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Cancer genomics

Qiyu Liu, Chong Lu, Wanjun Dai, Ke Li, Jing Xu, Yunke Huang, Guiling Li, Yu Kang, Anil K Sood, Congjian Xu
In order to elucidate the mechanisms underlying the biobehavioral factors responsible for cervical cancer from the perspective of lncRNAs. Tumor samples were obtained from patients with stage Ib-IIb squamous cervical cancer, which were divided into high- and low-risk groups according to biobehavioral risk factors. A lncRNA + mRNA microarray was performed, and the results were validated using qRT-PCR. Gene ontology (GO), pathway, and lncRNA-mRNA co-expression analysis were performed to predict the potential functions of the differentially expressed transcripts...
2018: Bioscience Trends
Chang Xu
Detection of somatic mutations holds great potential in cancer treatment and has been a very active research field in the past few years, especially since the breakthrough of the next-generation sequencing technology. A collection of variant calling pipelines have been developed with different underlying models, filters, input data requirements, and targeted applications. This review aims to enumerate these unique features of the state-of-the-art variant callers, in the hope to provide a practical guide for selecting the appropriate pipeline for specific applications...
2018: Computational and Structural Biotechnology Journal
Derrick S Haslem, Ingo Chakravarty, Gail Fulde, Heather Gilbert, Brian P Tudor, Karen Lin, James M Ford, Lincoln D Nadauld
The impact of precision oncology on guiding treatment decisions of late-stage cancer patients was previously studied in a retrospective analysis. However, the overall survival and costs were not previously evaluated. We report the overall survival and healthcare costs associated with precision oncology in these patients with advanced cancer. Building on a matched cohort study of 44 patients with metastatic cancer who received all of their care within a single institution, we evaluated the overall survival and healthcare costs for each patient...
February 23, 2018: Oncotarget
Madiha Kanwal, Xiao-Jie Ding, Xin Song, Guang-Biao Zhou, Yi Cao
Air pollution is one of the leading causes of lung cancer. Air pollution-related lung cancer is a deteriorating public health problem, particularly in developing countries. The MUC16 gene is one of the most frequently mutated genes in air pollution-related lung cancer. In the present study, MUC16 mRNA expression was increased in ∼50% of air pollution-related lung cancer samples obtained from patients residing in air-polluted regions (Xuanwei and Fuyuan, Yunnan, China), and MUC16 mRNA levels were correlated with the degree of air pollution...
February 23, 2018: Oncotarget
Mengfan Qi, Ye Tian, Wang Li, Dan Li, Tian Zhao, Yuxin Yang, Qiwen Li, Sujun Chen, Yan Yang, Zhixiong Zhang, Liang Tang, Zhonghua Liu, Bo Su, Fei Li, Yonghong Feng, Ke Fei, Peng Zhang, Fan Zhang, Lei Zhang
Gefitinib, an EGFR tyrosine kinase inhibitor, is used to treat non-small cell lung cancer (NSCLC) patients with activating EGFR mutations. However, the resistance to gefitinib eventually emerges in most of the patients. To understand its mechanism, we generated two acquired gefitinib-resistant NSCLC cell lines. The resistant cells have slower growth rates, but are more resistant to apoptosis in the presence of gefitinib, compared with their sensitive counterparts. In addition, our genome-wide transcriptome analysis reveals unexpected pathways, particularly autophagy, are dysregulated in the gefitinib-resistant cells...
February 23, 2018: Oncotarget
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
Jiaming Huang, Tianyu Liu, Chunliang Shang, Yunhe Zhao, Wei Wang, Yanchun Liang, Luyan Guo, Shuzhong Yao
Long non-coding RNAs (lncRNAs) have been acknowledged to serve a significant role in cancer biology and abnormal expression in tumors is frequently observed. However, their mechanisms in cervical cancer remain unclear. With a genome-wide analysis of lncRNA expression in cervical cancer tissues, the present study aimed to identify lncRNA targets for the further study of cervical cancer. To elucidate the specific role of lncRNAs in the pathogenesis of this type of cancer, 6 cervical cancer samples paired with normal cervical tissues were obtained...
