Indonesian cervical cancer specimens. METHODS: We cross-sectionally observed 23 DNA isolates of HPV16 positive cervical cancer specimens stored in the laboratory of the Center for Diagnostic and Research on Infectious Diseases (PDRPI Lab), Faculty of Medicine, Universitas Andalas, Padang, Indonesia. We detected and amplified the HPV16 L2 gene sequences in the samples, followed by sequencing, DNA alignment, single nucleotide polymorphisms (SNPs) analysis, and phylogenetic tree reconstruction. RESULTS: As many as 35 SNPs were found, consist of 18 synonymous SNPs (sSNPs) and 17 non-synonymous SNPs (nsSNPs). Amino acid variations were mostly detected at S269P (100%) and L330F (43.48%) with no variation in the immuno-protective region near L2 N-terminus. A total of 5 HPV16 phylogenetic sub-lineages were found closely related to A1 (n=5), A2 (n=12), A3 (n=2), A4 (n=3), and C (n=1). CONCLUSION: The variations of HPV16 L2 gene sequences are mainly located in the central region of the L2 sequences, and the cross-protective region near the L2 N-terminus is remarkably conserved. This study should enhance the information about HPV16 L2 gene variation in Indonesia.

Potential plasma biomarkers: miRNA-29c, miRNA-21, and miRNA-155 in clinical progression of Hepatocellular Carcinoma patients.

This study evaluated differences in the clinical appearance of patients with hepatocellular carcinoma (HCC) based on plasma level and regulation of microRNAs (miRNA-29c, miRNA-21, and miRNA-155). The observational-analytical study with a cross-sectional design was conducted on 36 HCC patients and 36 healthy controls. The blood samples were collected from 2 Province Hospitals (Dr. Sardjito Hospital and Prof. Dr. Margono Soekarjo Hospital) for HCC and the Blood Bank Donor of the Indonesian Red Cross for 36 healthy controls. These blood samples were treated as follows: plasma isolation, RNA isolation, cDNA synthesis, quantification by qRT-PCR using a sequence-specific forward primer, and normalization of miRNA using housekeeping-stably miRNA-16. There were only 27 HCC patients with complete clinical variables (neutrophil to lymphocyte ratio (NLR), platelet to lymphocyte ratio (PLR), platelet count, albumin, C-reactive protein (CRP), and cholinesterase (ChE)) that were able to analyses for regulation miRNAs based on its fold change expression miRNA target. All 27 HCC subjects were follow-up until 3-years of monitoring for their overall survival. The miRNA plasma expression was analyzed by Bio-Rad CFX 96 Manager software to determine the cycle of quantification, followed by the calculation of expression levels using Livak's methods. Data were analyzed using STATA 11.0, with a significant value of p<0.05. The miRNAs expression of HCC subjects were lower than that healthy control subjects in miRNA-29c (down-regulation 1.83-fold), higher than that healthy control subjects in miRNA 21 and miRNA-155 (up-regulation, 1.74-fold; 1.55-fold) respectively. NLR, CRP, ChE, and platelet count showed a significant difference in miRNA-29c regulation, though neutrophil count showed a significant difference in miRNA-21 and miRNA-155 regulation (p<0.05). Conclusion: Plasma biomarkers: miRNA-21 and miRNA-155 might be potential biomarkers as onco-miR in HCC subjects, while miRNA-29c might act as a tumor suppressor. Significant evidence was identified with clinical progression based on the regulation of miRNAs, which was consistent with miRNA -29c.

The potential of miRNA-based therapeutics in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: A review.

Since the World Health Organization (WHO) declared COVID-19, the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as a pandemic in March 2020, and more than 117 million people worldwide have been confirmed to have been infected. Scientists, medical professionals, and other stakeholders are racing against time to find and develop effective medicines for COVID-19. However, no drug with high efficacy to treat SARS-CoV-2 infection has been approved. With the increasing popularity of gene therapy, scientists have explored the utilization of small RNAs such as microRNAs (miRNAs) as therapeutics. miRNAs are non-coding RNAs with high affinity for the 3'-UTRs of targeted messenger RNAs (mRNAs). Interactions between host cells and viral genomes may induce the upregulation or downregulation of various miRNAs. Therefore, understanding the expression patterns of these miRNAs and their functions will provide insights into potential miRNA-based therapies. This review systematically summarizes the potential targets of miRNA-based therapies for SARS-CoV-2 infection and examines the viability of possible transfection methods.

