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bioinformatic cancer

W-B Kuang, Q -C Deng, C-T Deng, W-S Li, Y-G Zhang, S-W Shu, M-R Zhou
OBJECTIVE: Breast cancer cell infiltration, migration, and proliferation significantly affect its curative effect. Stemness gene octamer-binding transcription factor 4 (OCT4) upregulated in breast cancer tissue compared with normal control. MiRNA exhibits regulatory role in gene expression. This study adopted bioinformatics to predict the miRNA to regulate OCT4 gene and investigated its impact on breast cancer cell infiltration, migration, and proliferation. MATERIALS AND METHODS: MirBase database was analyzed to explore the potential miRNA in regulating OCT4 based on human OCT4 gene sequence...
March 2018: European Review for Medical and Pharmacological Sciences
X Yang, W Zhang, S-Q Cheng, R-L Yang
OBJECTIVE: To clarify the role of long non-coding RNA (lncRNA) GACAT3 in invasion and metastasis of non-small cell lung cancer (NSCLC) and its effect on radiotherapy. PATIENTS AND METHODS: The expression of GACAT3 and TIMP2 in cells and tissues of NSCLC were detected by quantitative Real-time PCR (qRT-PCR). The influence of GACAT3 on cell proliferation and the capacity of colony formation were estimated by MTT test and colony forming experiment respectively. Luciferase reporting assay was used to confirm the correlation between GACAT3 and TIMP2...
March 2018: European Review for Medical and Pharmacological Sciences
W-W Liao, C Zhang, F-R Liu, W-J Wang
OBJECTIVE: MiR-155 has been shown to be up-regulated in hepatocellular carcinoma (HCC) patients. B-cell lymphoma-2 (Bcl-2) interacting mediator of cell death (BIM) regulates cell proliferation and apoptosis, as its down-regulation is involved in HCC onset. Transcriptional factor FoxO3a mediates BIM expression and is related to HCC pathogenesis. Bioinformatics analysis showed targeted regulation of FoxO3a by miR-155. This study aims to investigate whether miR-155 plays a role in mediating FoxO3a/BIM signal pathway and HCC occurrence...
March 2018: European Review for Medical and Pharmacological Sciences
Dustin C Hancks
Chromothripsis is a mutational event driven by tens to hundreds of double-stranded DNA breaks which occur in a single event between a limited number of chromosomes. Following chromosomal shattering, DNA fragments are stitched together in a seemingly random manner resulting in complex genomic rearrangements including sequence shuffling, deletions, and inversions of varying size. This genomic catastrophe has been observed in cancer genomes and the genomes of patients harboring developmental and congenital defects...
2018: Methods in Molecular Biology
Yu-Yan Li, Guang Zheng, Liang Liu
OBJECTIVE: To decipher the possible mechanisms of Sinomenium Acutum (SA) in treating diseases by a bioinformatics method. METHODS: SA ingredients were searched according to Chinese Pharmacopoeia, Chinese Medicine Dictionary and Traditional Chinese Medicines Database (TCMD). Active compounds and target proteins of SA were acquired through the Pubchem platform. Pathway, network and function analyses of SA were performed with ingenuity pathway analysis (IPA), a bioinformatics analysis platform...
March 21, 2018: Chinese Journal of Integrative Medicine
Zhao-Xiong Zhang, Wan-Ni Zhang, Yuan-Yuan Sun, Yun-Hui Li, Zhen-Ming Xu, Wei-Neng Fu
Purpose: CREB, MYCY1 and NAT10 are involved in cancer cell migration. However, the relationship between these three proteins and their role in laryngeal cancer cell migration remains unknown. Methods: Transient gene transfection was performed in laryngeal cancer cells. Bioinformatics analysis was used to predict the binding of CREB to MYCT1 promoter. Binding of CREB to the promoter of MYCT1 was monitored by luciferase reporter assay and chromatin immuno-precipitation method in vitro and in vivo, respectively...
2018: OncoTargets and Therapy
Yang Cao, Xu Shi, Yingmin Liu, Ren Xu, Qing Ai
MicroRNA-338-3p has been reported to be a tumor suppressor in multiple cancer types. However, the biological role of miR-338-3p and underlying mechanism in multiple myeloma (MM) remains unclear. In the present study, we investigate the biological role and potential of miR-338-3p in MM. We found that miR-338-3p was significantly decreased in MM newly diagnosed and relapsed tissues and cell lines. Overexpression of miR-338-3p in MM cells significantly inhibited proliferation and promoted apoptosis, and caspase-3 and caspase-8 activity...
