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All Journal The Indonesian Biomedical Journal
Rafika Indah Paramita
Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jl. Salemba Raya No.6, Jakarta 10430
Biochemistry, Genetics & Molecular Biology Public Health

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Amino Acid Profile of Luminal A and B Subtypes Breast Cancer Sonar Soni Panigoro; Arif Kurniawan; Ramadhan Ramadhan; Ninik Sukartini; Herqutanto Herqutanto; Rafika Indah Paramita; Ferry Sandra
The Indonesian Biomedical Journal Vol 15, No 3 (2023)
Publisher : The Prodia Education and Research Institute (PERI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18585/inabj.v15i3.2109

Abstract

BACKGROUND: Amino acids are important for proliferation and maintenance of tumor cells. Breast cancer patients were found to have significant changes in the number of amino acids, which are assumed to be correlated with the molecular subtypes of breast cancer. Therefore, current study was conducted to analyze plasma amino acids in breast cancer patients with luminal A and B subtypes.METHODS: Breast cancer and control subjects were recruited, and venous blood was collected for the measurement of plasma amino acids. Total 19 plasma amino acids were measured using reverse-phase high-performance liquid chromatography with C18 column. Mean comparison for normally distributed and homogeneous data was further analzyed using independent sample T-test, with p<0.05 was considered as significant.RESULTS: From total 19 amino acids, only 7 amino acids; cysteine, glutamic acid, histidine, ornithine, threonine, tyrosine, valine, were statistically different between the healthy control and breast cancer subjects. Eventhough no amino acids was found to be statistically different between breast cancer subjects with luminal A and B subtypes, but some amino acids were found to be significantly different when correlated to various breast cancer risk factors.CONCLUSION: Amino acid profile of patients with Luminal A and B subtypes of breast cancer differs compared to healthy controls and is also correlated with breast cancer risk factors. Increase in cysteine level in Luminal A subtype patients and decrease of alanine and leucine in Luminal B subtype patients can be used as a biomarker.KEYWORDS: amino acid, plasma, breast cancer, risk factor, biomarker
Identification of Novel Intronic Variants Implicating L3MBTL4 and AOAH in Indonesian Ovarian Endometriosis Trijayani Trijayani; Surya Dwira; Raden Muharam; Rafika Indah Paramita
The Indonesian Biomedical Journal Vol 17, No 6 (2025)
Publisher : The Prodia Education and Research Institute (PERI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18585/inabj.v17i6.3732

Abstract

BACKGROUND: Genetic factors are contributing substantially to endometriosis risk, however, there is limited data on genetic variant associations specific to ovarian endometriosis, especially in Indonesian populations. Understanding the genetic variants associated with this condition is essential for improving diagnosis and identifying potential therapeutic targets. Therefore, this study was conducted to analyze the association of genetic variants with ovarian endometriosis in Indonesian women using the single nucleotide polymorphisms (SNP)-array method, followed by an in-silico functional enrichment and gene expression analysis to explore their biological context.METHODS: This case-control study utilized the Infinium Asian Screening Array microarray platform to examine 46 samples, consisting of 22 ovarian endometriosis and 24 controls. The analysis included quality control, genetic association testing, and enrichment analysis. Genotypes were analyzed under dominant and recessive inheritance models, and functional insights were explored using gene expression databases.RESULTS: Ten intronic SNPs were significantly associated with endometrioma (p<0.05). Eight variants conferred increased risk (OR>1): rs77360595 (IFNLR1), rs2325558 (KLF12), rs1654499 (NLRP2), rs4809494 (LOC105376996), rs168482 (TMPRSS11A), rs17026725 (STPG2-AS1), rs59330070 (GFOD1), and rs58909364 (AOAH). Two variants were protective (OR<1): rs180732 (L3MBTL4) and rs7356507 (CRMP1). Notably, AOAH variant showed the highest odds ratio among risk variants, while L3MBTL4 variant showed the strongest statistical significance among protective variants in the dominant model. In-silico expression analysis confirmed that key implicated genes (KLF12, L3MBTL4, AOAH, and GFOD1) are expressed in relevant female reproductive tissues, generally at low-to-moderate levels.CONCLUSION: Ten novel genetic variants associated with ovarian endometriosis in Indonesian were identified. In particular, variants in L3MBTL4 and AOAH represent promising candidates that may play roles in disease pathophysiology of endometriosis, suggesting the importance of population-specific genetic studies and these specific loci as potential biomarkers or therapeutic targets.KEYWORDS: ovarian endometriosis, SNP, microarray, genetic association, plink, bioinformatics
Co-Authors Arif Kurniawan Ferry Sandra Herqutanto Herqutanto Raden Muharam Ramadhan Ramadhan Sonar Soni Panigoro Sukartini, Ninik Surya Dwira Trijayani Trijayani