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
Pei-Hua Li, Lin Wang, Yao-Jie Pan, Miao-Miao Sang, Jun-Nian Zheng, Dong-Sheng Pei
c-Jun activation domain-binding protein-1 (Jab1) is a multifunctional protein involved in cell proliferation and apoptosis, DNA damage and repair and genome stability. In a number of types of human carcinoma, the abnormal expression of Jab1 is associated with poor prognosis, suggesting that Jab1 serves a vital function in tumorigenesis. However, the functional effects and the underlying molecular mechanisms of Jab1 in laryngeal squamous cell carcinoma (LSCC) progression remain poorly understood. The results of the present study demonstrate that downregulating Jab1 expression promotes LSCC apoptosis while inhibiting the proliferation of LSCC cells...
April 2018: Oncology Letters
Li-Qiang Zheng, Shan-Yi Li, Cheng-Xin Li
The aim of the present study was to identify the potential autophagy-related genes and to explore the underlying molecular mechanisms involved in cutaneous squamous cell carcinoma of head and neck (cSCCHN) by bioinformatics analysis. The Gene Expression Omnibus (GEO) series GSE86544 was downloaded from the GEO database. The primary data was generated from cSCCHN with clinical perineural invasion (PNI) and cSCCHN without PNI, and was further analyzed in order to identify differentially expressed genes (DEGs)...
April 2018: Oncology Letters
Choon Sen Seah, Shahreen Kasim, Mohd Farhan Md Fudzee, Jeffrey Mark Law Tze Ping, Mohd Saberi Mohamad, Rd Rohmat Saedudin, Mohd Arfian Ismail
Microarray technology has become one of the elementary tools for researchers to study the genome of organisms. As the complexity and heterogeneity of cancer is being increasingly appreciated through genomic analysis, cancerous classification is an emerging important trend. Significant directed random walk is proposed as one of the cancerous classification approach which have higher sensitivity of risk gene prediction and higher accuracy of cancer classification. In this paper, the methodology and material used for the experiment are presented...
December 2017: Saudi Journal of Biological Sciences
Xiaofu Wang, Bin Hao, Changbao Xu, Xinghua Zhao, Changwei Liu, Xiaohan Chu, Yuan Lv, Yongli Zhao, Shengwei Zhang, Pengsen Wang, Youzhi Wang
Background: Renal carcinoma is a common urologic tumor, and there is no ideal tumor marker for clinical diagnosis except for imaging diagnosis. This study aims to screen the serum tumor markers closely related with the benign and malignant of renal carcinoma out and chart out the regulatory network that involves renal carcinoma-related genes. Methods: Based on 96 pathologically diagnosed renal cancer patients, factors strongly linked to renal carcinoma character were selected using Fisher discriminant analysis...
December 2017: Saudi Journal of Biological Sciences
Jing Dong, David M Levine, Matthew F Buas, Rui Zhang, Lynn Onstad, Rebecca C Fitzgerald, Douglas A Corley, Nicholas J Shaheen, Jesper Lagergren, Laura J Hardie, Brian J Reid, Prasad G Iyer, Harvey A Risch, Carlos Caldas, Isabel Caldas, Paul D Pharoah, Geoffrey Liu, Marilie D Gammon, Wong-Ho Chow, Leslie Bernstein, Nigel C Bird, Weimin Ye, Anna H Wu, Lesley A Anderson, Stuart MacGregor, David C Whiteman, Thomas L Vaughan, Aaron P Thrift
BACKGROUND & AIMS: Genome-wide association studies (GWAS) have identified more than 20 susceptibility loci for esophageal adenocarcinoma (EA) and Barrett's esophagus (BE). However, variants in these loci account for a small fraction of cases of EA and BE. Genetic factors might interact with environmental factors to affect risk of EA and BE. We aimed to identify single nucleotide polymorphisms (SNPs) that may modify the associations of body mass index (BMI), smoking, and gastroesophageal reflux disease (GERD), with risks of EA and BE...
March 15, 2018: Clinical Gastroenterology and Hepatology
Liang-Qing Dong, Yang Shi, Li-Jie Ma, Liu-Xiao Yang, Xiao-Ying Wang, Shu Zhang, Zhi-Chao Wang, Meng Duan, Zhao Zhang, Long-Zi Liu, Bo-Hao Zheng, Zhen-Bin Ding, Ai-Wu Ke, Da-Ming Gao, Ke Yuan, Jian Zhou, Jia Fan, Ruibin Xi, Qiang Gao
BACKGROUND & AIMS: Intrahepatic cholangiocarcinoma (ICC) is the second-most lethal primary liver cancer. Little is known about intratumoral heterogeneity (ITH) and its impact on ICC progression. We aim to investigate its ITH in hope of helping develop new therapeutic strategies. METHODS: We obtained 69 spatially distinct regions from 6 operable ICCs. Patient-derived primary cancer cells (PDPCs) were established for each region, followed by whole-exome sequencing(WES) and multi-level validation...