Chemotherapy Negates the Effect of SDF1 mRNA to Distant Metastasis and Poor Overall Survival in Breast Cancer Patients.

OBJECTIVE: Investigate the effect of SDF1a, nuclear, and cytoplasmic CXCR4 breast cancer tissue on metastasis and overall survival in patients with complete-chemotherapy and no-chemotherapy. METHODS: Cohort ambidirectional design was employed with survival analysis that followed the patient's diagnosis until obtaining the outcome, distant metastasis, or death. We analyzed samples in three groups (all-patient, no-chemotherapy, and complete-chemotherapy groups).  Breast cancer cell nuclear and cytoplasm expressions of CXCR4 protein were examined using immunohistochemistry. Amplification of mRNA SDF1a of breast cancer tissue was examined using rtPCR on 131 samples from the same initial paraffin block. RESULTS: In the distant metastasis and Overall Survival (OS) analysis, there was no correlation between cytoplasmic and nuclear CXCR4 in all-patient, no-chemotherapy, and complete-chemotherapy groups. SDF1a was significantly correlated to shorter distant metastasis and poor OS in the all-patient (p=0.004 and p=0.04, respectively) and no-chemotherapy group (p=0.008 and p=0.026, respectively). However, in the complete-chemotherapy group, SDF1a was not correlated to either metastasis (p=0.527) or OS (p=0.993), advanced stage demonstrated a strong association on shorter distant metastatic in no-chemotherapy (p=0.021) and complete-chemotherapy group (p=0.004) and also poor OS in both groups (p=0.006 and p=0.002, respectively). The hormone receptor showed a protective effect on the no-chemotherapy group's OS (p= 0.019). Meanwhile, not undergoing chemotherapy was associated with poor OS in the all-patient group (p= 0.011). CONCLUSION: SDF1a mRNA amplification has a significant correlation with the occurrence of metastasis and OS in all-patient and no-chemotherapy group. Undergoing chemotherapy negates the effect of SDF1a for distant metastasis and OS.

The Potential of hsa-mir-106b-5p as Liquid Biomarker in Prostate Cancer Patients in Indonesia.

PURPOSE: This study aims to explore the potential of hsa-mir-106b-5p as a new liquid biomarker for prostate cancer sufferers in Indonesia. METHODS: Analysis of hsa-mir-106b-5p expression of two tissue samples from BPH patients and two PCa patients used NanoString nCounter Expression Assay then validated by qRT-PCR using 10 patient urine samples for prostate cancer and BPH. Furthermore, analysis of the role of hsa-mir-106b-5p in prostate cancer was carried out bioinformatically. RESULTS: The results of this study indicated that the expression of hsa-mir-106b-5p in prostate cancer tissue was 1.23 times higher than that of BPH and urine of Indonesian patients (1.72 times). Moreover, this miRNA was upregulated in prostate cancer cells compared to normal cells 1.37 times. The hsa-mir-106b-5p appeared to be involved in the development of prostate cancer through the binding of genes involved in endoplasmic reticulum stress pathways and tumor suppressor genes. CONCLUSION: hsa-mir-106b-5p could modulate prostate cancer by interfering with the endoplasmic reticulum stress repair pathways and decreasing the expression of tumor suppressor genes involved in many biological processes. These updates our understanding of the role of hsa-mir-106b-5p in cancer and its potential as a candidate of a biomarker for clinical diagnosis of prostate cancer.

Cytokines as Prognostic Biomarkers of Epithelial Ovarian Cancer (EOC): A Systematic Review and Meta-Analysis.

