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Anwar, Sumadi Lukman

Department Of Surgery, Faculty Of Medicine Universitas Gadjah Mada

Author-ID : 912936

Immunology & microbiology Neuroscience

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Variation of the breast cancer susceptibility marker, rs4245739, is associated with differential miRNA binding and MDM4 expression Sumadi Lukman Anwar; Angel Carlos-Roman; Wahyu Wulaningsih; Johnathan Watkins
Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Vol 48, No 4 (2016): SUPPLEMENT
Publisher : Journal of the Medical Sciences (Berkala Ilmu Kedokteran)

A polymorphism, rs4245739, has been associated with susceptibility of several cancers including ER-negative breast cancer. Rs4245739 is located at the 3’UTR of MDM4 gene, an oncogene that negatively regulates p53. The polymorphism has been associated with binding changes of miR-191. We studied, the influence of SNP rs4245739 to the binding of microRNAs, expression of microRNAs and MDM4. Using FindTar software, we detected potential microRNAs affected by the SNP-flanking sequence. We then used RNA sequencing data from ER-negative breast cancer to compare expression of miR-184, miR-191, miR-193a, miR-378, and MDM4 in different genotypes. Comparison of ER-negative patients with and without expression of miR-191 as well as profile microRNAs (miR-184, miR-191, miR-193a and miR-378 altogether) can differentiate expression of MDM4between different alleles. In addition, the number of lymphatic nodes affected in the individuals was also found to be significantly reduced in the risk group obtained by the miRNA profile method. We show our methods especially miRNA profile approach, are able to obtain new molecular and clinical features related to the rs4245739 SNP, a variant located in the 3’UTR of MDM4 gene and known to appear in different types of cancer. Keywords: ER negative breast cancer, rs4245739, microRNA, MDM4, p53

DNA extraction, Polymerase Chain Reaction, and Sequencing : Workshop in Clinical Genetics Sumadi Lukman Anwar
Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Vol 48, No 4 (2016): SUPPLEMENT
Publisher : Journal of the Medical Sciences (Berkala Ilmu Kedokteran)

AbstractDNA extraction, Polymerase Chain Reaction (PCR), and Sequencing are basic methods in molecular biology and genetics. Those there are routinely performed as basic methods in genetic research and currently also for diagnostic lab especially for pathology and human genetics. With the advance in the genetics and clinical service for cancer management, mutation analysis is very important not only for diagnosis but also for prediction of therapeutic response. Detection of KRAS, BRAF, EGFR, and c-KIT mutations is presently performed in almost every molecular pathology lab as part of daily clinical service in cancer management. In this workshop we will discuss tips and tricks for those three basic lab methods. How to improve amount and purity of DNA extraction from blood and tissues, how to avoid DNA degradation during the procedure and storage, how to perform PCR, factors and substance that inhibit polymerases during PCR, how to design effective primer pairs, and how basic theory for sequencing, and interpretation of sequencing will be discussed. Although it has been widely discussed, this workshop is especially important for clinicians who previous do not have hands-on laboratory experience. In addition, number of labs with ability to perform and serve basic genetic and molecular analysis are still limited in Indonesia. With this workshop, we expect to improve knowledge and skill in DNA extraction, PCR, and Sequencing.Keywords : DNA, PCR, sequencing

The Expression of hsa-miR-155-5p in Plasma Samples Of Breast Cancer Before And After Chemotherapy Meutia Srikandi Fitria; Sofia Mubarika Haryana; Sumadi Lukman Anwar; Teguh Aryandono; Dewi Sahfitri Tanjung; Aprilia Indra Kartika; Risky Oktriani; . Irianianiwati; Dwi Nur Indah Sari
Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Vol 48, No 4 (2016): SUPPLEMENT
Publisher : Journal of the Medical Sciences (Berkala Ilmu Kedokteran)

Breast cancer has emerged as the most common cancer-related mortality among women worldwide. Therefore, early cancer detection using biomarkers such as microRNA is needed. One of microRNAs that has an important role in breast cancer development is miR-155. Hsa-miR-155-5p is an oncomir that is commonly dysregulated in breast cancer. This study aims to determine the expression of hsa-miR-155-5p in breast cancer patient’s plasma before and after chemotherapy. We collected 64 samples from breast cancer patients admitted to Dr. Sardjito Hospital in Yogyakarta. RNA from plasma was extracted using RNA Isolation Kit miRCURY-Biofluid. cDNA synthesis was performed using cDNA Synthesis kit II and quantification of miR-155-5p using ExiLent SYBR Green master mix (Exiqon). qRT-PCR results were then analyzed with Livak's method and compared (before and after chemotherapy) with t-test. Expression of miR-155-5p in the breast cancer patients’ plasma after chemotherapy was significantly increased (10.59 times) when compared to before chemotherapy (p = 0.001). We concluded that there was upregulated expression of miR-155-5p after chemotherapy than before chemotherapy. There has not been a known, relevant pathway between hsa-miR-155-5p and chemotherapy regimens nor resistance to chemotherapy. Keywords: Breast cancer, plasma, hsa-miR-155-5p, oncomiR, chemotherapy.

