Read by QxMD icon Read

clinical bioinformatics

Manne Munikumar, Vagolu Siva Krishna, Varikasuvu Seshadri Reddy, Bolla Rajeswari, Dharmarajan Sriram, Mendu Vishnuvardhana Rao
Excess adiposity in obese inhibits negatively impacts immune function and host defence. Obesity is characterized by a state of low-grade, chronic inflammation in addition to disturbed levels of circulating nutrients and metabolic hormones. The impact of metabolic abnormalities on obesity-related co-morbidities has undergone intense scrutiny over the past decades. Thus, treatment of obesity and its associated immune-mediated diseases is challenging due to impaired function of leptin system. These disorders are managed through antibiotics and by cytokines replacement...
April 4, 2018: Journal of Molecular Graphics & Modelling
Jana Soukupova, Petra Zemankova, Klara Lhotova, Marketa Janatova, Marianna Borecka, Lenka Stolarova, Filip Lhota, Lenka Foretova, Eva Machackova, Viktor Stranecky, Spiros Tavandzis, Petra Kleiblova, Michal Vocka, Hana Hartmannova, Katerina Hodanova, Stanislav Kmoch, Zdenek Kleibl
BACKGROUND: Carriers of mutations in hereditary cancer predisposition genes represent a small but clinically important subgroup of oncology patients. The identification of causal germline mutations determines follow-up management, treatment options and genetic counselling in patients' families. Targeted next-generation sequencing-based analyses using cancer-specific panels in high-risk individuals have been rapidly adopted by diagnostic laboratories. While the use of diagnosis-specific panels is straightforward in typical cases, individuals with unusual phenotypes from families with overlapping criteria require multiple panel testing...
2018: PloS One
Xiaopeng Hu, Junping Ao, Xinyue Li, Huijuan Zhang, Ji Wu, Weiwei Cheng
Background: The etiology and pathogenesis of pre-eclampsia (PE) is unclear, and there is no ideal early clinical biomarker for prediction of PE. The competing endogenous RNA (ceRNA) hypothesis is a new approach to uncover the molecular pathology of PE. The first aim of this study was to perform messenger RNA, long non-coding RNA, and circular RNA (circRNA) expression profiling of human normal and severe pre-eclampsia (SPE) placentas. circRNA, which has a stable structure, is a more suitable biomarker than other types of RNA...
2018: Clinical Epigenetics
N Gao, F-X Wang, G Wang, Q-S Zhao
OBJECTIVE: Previous study reported that miR-498 served as a tumor suppressor in non-small cell lung cancer (NSCLC), but the underlying mechanism remains largely unknown. The aim of this study is to investigate the role of miR-498 and its target gene HMGA2 in NSCLC progression. PATIENTS AND METHODS: The expression of miR-498 was assessed in clinical NSCLC specimens and cell lines using RT-PCR. Overexpression of miR-498 and transfection of pLenti-HMGA2 were performed in A549 cells...
March 2018: European Review for Medical and Pharmacological Sciences
Motonobu Saito, Tomoyuki Momma, Koji Kono
Targeted therapy against actionable gene mutations shows a significantly higher response rate as well as longer survival compared to conventional chemotherapy, and has become a standard therapy for many cancers. Recent progress in next-generation sequencing (NGS) has enabled to identify huge number of genetic aberrations. Based on sequencing results, patients recommend to undergo targeted therapy or immunotherapy. In cases where there are no available approved drugs for the genetic mutations detected in the patients, it is recommended to be facilitate the registration for the clinical trials...
April 7, 2018: Fukushima Journal of Medical Science
Wen-Juan Wu, Yang Shen, Jing Sui, Cheng-Yun Li, Sheng Yang, Si-Yi Xu, Man Zhang, Li-Hong Yin, Yue-Pu Pu, Ge-Yu Liang
Cervical cancer (CC) is a common gynecological malignancy in women worldwide. Using an RNA sequencing profile from The Cancer Genome Atlas (TCGA) and the CC patient information, the aim of the present study was to identify potential long non‑coding RNA (lncRNA) biomarkers of CC using bioinformatics analysis and building a competing endogenous RNA (ceRNA) co‑expression network. Results indicated several CC‑specific lncRNAs, which were associated with CC clinical information and selected some of them for validation and evaluated their diagnostic values...
April 5, 2018: Molecular Medicine Reports
Shixiang Guo, Xuejun Xu, Yongsheng Ouyang, Yunchao Wang, Jiali Yang, Liangyu Yin, Jiayun Ge, Huaizhi Wang
Pancreatic cancer remains one of the most malignant tumors with a poor prognosis. Despite advances in diagnosis and treatment, no reliable biomarkers are available for clinical practice. Circular RNAs (circRNAs) are a novel class of endogenous non‑coding RNA, which are abundant, stable and conserved, and serve crucial roles in disease, particularly in cancer. The purpose of the present study was to investigate the expression profile of circRNAs in 20 pancreatic cancer tissues and corresponding paracancerous tissues using arraystar human circRNA array analysis, high‑throughput circRNA microarray, bioinformatic analysis and reverse transcription‑quantitative polymerase chain reaction...