OBJECTIVES: The value of cytokines as epithelial ovarian cancer (EOC) prognostic factors has been widely investigated. This study aimed to determine the role of single cytokine as a biomarker prognosis in EOC. MATERIALS AND METHODS: We conducted a systematic review and meta-analysis of studies reporting cytokine as the prognostic predictor in EOC based on PRISMA guideline. We included English articles investigating associations of preoperative cytokines level in tissue, blood or ascites with overall survival (OS) or disease-free survival (DFS) from PUBMED and EBSCO. Summary hazard ratios (HRs) and confidence intervals (CIs) were calculated. RESULTS: Fifty studies investigating twenty types of cytokines in tumor tissue, serum, and ascites from 5,376 patients were included. Pre-operative high VEGF level was associated with poor OS (HR 2.28, 95%CI [1.28, 3.28]) and DFS (HR 2.13, 95%CI [1.63, 2.78]) in serum and OS (HR 1.80, 95%CI [1.45, 2.23]) in tissue. IL-6 level in blood was associated with DFS (HR 1.60, 95%CI [1.21, 2.11]). There was no single cytokine which investigated by at least 2 studies reporting hazard ratio in ascites, so we did not conduct the meta-analysis. Other cytokines (serum IL-8; ascites fluid IL-8, IL-10, IFN-γ, TNF-α; and ovarian tissue TGF-α, CSF-1, IL-10 ,TGF-ß1, IL-17) associated with the poorer prognosis, could not be pooled due to lack of studies. CONCLUSION: Pre-operative VEGF level in serum and tissue specimen seem to be the potential candidate of an unfavorable prognostic biomarker for EOC. The evidence was lacking to support the other cytokines investigated in blood, tissue and ascites as prognostic biomarkers for EOC.

The potential of miRNA-based therapeutics in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection:A review / 药物分析学报

Since the World Health Organization (WHO) declared COVID-19,the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2),as a pandemic in March 2020,and more than 117 million people worldwide have been confirmed to have been infected.Scientists,medical professionals,and other stakeholders are racing against time to find and develop effective medicines for COVID-19.However,no drug with high efficacy to treat SARS-CoV-2 infection has been approved.With the increasing popularity of gene therapy,scientists have explored the utilization of small RNAs such as microRNAs (miRNAs) as therapeutics.miRNAs are non-coding RNAs with high affinity for the 3'-UTRs of targeted messenger RNAs (mRNAs).Interactions between host cells and viral genomes may induce the upregulation or downregulation of various miRNAs.Therefore,understanding the expression patterns of these miRNAs and their functions will provide insights into potential miRNA-based therapies.This re-view systematically summarizes the potential targets of miRNA-based therapies for SARS-CoV-2 infec-tion and examines the viability of possible transfection methods.

MicroRNA-155-5p Diminishes in Vitro Ovarian Cancer Cell Viability by Targeting HIF1α Expression.

Purpose: Ovarian cancer is the most lethal of gynecological malignancies. Recently, the development of microRNA (miRNA) -based therapeutics that could impact broad cellular programs, leading to inhibition of cancer cell viability, is gaining attention in the therapeutic landscape. The therapy is based on the presence of aberrant expressions of miRNA in cancer cells. Decreasing of tumor suppressor miRNA expression causes upregulation of oncoprotein, which worsens the prognosis of the ovarian cancer. Methods: miR-155-5p mimics were carried by chitosan nanoparticles using new nanotechnology methods. Cellular uptake of miRNA was assessed by fluorescence microscope while MTT and qPCR assay were used to determine miRNA profile and the effect of CS-NP/miRNA on SKOV3 cells. Results: Results of profiling validated using quantitative realtime-polymerase chain reaction (PCR) found one of the most altered tumor suppressor miRNAs, miR-155-5p was downregulated 892.15-fold. According to bioinformatic analysis we identified the miRNA could recognize and regulate HIF1α expression. Transfection of mimics for miR-155-5p showed significantly increased miR-155-5p endogen SKOV3 expression level compared to the control group. We found differences after transfection mimics for miR-155-5p 31.5 and 63 nanoMolar. Increasing of miR-155-5p endogen lead to diminished SKOV3 viability (by 30%; <0.05 at concentration 80 nanoMolar). These mimics may cause an increase in upregulated miR-155-5p endogen that can reduce HIF1α expression. Here we found 2-fold and 2.8-fold reduction of HIF1α expression level after transfection compared to the control group. Conclusion: According to these findings, the mimics miR-155-5p can inhibit ovarian cancer cell proliferation by regulating HIF1α expression.