March 21, 2018: Oncology Research
Widodo, Nadya Veronica Margarecaesha Anyndita, Nurul Dluha, Muhaimin Rifa'i, Karimatul Himmah, Mulya Dwi Wahyuningsih
Background: Epstein-Barr virus (EBV) can cause cancer in people from around the world. There is no EBV vaccine available for use on a global scale. However, emerging evidence suggests that the epitope on the gp350/220 capsid protein may be developed into an EBV vaccine. Nevertheless, the production of small, single epitope is challenging of stability issues and possible alteration of peptide structure. In this study, a tandem epitope was developed consisting of three single epitopes, aimed to improve stability, antigenicity and preserve epitope structure...
March 2018: Heliyon
Balázs Győrffy, Lőrinc Pongor, Giulia Bottai, Xiaotong Li, Jan Budczies, András Szabó, Christos Hatzis, Lajos Pusztai, Libero Santarpia
BACKGROUND: Sequence variations in coding and non-coding regions of the genome can affect gene expression and signalling pathways, which in turn may influence disease outcome. METHODS: In this study, we integrated somatic mutations, gene expression and clinical data from 930 breast cancer patients included in the TCGA database. Genes associated with single mutations in molecular breast cancer subtypes were identified by the Mann-Whitney U-test and their prognostic value was evaluated by Kaplan-Meier and Cox regression analyses...
March 21, 2018: British Journal of Cancer
Jude Masannat, Hamsa Thayele Purayil, Yushan Zhang, Michelle Russin, Iqbal Mahmud, Wanju Kim, Daiqing Liao, Yehia Daaka
Renal Cell Carcinoma (RCC) is one of the most lethal urological cancers worldwide. The disease does not present early clinical symptoms and is commonly diagnosed at an advanced stage. Limited molecular drivers have been identified for RCC, resulting in the lack of effective treatment for patients with progressive disease. Ubiquitous βArrestin2 (βArr2) is well established for its function in the desensitization and trafficking of G protein-coupled receptors. More recently, βArr2 has been implicated in the regulation of fundamental cellular functions, including proliferation and invasion...
March 20, 2018: Scientific Reports
Li Gao, Li-Jie Zhang, Sheng-Hua Li, Li-Li Wei, Bin Luo, Rong-Quan He, Shuang Xia
BACKGROUND: MiR-452-5p has been reported to be down-regulated in prostate cancer, affecting the development of this type of cancer. However, the molecular mechanism of miR-452-5p in prostate cancer remains unclear. Therefore, we investigated the network of target genes of miR-452-5p in prostate cancer using bioinformatics analyses. MATERIALS AND METHODS: We first analyzed the expression profiles and prognostic value of miR-452-5p in prostate cancer tissues from a public database...
March 6, 2018: Pathology, Research and Practice
Amit A Upadhyay, Robert C Kauffman, Amber N Wolabaugh, Alice Cho, Nirav B Patel, Samantha M Reiss, Colin Havenar-Daughton, Reem A Dawoud, Gregory K Tharp, Iñaki Sanz, Bali Pulendran, Shane Crotty, F Eun-Hyung Lee, Jens Wrammert, Steven E Bosinger
B cells play a critical role in the immune response by producing antibodies, which display remarkable diversity. Here we describe a bioinformatic pipeline, BALDR (BCR Assignment of Lineage using De novo Reconstruction) that accurately reconstructs the paired heavy and light chain immunoglobulin gene sequences from Illumina single-cell RNA-seq data. BALDR was accurate for clonotype identification in human and rhesus macaque influenza vaccine and simian immunodeficiency virus vaccine induced vaccine-induced plasmablasts and naïve and antigen-specific memory B cells...
March 20, 2018: Genome Medicine
Dawei Cai, Zongjian Liu, Guangqi Kong
BACKGROUND Circular RNAs (circRNAs) have emerged as important regulators in carcinogenesis and metastasis. However, the knowledge of circRNAs in bladder cancer remains limited. This study aimed to investigate the role and mechanism of circRNAs in the development and progression of bladder cancer. MATERIAL AND METHODS Three pairs of bladder carcinomas (including high- and low-grade tumors) and adjacent normal tissues were collected from patients. The total RNAs were extracted from these samples and subjected to Clariom D microarray assays to detect the differentially expressed circRNAs and mRNAs...