March 29, 2018: Molecular Medicine Reports
Dan-Dan Xiong, Hao Chen, Rong-Quan He, Ai-Hua Lan, Jin-Cai Zhong, Gang Chen, Zhen-Bo Feng, Kang-Lai Wei
MicroRNAs (miRNAs or miRs) are highly conserved small noncoding RNA molecules involved in gene regulation. An increasing number of studies have demonstrated that miRNAs act as oncogenes or antioncogenes in various types of cancer, including breast cancer (BC). However, the exact role of miR‑671‑3p in BC has not yet been reported. In the present study, in vitro experiments were implemented to explore the effects of miR‑671‑3p on the proliferation and apoptosis of BC cells, and reverse transcription‑quantitative polymerase chain reaction was conducted using in‑house clinical BC samples to address the expression level and clinical value of miR‑671‑3p in BC...
March 28, 2018: International Journal of Oncology
Lukasz Roguski, Idoia Ochoa, Mikel Hernaez, Sebastian Deorowicz
Motivation: The affordability of DNA sequencing has led to the generation of unprecedented volumes of raw sequencing data. These data must be stored, processed, and transmitted, which poses significant challenges. To facilitate this effort, we introduce FaStore, a specialized compressor for FASTQ files. FaStore does not use any reference sequences for compression, and permits the user to choose from several lossy modes to improve the overall compression ratio, depending on the specific needs...
March 29, 2018: Bioinformatics
Aleksandar Poleksic, Lei Xie
Motivation: Adverse drug reactions (ADRs) are one of the main causes of death and a major financial burden on the world's economy. Due to the limitations of the animal model, computational prediction of serious, rare ADRs is invaluable. However, current state-of-the-art computational methods do not yield significantly better predictions of rare ADRs than random guessing. Results: We present a novel method, based on the theory of "compressed sensing", which can accurately predict serious side-effects of candidate and market drugs...
March 29, 2018: Bioinformatics
Reyka G Jayasinghe, Song Cao, Qingsong Gao, Michael C Wendl, Nam Sy Vo, Sheila M Reynolds, Yanyan Zhao, Héctor Climente-González, Shengjie Chai, Fang Wang, Rajees Varghese, Mo Huang, Wen-Wei Liang, Matthew A Wyczalkowski, Sohini Sengupta, Zhi Li, Samuel H Payne, David Fenyö, Jeffrey H Miner, Matthew J Walter, Benjamin Vincent, Eduardo Eyras, Ken Chen, Ilya Shmulevich, Feng Chen, Li Ding
For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function...
April 3, 2018: Cell Reports
Xiao-Ning Gan, Ting-Qing Gan, Rong-Quan He, Jie Luo, Rui-Xue Tang, Han-Lin Wang, Hong Zhou, Hui Qing, Jie Ma, Xiao-Hua Hu, Gang Chen
The role of microRNA (miRNA)-452-5p in lung squamous cell carcinoma (LUSC) remains unclear. Therefore, the present systematic study was performed to investigate the clinical significance and the rudimentary mechanism of the function of miR-452-5p in LUSC. The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were utilized to confirm the expression level and clinical value of miR-452-5p in LUSC. Using online databases and bioinformatic software, gene ontology (GO), pathway and protein-protein interaction (PPI) analyses of miR-452-5p target genes were performed to examine the molecular mechanism of miR-452-5p...
May 2018: Oncology Letters
Jia-Min Gao, Lin-Zhen Huang, Zhi-Guang Huang, Rong-Quan He
The clinicopathological value and exploration of the potential molecular mechanism of microRNA-183-5p (miR-183-5p) have been investigated in various cancers; however, to the best of the author's knowledge, no similar research has been reported for bladder cancer. In the present study, it was revealed that the expression level of miR-183-5p was notably increased in bladder cancer tissues compared with adjacent non-cancerous tissues (P=0.001) and was markedly increased in the tissue samples of papillary, pathological T stage (T0-T2) and pathological stage (I-II) compared with tissue samples of their counterparts (P=0...