Transcriptome Profile of Next-Generation Sequencing Data Relate to Proliferation Aberration of Nasopharyngeal Carcinoma Patients in Indonesia.

OBJECTIVE: Nasopharyngeal carcinoma (NPC) is the most common cancer arising from epithelial cells of the nasopharynx in  Indonesia. This study aims to determine the differential level of gene expression in NPC patients when compared with normal individuals. Transcriptome profiling analysis was performed using RNA-Seq technology to determine the differential gene expression relate to proliferation aberration that occurs in NPC patients compared with normal individuals. So we get the transcriptomic profile of Indonesia NPC patients. METHODS: In this study, we used 9 samples, 7 NPC samples and 2 normal samples as control.  Fresh tissue of tumor samples was collected from biopsy, and normal samples were collected brushing technique. The total RNA was isolated from fresh tissue samples and brushing samples using the Rneasy® RNA Extraction Mini Kit. The cDNA library was generated using TruSeq® RNA Library Preparation Kit V2, and its concentration was determined using qPCR. The library was sequenced using the Next-Generation Sequencing (NGS) Illumina Next Seq 550 platform. The raw sequence data quality was analyzed using FastQC and interpreted using HISAT2, HTSeq, edgeR, and PANTHER. RESULTS: From the analysis, 25493 gene transcripts were expressed, with 1956 genes were significantly upregulated, 90 genes were significantly downregulated in NPC samples, and 23897 genes didn't change the expression level significantly (p <0.05), 10 of which genes were associated with cell proliferation. These genes are involved in the regulation of cancer cell proliferation through several signaling pathways, which are the apoptosis signaling pathway, IGF signaling pathway, Notch signaling pathway, and P13K signaling pathway. CONCLUSION: There were significant differences in gene expression levels between NPC patients and normal individuals. Each gene that has changed the expression level plays a role in regulating various pathways that lead to cell proliferation aberration in NPC cases.

Transcriptome Related to Avoiding Immune Destruction in Nasopharyngeal Cancer in Indonesian Patients Using Next-Generation Sequencing.

OBJECTIVE: This study aims to obtain the transcriptomes profile associated with avoiding immune destruction from nasopharyngeal cancer patients in Indonesia using next-generation sequencing. METHODS: The samples are divided into two types of samples; 1) biopsy of nasopharyngeal cancer tissue samples, 2) brushing tissue of people without nasopharyngeal cancer as control samples. The sequencing results were mapped (HISAT2) and quantified (HTSeq) for differential expression analysis using edgeR software. Transcripts data analyzed with Pantherdb and DAVID software to find genes related to the immune system and pathways related to immune destruction by cancer. RESULTS: The differential expression results show that 2,046 genes that have a significant differential expression. The 90 genes expression has down-regulated and 1,956 genes expression up-regulated, there are 20 genes related to the immune system. The 20 genes related to the immune system by analyzing lionproject.net that directly related to hallmark avoiding immune destruction that genes are CXCL9/10/11. The gene expression of CXCL9/10/11 regulates PD-L1 expressions via the Jak/STAT signaling pathway. The interaction between the extracellular domain PD-1 and PD-L1 in cancer cells have avoiding immune destruction. CONCLUSION: The results of this study suggest that the gene expression of CXCL9/10/11 have up-regulated is related to avoiding immune destruction that can use as an early detection biomarker of nasopharyngeal cancer in Indonesian patients.

The Effects of Combination of Mimic miR-155-5p and Antagonist miR-324-5p Encapsulated Chitosan in Ovarian Cancer SKOV3.

