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Shuaib M, Prajapati KS, Singh AK, Kushwaha PP, Waseem M, Kumar S. Identification of miRNAs and related hub genes associated with the triple negative breast cancer using integrated bioinformatics analysis and in vitro approach. J Biomol Struct Dyn 2022; 40:11676-11690. [PMID: 34387138 DOI: 10.1080/07391102.2021.1961869] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Triple negative breast cancer (TNBC) is an aggressive breast cancer subtype generally associated with younger women. Due to the lack of suitable drugable targets in TNBC, the microRNAs are considered as a better hope as therapeutic agents for the management of the disease. In this study, we identified differentially expressed miRNAs (DEMs) and associated hub genes in TNBC microarray data (GSE38167, GSE60714, and GSE10833) using bioinformatics tools. The identified miRNAs and genes were validated in the TNBC cell line model (MDA-MB-231) compared with the normal breast cells (MCF-10A) using the qRT-PCR technique. False-positive DEMs were avoided by comparing the DEMs profile of TNBC and triple positive breast cancer (TPBC) cell line model (BT474) compared with the MCF-10A cells data. In addition, we studied the effect of anticancer phytochemicals on the differential expression of miRNAs and genes in MDA-MB-231 cells. Furthermore, target predictions, functional enrichment and KEGG pathway analysis, mutation and copy number alterations, and overall survival analysis of DEMs in TNBC sample was investigated using standard computational tools. The study identifies first time the association of hsa-miR-1250, has-miR-1273, and has-miR-635 with the TNBC. DEMs showed significant association with the Wnt, ErbB, PI3-Akt and cAMP signaling pathways having clinical implications in TNBC tumorigenesis. The DEMs and hub genes (HOXC6 and ACVR2B) showed survival disadvantages in TNBC patients. In summary, the identified miRNAs and hub genes show important implications in TNBC tumorigenesis and patient survival. We recommend further experimental studies on pathophysiological mechanism of the identified miRNAs and hub genes in TNBC.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohd Shuaib
- Molecular Signaling and Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
| | - Kumari Sunita Prajapati
- Molecular Signaling and Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
| | - Atul Kumar Singh
- Molecular Signaling and Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
| | - Prem Prakash Kushwaha
- Molecular Signaling and Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
| | - Mohammad Waseem
- Department of Zoology, Jagdam College, Jai Prakash University, Chapra, Bihar, India
| | - Shashank Kumar
- Molecular Signaling and Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
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Wang YC, Lu S, Zhou XJ, Yang L, Liu P, Zhang L, Hu Y, Dong XZ. miR-1273h-5p suppresses CXCL12 expression and inhibits gastric cancer cell invasion and metastasis. Open Med (Wars) 2022; 17:930-946. [PMID: 35647303 PMCID: PMC9113083 DOI: 10.1515/med-2022-0486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 04/15/2022] [Accepted: 04/28/2022] [Indexed: 02/06/2023] Open
Abstract
The aim of this study was to verify the biological function of miR-1273h-5p in gastric cancer (GC) and its underlying mechanisms. The differential expression of microRNAs between GC and tumor-adjacent normal tissues was detected using microarrays, miR-1273h-5p, and chemokine (C-X-C motif) ligand 12 (CXCL12) mRNA, and protein levels were evaluated using polymerase chain reaction and Western blotting methods, cell proliferation, apoptosis, migration, and invasion were determined by CCK-8, flow cytometry, and transwell assay. Compared to tumor-adjacent normal tissue and gastric epithelial mucosa cell line cells, miR-1273h-5p was significantly downregulated in tissues and cells of GC. The overexpression of miR-1273h-5p could inhibit cell proliferation, migration, invasion, and promote cell apoptosis; in contrast, inhibition of miR-1273h-5p expression could reverse this process. Moreover, a significant upregulation of CXCL12 was observed when the miR-1273h-5p was downregulated in GC cells. Additionally, miR-1273h-5p significantly reduces tumor volume and weight. Thus, this study suggests that miR-1273h-5p regulates cell proliferation, migration, invasion, and apoptosis during GC progression by directly binding to CXCL12 mRNA 3′-untranslational regions, which may be a novel diagnostic and therapeutic target in GC.
