In silico screening of proteins targeting circulating miRNAs for improved diagnosis of multiple myeloma
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
Authors: Suyal, Shradha; Singh, Manish Pratap; Shekhar, Himanshu; Srivastava, Sameer
Abstract
Multiple Myeloma (MM) is a B-cell malignancy, which is characterized by the expansion of clonal plasma cells in the bone marrow, leading to abnormal accumulation of monoclonal antibodies in circulation. Certain circulating miRNAs are deregulated in MM and their differential expression profiles in body fluids can be quantified and used to discriminate between the premalignant and malignant stages of MM. Our study identifies protein which would show affinity for a selected panel of circulating miRNAs deregulated in MM. Human RNA binding proteins were identified based on their unique RNA binding domains and their interacting probabilities with the panel of miRNAs deregulated in MM. miR-26 was used as a negative control for interaction studies. 3-D structure of candidate proteins were determined and molecular docking was performed to confirm the results. Five RNA binding proteins TROVE2, CUGBP2, DHX8, PUM2 and DKC1 were used for molecular docking studies. DKC1 showed significant hydrogen bonding as well as remarkable binding affinity values of -17.4 kcal/mol with miR-720 (2 H-bonds), 16 kcal/mol with miR-1246 (1 H-bond) and -16.9 kcal/mol with miR-1308 (3 H-bonds). Identified protein-miRNA interaction could be used to develop an economical and reliable ELISA based methodology for improved and sensitive diagnosis of MM patients. (C) 2018 Elsevier Inc. All rights reserved.
Proteomic screening and identification of microRNA-128 targets in glioma cells
PROTEOMICS
Authors: Yang, Bin; Wang, Shan; Zeng, Jiawei; Zhang, Yu; Ruan, Xiangbin; Han, Wei; Yin, Bin; Yuan, Jiangang; Qiang, Boqin; Ying, Wantao; Qian, Xiaohong; Peng, Xiaozhong
Abstract
Brain-enriched miR-128 is repressed in glioma cells, and could inhibit the proliferation of gliomas by targeting genes such as E2F3a and BMI1. To identify more targets of miR-128 in glioblastoma multiforme, the pulse stable isotope labeling with amino acids in cell culture (pSILAC) technique was used to test its impact on whole protein synthesis in T98G glioma cells. We successfully identified 1897 proteins, of which 1459 proteins were quantified. Among them, 133 proteins were downregulated after the overexpression of miR-128. Through predictions using various bioinformatics tools, 13 candidate target genes were chosen. A luciferase assay validated that 11 of 13 selected genes were potential targets of miR-128, and a mutagenesis experiment confirmed CBFB, CORO1C, GLTP, HnRNPF, and TROVE2 as the target genes. Moreover, we observed that the expression of CORO1C, TROVE2, and HnRNPF were higher in glioma cell lines compared to normal brain tissues and presented a tendency toward downregulation after overexpression of miR-128 in T98G cells. Furthermore, we have validated that CORO1C, TROVE2, and HnRNPF could inhibit glioma cell proliferation. In sum, our data showed that the integration of pSILAC and bioinformatics analysis was an efficient method for seeking the targets of miRNAs, and plentiful targets of miR-128 were screened and laid the foundation for research into the miR-128 regulation network.