OBJECTIVE: Ovarian cancer is a malignant tumor that attacks reproductive organs of women. MicroRNA is known to have an involvement in the prognosis of ovarian cancer. One of them is miR-155-5p which is down regulated and miR-324-5p which is up regulated. Chitosan is used as microRNA delivery system. The aims of this study is to find out the effects of combination microRNA encapsulated chitosan in cell line SKOV3. METHODS: Cell line SKOV3 obtained from Stem Cell and Cancer Institute (Kalbe). Mimic miR-155-5p and Antagonist miR-324-5p formulated with chitosan. Total RNA was extracted from nine samples (three as control and six as treatment), and prepared for cDNA synthesis. Expression of RNA and mRNA target was measured using q-PCR Biorad CFX96 C.100 and Gen Ex 7 software. Statistics analysis was measured using SPSS 16.0. RESULTS: The administration of combination microRNA encapsulated with chitosan affect the expression of miR-155-5p and miR-324-5p endogen (p <0.05). The expression of mRNA target HIF1α and GLI1 was down regulated after treatment. The correlation between expression of microRNA and mRNA target was strongly (p <0.05). CONCLUSION: This study successfully presented effects of combination of mimic miR-155-5p and antagonist miR-324-5p encapsulated chitosan which be considered as a potential therapy targets for ovarium cancer.

Transcriptome Profile of Next Generation Sequence Data Related to Inflammation on Nasopharyngeal Carcinoma Cases in Indonesia.

OBJECTIVE: Transcriptomic Profile Analysis Related to Inflammation in Nasopharyngeal Carcinoma Cases. METHODS: This study used 2 control samples taken using the brushing technique and 7 cancer samples with tissue biopsy. Isolate total RNA using Rneasy® RNA Extraction Mini Kit. Measurement of total RNA concentration and purity using a fluorometer and nanodrop Qubit. Synthesis of cDNA library uses TruSeq® RNA Library Preparation Kit V2 and concentration is measured using qPCR. Sequencing samples using NGS Illumina NextSeq 550 platform engine. Quality control results of sequencing using FASTQC, and raw data processing using HISAT2. Differential analysis of gene expression (DEGs) using edgeR and pathway analysis using DAVID and PANTHER. RESULTS: From the 25,493 genes that experienced a significant change in expression level (P <0.05) from DEG analysis there were 13 genes that play a role in the inflammatory process. Based on DAVID pathway analysis software, there are 8 genes detected based on the KEGG pathway database found in 2 pathways, namely Inflammatory Mediator Regulation of TRP Channels pathway with genes that play HTR2A, NGF, TRPA1, PRKCG, and ADCY8. CXCL9, CXCL10, and CXCL11 genes are found in the Toll-Like Receptor Signaling pathway. Based on PANTHER pathway analysis software, 6 genes were found, namely CXCL10, MYLK2, COL20A1, MYH2, ACTC1, and ALOX15 in the Inflammation Mediated by Chemokine and Cytokine Signaling pathways. Almost all genes found from DEGs are upregulated, except the ALOX15 gene that is downregulated. CONCLUSION: There are 13 genes that play a role in the inflammatory process in Nasopharyngeal Carcinomafrom a sample of the Indonesian population. Genes CXCL9, CXCL10, CXCL11, MYLK2, COL20A1, MYH2, ACTC1, HTR2A, NGF, TRPA1, PRKCG, and ADCY8 have been upregulated and ALOX15 has been downregulated. These genes play a role in the Inflammation Mediated by Chemokine and Cytokine Signaling pathways, Inflammatory Mediator Regulation of TRP Channels, and Toll-Like Receptor Signaling.

Circulation EBV Mir-Bart-7 Relating to Clinical Manifestation in Nasopharyngeal Carcinoma.

OBJECTIVE: Nasopharyngeal Carcinoma (NPC) is an endemic head and neck malignancy in Asia Pacific regions that is associated with chronic infection by Epstein-Barr virus (EBV). EBV miR-BART-7 is a microRNA (miRNA) encoded by EBV that regulates malignant behavior of NPC. However, the role and function of miR-BART7 are not clear, particularly the relation of circulating levels and patient's clinical presentation. METHODS: Circulating miR-BART-7 levels were measured by using qRT-PCR and were correlated with clinical and pathological data. RESULT: Of 52 NPC patients included in this study, 85% were diagnosed in the late stages (Stage III-IV). 73% of tumors were non-keratinizing undifferentiated NPC, 92% of tumors were WHO class III histology and all cases were EBV-IgA positive. Over-expression of miR-BART7-3p was correlated with positive regional lymph nodes in newly diagnosed (4.61 fold changes, p <0.05). CONCLUSION: Over-expression of circulating EBV miR-BART7 correlated with positive regional lymph nodes reflecting the diagnostic and prognostic values of circulating miR-BART7 for patients with NPC.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): An overview of viral structure and host response.