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Affiliation(s)
- Yi-Chen Wang
- Department of Pharmacy, Medical Supplier Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Song Lu
- Department of Pharmacy, Xuanwu Hospital of Capital Medical University, Beijing 100053, China.,College of Pharmacy, Zunyi Medical University, Zunyi 563000, China
| | - Xiao-Jiang Zhou
- Department of Pharmacy, Medical Supplier Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Li Yang
- Department of Pharmacy, Xuanwu Hospital of Capital Medical University, Beijing 100053, China.,College of Pharmacy, Zunyi Medical University, Zunyi 563000, China
| | - Ping Liu
- Department of Pharmacy, Medical Supplier Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Lan Zhang
- Department of Pharmacy, Xuanwu Hospital of Capital Medical University, Beijing 100053, China
| | - Yuan Hu
- Department of Pharmacy, Medical Supplier Center, Chinese PLA General Hospital, No. 28 FuXing Road, Haidian District, Beijing 100853, China
| | - Xian-Zhe Dong
- Department of Pharmacy, Xuanwu Hospital of Capital Medical University, 45 Changchun Road, Xicheng District, Beijing 100053, China
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Crane MM, Sands B, Battaglia C, Johnson B, Yun S, Kaeberlein M, Brent R, Mendenhall A. In vivo measurements reveal a single 5'-intron is sufficient to increase protein expression level in Caenorhabditis elegans. Sci Rep 2019; 9:9192. [PMID: 31235724 PMCID: PMC6591249 DOI: 10.1038/s41598-019-45517-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/06/2019] [Indexed: 11/29/2022] Open
Abstract
Introns can increase gene expression levels using a variety of mechanisms collectively referred to as Intron Mediated Enhancement (IME). IME has been measured in cell culture and plant models by quantifying expression of intronless and intron-bearing reporter genes in vitro. We developed hardware and software to implement microfluidic chip-based gene expression quantification in vivo. We altered position, number and sequence of introns in reporter genes controlled by the hsp-90 promoter. Consistent with plant and mammalian studies, we determined a single, natural or synthetic, 5'-intron is sufficient for the full IME effect conferred by three synthetic introns, while a 3'-intron is not. We found coding sequence can affect IME; the same three synthetic introns that increase mcherry protein concentration by approximately 50%, increase mEGFP by 80%. We determined IME effect size is not greatly affected by the stronger vit-2 promoter. Our microfluidic imaging approach should facilitate screens for factors affecting IME and other intron-dependent processes.
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Affiliation(s)
- Matthew M Crane
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA
| | - Bryan Sands
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA
| | - Christian Battaglia
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA
| | - Brock Johnson
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA
| | - Soo Yun
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA
| | - Matt Kaeberlein
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA
| | - Roger Brent
- Fred Hutchinson Cancer Research Center, Division of Basic Science, Seattle, WA, USA
| | - Alex Mendenhall
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA.
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Liu Z, Zheng WJ, Allen GI, Liu Y, Ruan J, Zhao Z. The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools. BMC Bioinformatics 2017; 18:405. [PMID: 28984189 PMCID: PMC5629550 DOI: 10.1186/s12859-017-1797-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The 2016 International Conference on Intelligent Biology and Medicine (ICIBM 2016) was held on December 8-10, 2016 in Houston, Texas, USA. ICIBM included eight scientific sessions, four tutorials, one poster session, four highlighted talks and four keynotes that covered topics on 3D genomics structural analysis, next generation sequencing (NGS) analysis, computational drug discovery, medical informatics, cancer genomics, and systems biology. Here, we present a summary of the nine research articles selected from ICIBM 2016 program for publishing in BMC Bioinformatics.
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Affiliation(s)
- Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA. .,Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - W Jim Zheng
- School of Biomedical Informatics, The University of Texas Health Science Center, Houston, TX, 77030, USA
| | - Genevera I Allen
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA.,Department of Statistics, Rice University, Houston, TX, 77030, USA.,Department of Electrical and Computer Engineering, Rice University, Houston, TX, 77030, USA
| | - Yin Liu
- Department of Neurobiology and Anatomy, The University of Texas Medical School at Houston, Houston, TX, 77030, USA
| | - Jianhua Ruan
- Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA. .,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
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