March 15, 2018: Journal of Hepatology
Xi Ouyang, Guanping Zhang, Hua Pan, Jun Huang
PURPOSE: To explore the correlation between the SERT gene promoter single nucleotide polymorphisms (SNPs) rs25531 and rs956304 and the cancer-related fatigue (CRF) of colon and rectal cancer, and also to analyze the correlation of the interaction of genetic and non-genetic factors. METHOD: A sample of 568 colon and rectal cancer patients were recruited from the Second Affiliated Hospital of Nanchang University from October 2013 to December 2015. The Chinese version of the Brief Fatigue Inventory (BFI-C) was used to evaluate the CRF...
April 2018: European Journal of Oncology Nursing: the Official Journal of European Oncology Nursing Society
María Del Mar Sáez Freire, Adrián Blanco Gómez, Sonia Castillo Lluva, Aurora Gómez Vecino, Julie Milena Galvis Jiménez, Carmen Martín Seisdedos, María Isidoro García, Lourdes Hontecillas Prieto, María Begoña García-Cenador, Francisco Javier García Criado, María Carmen Patino Alonso, Purificación Galindo Villardón, Jian-Hua Mao, Carlos Prieto, Andrés Castellanos Martín, Lars Kaderali, Jesús Pérez Losada
The incidence of breast cancer increases with age until menopause, and breast cancer is more aggressive in younger women. The existence of epidemiological links between breast cancer and aging indicates that both processes share some common mechanisms of development. Oxidative stress is associated with both cancer susceptibility and aging. Here we observed that ERBB2-positive breast cancer, which developed in genetically heterogeneous ERBB2-positive transgenic mice generated by a backcross, is more aggressive in chronologically younger than in older mice (differentiated by the median survival of the cohort that was 79 weeks), similar to what occurs in humans...
March 14, 2018: Free Radical Biology & Medicine
Ahmed H Ghobashi, Maher A Kamel
The maintenance of genome integrity is essential for organism survival. Therefore, eukaryotic cells possess many DNA repair mechanisms in response to DNA damage. Acetyltransferase, Tip60, plays a central role in ATM and p53 activation which are involved in DNA repair. Recent works uncovered the roles of Tip60 in ATM and p53 activation and how Tip60 is recruited to double-strand break sites. Moreover, recent works have demonstrated the role of Tip60 in cancer progression. Here, we review the current understanding of how Tip60 activates both ATM and p53 in response to DNA damage and his new roles in tumorigenesis...
March 16, 2018: Journal of Applied Genetics
David Wu, Adam Waalkes, Kelsi Penewit, Stephen J Salipante
BACKGROUND: Genomic chimerism, the co-occurrence of cells from different genetic origins, provides important diagnostic information in diverse clinical contexts, including graft injury detection and longitudinal surveillance of hematopoietic stem cell transplantation patients, but existing assays are limiting. Here we applied single-molecule molecular inversion probes (smMIPs), a high-throughput sequencing technology combining multiplexed target capture with read quantification mediated by unique molecular identifiers, to detect chimerism based on the presence or absence of polymorphic genomic loci...
March 16, 2018: Clinical Chemistry
Pauline Funchain, Ahmad A Tarhini
Rapidly advancing genomic sequencing technologies are changing all areas of cancer, from diagnosis to surveillance, and prognostication to treatment. The role of genomic testing in melanoma is expanding, and multiple genomically based tests are available, including somatic tumor sequencing for actionable genetic alterations and tumor mutational burden, prognostic gene expression profiling from tumor tissue, and germline genetic testing from blood. The available testing options have varying levels of supporting data, from robust to preliminary...
March 15, 2018: Oncology (Williston Park, NY)
Anna S Berghoff, Priscilla K Brastianos
Brain metastases (BMs) reflect an area of high clinical need, as up to 40% of patients with metastatic cancer will develop this morbid and highly fatal complication. Historically, treatment strategies have relied on local approaches including radiosurgery, whole-brain radiotherapy, and neurosurgical resection. Recently, targeted and immune-modulating therapies have shown promising responses and have been introduced in the clinical management of patients with BMs. Recent improvements in genomic technologies have enriched our understanding of BMs and have demonstrated that BMs present with significant genetic divergence from the originating primary tumor, such that potentially targetable genetic alterations are detected only in the BMs...
February 2018: Seminars in Neurology
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