DNA methylation and expression of Homeobox gene family as diagnostic and prognostic markers in human hepatocellular carcinoma Sumadi Lukman Anwar; Ulrich Lehmann
Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Vol 48, No 4 (2016): SUPPLEMENT
Publisher : Journal of the Medical Sciences (Berkala Ilmu Kedokteran)

ABSTRACTHomeobox genes consist of a family of evolutionarily conserved genes that play important roles in morphogenesis, embryogenesis, and cell fate determination. Re-expression of embryogenic genes has been associated with carcinogenesis of human cancers. Aberrant expression of homeobox genes has been increasingly found to modulate diverse processes such as cell proliferation, cell death, metastasis, angiogenesis and DNA repair. We studied DNA methylation and expression of homeobox gene family in human hepatocellular carcinoma (HCC), the fifth most common cancer and the third leading cause of cancer mortality worldwide. We performed microarray for comprehensive DNA methylation and gene expression using primary HCC samples and healthy liver tissues. Confirmation using pyrosequencing and RT-PCR was then performed. Clustering both unsupervised and supervised methods using Qlucore software was then performed. Enrichment of homeobox genes both for DNA methylation and gene expression could differentiate HCC and the healthy liver tissues. Profile of homeobox gene methylation could further predict clinical outcome. Inverse correlation between DNA methylation and gene expression was shown (HOXA9, Spearman r=-0.49, p=0.002). Gain of DNA methylation in HOXA9, HOXA13, and MEOX1 correlated with shorter HCC survival (log-rank Mantel-Cox test p=0.02, with median survival 50 and 490 weeks, respectively). We demonstrated potential roles of DNA methylation and gene expression profiles of Homeobox gene family as diagnostic and prognostic marker in patients with HCC.

The accuracy of fine needle aspiration biopsy to diagnose breast neoplasm Hifdza Faza Felisha; Hanggoro Tri Rinonce; Sumadi Lukman Anwar; Ery Kus Dwianingsih
Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Vol 51, No 3 (2019)
Publisher : Journal of the Medical Sciences (Berkala Ilmu Kedokteran)

Breast lump is a very common complaint among women, especially during the reproductive year. Fine needle aspiration biopsy (FNAB) is a less invasive procedure. It is usually performed as an initial diagnosis prior to the operative procedure. The accuracy of the FNAB in Indonesia needs to be elaborated. The study aimed to evaluate the sensitivity and specificity of FNAB in diagnosing breast neoplasm. This is a retrospective study with cross sectional design, involving 145 patients with breast lump who underwent FNAB and histopathology examination in Dr. Sardjito General Hospital, Yogyakarta, from 2012 to 2014. Data analysis showed that female to male ratio was 23. 2:1 commonly occurred at 41-50 years old. Forty-one cases (28.28%) diagnosed as a benign lesion with fibrocystic changes as the most frequentcase (11.19%). The malignant case was 104 cases (71.72%) with ductal carcinoma as the highest case (51.49%). FNAB achieved a sensitivity of 85.58%, a specificity of 100% and a total accuracy of 89.66% in determining the benign or malignant breast lump. The accuracy, sensitivity and specificity of FNAB in diagnosing ductal carcinoma were 83.58%, 85.51% and 81.54%, respectively. The accuracy, sensitivity and specificity of FNAB to diagnose fibrocystic changes lesion were 85.82%, 26.67% and 93.28%, respectively. FNAB can be used as an alternative diagnostic tool to diagnose breast neoplasm. It provides rapid, cheaper, effective, valuable, and less invasive procedure in diagnosis of breast lump.

Over- and down-expression mir-29c and mir-21 after chemotherapy and radio-therapy in nasopharyngeal carcinomas and the down-regulating proteins encoding eipstein barr virus and c-Myc. Tirta wardana; Cita Herawati; Risky Oktriani; Sumadi Lukman Anwar; Indwiani Astuti; Teguh Aryandono; Sofia Mubarika Haryana
Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Vol 48, No 4 (2016): SUPPLEMENT
Publisher : Journal of the Medical Sciences (Berkala Ilmu Kedokteran)

Nasopharyngeal carcinoma (NPC) is the type of cancer related to multiple risk factors, including infection by Epstein Barr Virus (EBV). Standard treatment of NPC involves radiotherapy and chemotherapy in local and advanced tumors, while metastatic cases are treated with systemic chemotherapy. However, there is limited data on the causes of tumor recurrence, resistance, and progression. Moreover, the initial symptoms of NPC were often neglected until later enlarged, thus making it difficult to manage. MicroRNA (miRNA) is short molecule with 18-24 nucleotides and functions as protein-expression regulator protein in post-transcription. This study was aimed to determine miRNA expression and its relationship with the incidence of NPC. miR-21 and miR-29c were known to be involved in the development of NPC and resistance. A total of 51 plasma samples and 17 tissue samples were collected from Dharmais Hospital. The samples were taken from 17 untreated patients, 17 treated patients, and 17 healthy participants as control. We examined miRNA, protein of protein EBV (EBNA), and c-Myc expression using immunohistochemistry and quantitative polymerase chain reaction (qPCR). Our study revealed an increased expression of miR-21 and decreased expression of miR-29c in patients with NPC. There was also a correlation between the regulation of expression of miR-21 and c-Myc in the treated group of patients, and decreased expression in patients with complete response (CR) (4.13 ± 3.65: 2.74 ± 3.23; p <0.1). The parameters tend to increase in patients with partial response (PR) (3.00 ± 5, 86 compared to 8.77 ± 8.43; p <0.5), while no significant difference in expression of miR-29c in patients with CR and PR was detected. We concluded that miRNA might be detected in the plasma of NPC patients, and miR-21 might become a useful biomarker to determine therapeutic outcome in NPC patients.Keywords: nasopharyngeal cancer; miRNA; biomarker

Co-Authors . Irianianiwati Angel Carlos-Roman Aprilia Indra Kartika Cita Herawati Dewi Sahfitri Tanjung Dwi Nur Indah Sari Dwianingsih, Ery Kus Hanggoro Tri Rinonce Hifdza Faza Felisha Indwiani Astuti Johnathan Watkins Meutia Srikandi Fitria Risky Oktriani Sofia Mubarika Haryana Sofia Mubarika Haryana Teguh Aryandono Tirta wardana Ulrich Lehmann Wahyu Wulaningsih

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