March 20, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Qian Zhou, Hui Zeng, Peng Ye, Yu Shi, Juan Guo, Xinghua Long
Increasing evidence has shown that the dysregulation of microRNAs (miRNAs) is associated with drug resistance. Fulvestrant and tamoxifen represent the major endocrine drugs for the treatment of breast cancer patients, and yet little is known about the biological mechanisms of acquiring resistance to fulvestrant and tamoxifen, let alone the differences between cell lines resistant to these two drugs. Exploration of the differential miRNA profiles between these two cell lines is a useful way to further clarify these resistance mechanisms...
March 19, 2018: Anti-cancer Drugs
Xiaolei Hu, Jie Wang, Wan He, Pan Zhao, Changsheng Ye
Breast cancer is the most frequently diagnosed malignancy in women. However, the molecular mechanisms underlying breast cancer pathogenesis are not fully understood. The present study examined the role of miR-433 in breast cancer and investigated its underlying molecular mechanisms of action. Reverse transcription-quantitative polymerase chain reaction and western blot analysis were performed to analyze the level of microRNA (miRNA/miR)/mRNA and protein expression, respectively. Additionally, MTT assay was used to determined cell proliferation and viability...
March 2018: Oncology Letters
Fangfang Tao, Xinxin Tian, Zhiqian Zhang
Long non-coding RNAs (lncRNAs) have been reported to be of great importance in the formation and progression of a wide range of human carcinomas including prostate cancer (PCa). Among them, PCAT3 and PCAT9 have been identified as two prostate tissue-specific lncRNAs and are up-regulated in PCa. However, their roles in the biological characteristics of PCa have not been fully elucidated. In the present study, our data revealed that knockdown of PCAT3 and PCAT9 suppressed cellular proliferation, invasion, migration, angiogenesis and stemness in androgen-dependent LNCaP and 22Rv1 cells...
February 23, 2018: Oncotarget
Qiang Wang, Yiwan Teng, Rong Wang, Danni Deng, Yijie You, Ya Peng, Naiyuan Shao, Feng Zhi
Malignant glioma is one of the most common types of primary brain tumours. Long non-coding RNAs (lncRNAs) have recently emerged as a new class of therapeutic targets for many cancers. In this study, we aimed to explore the functional involvement of small nucleolar RNA host gene 14 (SNHG14) and its potential regulatory mechanism in glioma progression. SNHG14 was found to be downregulated in human glioma tissues and cell lines. SNHG14 significantly inhibited cell viability, reduced cell invasion, and induced apoptosis in glioma cell lines...
February 23, 2018: Oncotarget
Xuechun Yu, Chaojian Ma, Ling Fu, Jingwu Dong, Jie Ying
The expression, function and underlying mechanisms of microRNA-139 (miR-139) in gastric cancer were investigated in the present study. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was performed to detect miR-139 expression in gastric cancer tissues and cell lines. The effects of miR-139 overexpression on gastric cancer cell proliferation, migration and invasion were evaluated. ρ-associated protein kinase 1 (ROCK1) was predicted as a downstream target of miR-139 and its role in gastric cancer was assessed by bioinformatics analysis, luciferase reporter assay, RT-qPCR and western blot analysis...
April 2018: Oncology Letters
Feilun Cui, Jianpeng Hu, Yu Fan, Jian Tan, Huaming Tang
Prostate cancer (PCa) is the most frequently diagnosed type of cancer in Chinese males. Cell-cycle aberration is a hallmark of cancer. Spindle pole body component 25 homolog (SPC25), a component of the Ndc80 complex, serves an important role in regulating mitotic chromosome segregation. However, the functional roles of SPC25 in PCa remain poorly understood. To the best of our knowledge, the present study was the first to demonstrate that SPC25 is significantly upregulated in PCa. In order to investigate the molecular roles of SPC25, a loss of function assay was performed, revealing that SPC25 knockdown inhibited cell proliferation, and induced a decrease in the number of cells in the S phase and an increase in the number of cells in the G2/M phase...
April 2018: Oncology Letters
Rong-Quan He, Xia Yang, Liang Liang, Gang Chen, Jie Ma
The present study aimed to explore the potential clinical significance of microRNA (miR)-124-3p expression in the hepatocarcinogenesis and development of hepatocellular carcinoma (HCC), as well as the potential target genes of functional HCC pathways. Reverse transcription-quantitative polymerase chain reaction was performed to evaluate the expression of miR-124-3p in 101 HCC and adjacent non-cancerous tissue samples. Additionally, the association between miR-124-3p expression and clinical parameters was also analyzed...
April 2018: Oncology Letters
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