April 2018: Oncology Letters
Manuel Ares-Arroyo, Cristina Bernabe-Balas, Alfonso Santos-Lopez, Maria R Baquero, Kashi N Prasad, Dolores Cid, Carmen Martin-Espada, Alvaro San Millan, Bruno Gonzalez-Zorn
ColE1 plasmids are important vehicles for the spread of antibiotic resistance in the Enterobacteriaceae and Pasteurellaceae families of bacteria. Their monitoring is essential, as they harbor important resistant determinants in humans, animals and the environment. In this work, we have analyzed ColE1 replicons using bioinformatic and experimental approaches. First, we carried out a computational study examining the structure of different ColE1 plasmids deposited in databases. Bioinformatic analysis of these ColE1 replicons revealed a mosaic genetic structure consisting of a host-adapted conserved region responsible for the housekeeping functions of the plasmid, and a variable region encoding a wide variety of genes, including multiple antibiotic resistance determinants...
2018: Frontiers in Microbiology
Wen Yuan, Songping Xie, Meng Wang, Shan Pan, Xiaoxing Huang, Meng Xiong, Rui-Jing Xiao, Jie Xiong, Qiu-Ping Zhang, Liang Shao
Background: ZWINT is a crucial component of the mitotic checkpoint. However, its possible role in lung cancer is unclear. In this study, we determined its correlation with lung cancer. Methods: Real-time PCR and immunohistochemistry (IHC) were used to determine 40 collected clinical lung cancer samples. Chi-square test was used to examine possible correlations between ZWINT expression and clinicopathological factors. The prognostic significance of mRNA expression of ZWINT in lung cancer was evaluated using the Kaplan-Meier plotter...
2018: OncoTargets and Therapy
Kentaro Miyazaki, Kei Kitahara
Our knowledge as to how bacteria acquire antibiotic resistance is still fragmented, especially for the ribosome-targeting drugs. In this study, with the aim of finding novel mechanisms that render bacteria resistant to the ribosome-targeting antibiotics, we developed a general method to systematically screen for antibiotic resistant 16 S ribosomal RNAs (rRNAs), which are the major target for multiple antibiotics (e.g. spectinomycin, tetracycline, and aminoglycosides), and identify point mutations therein...
April 3, 2018: Scientific Reports
Margherita Francescatto, Marco Chierici, Setareh Rezvan Dezfooli, Alessandro Zandonà, Giuseppe Jurman, Cesare Furlanello
BACKGROUND: High-throughput methodologies such as microarrays and next-generation sequencing are routinely used in cancer research, generating complex data at different omics layers. The effective integration of omics data could provide a broader insight into the mechanisms of cancer biology, helping researchers and clinicians to develop personalized therapies. RESULTS: In the context of CAMDA 2017 Neuroblastoma Data Integration challenge, we explore the use of Integrative Network Fusion (INF), a bioinformatics framework combining a similarity network fusion with machine learning for the integration of multiple omics data...
April 3, 2018: Biology Direct
Panagiotis G Adamopoulos, Christos K Kontos, Andreas ScorilasP
Tissue kallikrein, kallikrein-related peptidases (KLKs), and plasma kallikrein form the largest group of serine proteases in the human genome, sharing many structural and functional properties. Several KLK transcripts have been found aberrantly expressed in numerous human malignancies, confirming their prognostic or/and diagnostic values. However, the process of alternative splicing can now be studied in-depth due to the development of Next-Generation Sequencing (NGS). In the present study, we used NGS to discover novel transcripts of the KLK1 and KLK2 genes, after nested touchdown PCR...
March 31, 2018: Genomics
Lei Cao, Shiyan Wang, Yanquan Zhang, Ka-Chun Wong, Geicho Nakatsu, Xiaohong Wang, Sunny Wong, Jiafu Ji, Jun Yu
Zinc-finger protein 471 (ZNF471) was preferentially methylated in gastric cancer using promoter methylation array. The role of ZNF471 in human cancer is unclear. Here we elucidated the functional significance, molecular mechanisms and clinical impact of ZNF471 in gastric cancer. ZNF471 mRNA was silenced in 15 out of 16 gastric cancer cell lines due to promoter hypermethylation. Significantly higher ZNF471 promoter methylation was also observed in primary gastric cancers compared to their adjacent normal tissues (P < 0...
April 3, 2018: Oncogene
Qinglian Tang, Jinchang Lu, Changye Zou, Yang Shao, Yan Chen, Swami Narala, Hui Fang, Huaiyuan Xu, Jin Wang, Jingnan Shen, Rama Khokha
The era of cancer genomics now provides an opportunity to discover novel determinants of osteosarcoma (OS), the most common primary bone cancer in children and adolescents known for its poor prognosis due to lung metastasis. Here, we identify CDH4 amplification in 43.6% of human osteosarcoma using array CGH and demonstrate its critical role in osteosarcoma development and progression. Gain or loss-of-function of CDH4, which encodes R-cadherin, causally impacts multiple features of human OS cells including cell migration and invasion, osteogenic differentiation, and stemness...
April 3, 2018: Oncogene
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"