BACKGROUND AND AIM: As a result of its rapid spread in various countries around the world, on March 11, 2020, WHO issued an announcement of the change in coronavirus disease 2019 status from epidemic to pandemic disease. The virus that causes this disease is indicated originating from animals traded in a live animal market in Wuhan, China. Severe Acute Respiratory Syndrome Coronavirus 2 can attack lung cells because there are many conserved receptor entries, namely Angiotensin Converting Enzyme-2. The presence of this virus in host cells will initiate various protective responses leading to pneumonia and Acute Respiratory Distress Syndrome. This review aimed to provide an overview related to this virus and examine the body's responses and possible therapies. METHOD: We searched PubMed databases for Severe Acute Respiratory Syndrome Coronavirus-2, Middle East respiratory syndrome-related coronavirus and Severe Acute Respiratory Syndrome Coronavirus. Full texts were retrieved, analyzed and developed into an easy-to-understand review. RESULTS: We provide a complete review related to structure, origin, and how the body responds to this virus infection and explain the possibility of an immune system over-reaction or cytokine storm. We also include an explanation of how this virus creates modes of avoidance to evade immune system attacks. We further explain the therapeutic approaches that can be taken in the treatment and prevention of this viral infection. CONCLUSION: In summary, based on the structural and immune-evasion system of coronavirus, we suggest several approaches to treat the disease.

Dynamic Changes of Circulating Mir-155 Expression and the Potential Application as a Non-Invasive Biomarker in Breast Cancer.

BACKGROUND: Breast cancer incidence rates have been continuously increasing in majority nations with significant higher portion of cancer-related mortality in low- and middle-income countries. Developing new biomarker is an emerging field in the breast cancer research. Application of a promising minimally invasive biomarker, circulating microRNA, for additional improvement of diagnosis, prognosis, and therapeutic monitoring in breast cancer is not well corroborated. MATERIALS AND METHODS: To uncover the potential use of circulating miR-155 expression as a clinical biomarker in breast cancer, we analyzed 102 breast cancer patients at diagnosis and after treatment as well as 15 healthy women. Total RNA was isolated from patient's plasma and expression of circulating miR-155 was measured with quantitative reverse transcription polymerase chain reaction (qRT-PCR). The expression levels of circulating miR-155 were compared according to the effect of treatment, clinicopathological variables, and progression-free survival.  Results: In comparison to the healthy women, expression of circulating miR-155 levels were significantly higher (medians were 18.49±19 and 1.28±0.18, respectively; p<0.0001). The expression levels of miR-155 were significantly diminished after patients completed surgery and chemotherapy (medians were 18.49±19 at diagnosis and 1.32±0.22 after treatment, respectively; p<0.0001). Patients older than 40 years old expressed higher circulating miR-155 than those younger than 40 years-old (medians were 28.92±22 and 4.19±2.49, respectively; p<0.0001). Circulating miR-155 was significantly higher in patients with tumors larger than 5 cm (44.27±2.6 vs 9.17±6.9, p=0.03). MiR-155 expression levels were not significantly different according to various tumor grades, subtypes, and clinical stages. Although longer follow-up is required, progression-free survivals of patients with upregulation of circulating miR-155 were significantly longer (mean survivals were 77 and 65 weeks, Log-rank (Mantel-Cox) test p=0.038). CONCLUSION: Expression of circulating miR-155 expression was significantly elevated in breast cancer patients and was decreased after treatment. Therefore, circulating miR-155 is potentially applicable as diagnostic therapeutic monitoring marker in breast cancer.
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