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RNA sequencing Cancer

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https://www.readbyqxmd.com/read/28641312/impact-of-novel-mir-145-3p-regulatory-networks-on-survival-in-patients-with-castration-resistant-prostate-cancer
#1
Yusuke Goto, Akira Kurozumi, Takayuki Arai, Nijiro Nohata, Satoko Kojima, Atsushi Okato, Mayuko Kato, Kazuto Yamazaki, Yasuo Ishida, Yukio Naya, Tomohiko Ichikawa, Naohiko Seki
BACKGROUND: Despite recent advancements, metastatic castration-resistant prostate cancer (CRPC) is not considered curative. Novel approaches for identification of therapeutic targets of CRPC are needed. METHODS: Next-generation sequencing revealed 945-1248 miRNAs from each lethal mCRPC sample. We constructed miRNA expression signatures of CRPC by comparing the expression of miRNAs between CRPC and normal prostate tissue or hormone-sensitive prostate cancer (HSPC)...
June 22, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28637221/digital-direct-detection-of-micrornas-using-single-molecule-arrays
#2
Limor Cohen, Mark R Hartman, Aaron Amardey-Wellington, David R Walt
MicroRNAs (miRNAs) are involved in many biological pathways, and detecting miRNAs accurately is critical for diagnosing a variety of diseases including cancer. However, most current methods for miRNA detection require lengthy sample preparation and amplification steps that can bias the results. In addition, lack of specificity and reproducibility give rise to various challenges in detection of circulating miRNAs in biological samples. In this work, we applied the Single Molecule Array (Simoa) technique to develop an ultra-sensitive sandwich assay for direct detection of multiple miRNAs without pre-amplification...
June 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28637169/novel-molecules-lncrnas-trfs-and-circrnas-deciphered-from-next-generation-sequencing-rna-sequencing-computational-databases-and-tools
#3
A Saleembhasha, Seema Mishra
Powerful next-generation sequencing (NGS) technologies, more specifically RNA sequencing (RNA-seq), have been pivotal toward the detection and analysis and hypotheses generation of novel biomolecules, long noncoding RNAs (lncRNAs), tRNA-derived fragments (tRFs) and circular RNAs (circRNAs). Experimental validation of the occurrence of these biomolecules inside the cell has been reported. Their differential expression and functionally important role in several cancers types as well as other diseases such as Alzheimer's and cardiovascular diseases have garnered interest toward further studies in this research arena...
June 20, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28634199/characterising-cis-regulatory-variation-in-the-transcriptome-of-histologically-normal-and-tumour-derived-pancreatic-tissues
#4
Mingfeng Zhang, Soren Lykke-Andersen, Bin Zhu, Wenming Xiao, Jason W Hoskins, Xijun Zhang, Lauren M Rost, Irene Collins, Martijn van de Bunt, Jinping Jia, Hemang Parikh, Tongwu Zhang, Lei Song, Ashley Jermusyk, Charles C Chung, Bin Zhu, Weiyin Zhou, Gail L Matters, Robert C Kurtz, Meredith Yeager, Torben Heick Jensen, Kevin M Brown, Halit Ongen, William R Bamlet, Bradley A Murray, Mark I McCarthy, Stephen J Chanock, Nilanjan Chatterjee, Brian M Wolpin, Jill P Smith, Sara H Olson, Gloria M Petersen, Jianxin Shi, Laufey Amundadottir
OBJECTIVE: To elucidate the genetic architecture of gene expression in pancreatic tissues. DESIGN: We performed expression quantitative trait locus (eQTL) analysis in histologically normal pancreatic tissue samples (n=95) using RNA sequencing and the corresponding 1000 genomes imputed germline genotypes. Data from pancreatic tumour-derived tissue samples (n=115) from The Cancer Genome Atlas were included for comparison. RESULTS: We identified 38 615 cis-eQTLs (in 484 genes) in histologically normal tissues and 39 713 cis-eQTL (in 237 genes) in tumour-derived tissues (false discovery rate <0...
June 20, 2017: Gut
https://www.readbyqxmd.com/read/28628120/intestinal-cancer-progression-by-mutant-p53-through-the-acquisition-of-invasiveness-associated-with-complex-glandular-formation
#5
M Nakayama, E Sakai, K Echizen, Y Yamada, H Oshima, T-S Han, R Ohki, S Fujii, A Ochiai, S Robine, D C Voon, T Tanaka, M M Taketo, M Oshima
Tumor suppressor TP53 is frequently mutated in colorectal cancer (CRC), and most mutations are missense type. Although gain-of-functions by mutant p53 have been demonstrated experimentally, the precise mechanism for malignant progression in in vivo tumors remains unsolved. We generated Apc(Δ716) Trp53(LSL•R270H) villin-CreER compound mice, in which mutant p53(R270H) was expressed in the intestinal epithelia upon tamoxifen treatment, and examined the intestinal tumor phenotypes and tumor-derived organoids...
June 19, 2017: Oncogene
https://www.readbyqxmd.com/read/28625393/establishment-and-characterization-of-uterine-sarcoma-and-carcinosarcoma-patient-derived-xenograft-models
#6
Tine Cuppens, Jeroen Depreeuw, Daniela Annibali, Debby Thomas, Els Hermans, Ellen Gommé, Xuan Bich Trinh, David Debruyne, Philippe Moerman, Diether Lambrechts, Frédéric Amant
OBJECTIVE: Uterine sarcomas (US) and carcinosarcomas (CS) are rare, aggressive cancers. The lack of reliable preclinical models hampers the search for new treatment strategies and predictive biomarkers. To this end, we established and characterized US and CS patient-derived xenograft (PDX) models. METHODS: Tumor fragments of US and CS were subcutaneously implanted into immunocompromised mice. Engrafted xenograft and original tumors were compared by means of histology, immunohistochemistry, whole-genome low-coverage sequencing for copy number variations, and RNA sequencing...
June 16, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/28624202/2l-pirna-a-two-layer-ensemble-classifier-for-identifying-piwi-interacting-rnas-and-their-function
#7
Bin Liu, Fan Yang, Kuo-Chen Chou
Involved with important cellular or gene functions and implicated with many kinds of cancers, piRNAs, or piwi-interacting RNAs, are of small non-coding RNA with around 19-33 nt in length. Given a small non-coding RNA molecule, can we predict whether it is of piRNA according to its sequence information alone? Furthermore, there are two types of piRNA: one has the function of instructing target mRNA deadenylation, and the other does not. Can we discriminate one from the other? With the avalanche of RNA sequences emerging in the postgenomic age, it is urgent to address the two problems for both basic research and drug development...
June 16, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28622687/identification-of-a-novel-p53-target-col17a1-that-inhibits-breast-cancer-cell-migration-and-invasion
#8
Varalee Yodsurang, Chizu Tanikawa, Takafumi Miyamoto, Paulisally Hau Yi Lo, Makoto Hirata, Koichi Matsuda
p53 mutation is a marker of poor prognosis in breast cancers. To identify downstream targets of p53, we screened two transcriptome datasets, including cDNA microarrays of MCF10A breast epithelial cells with wild-type p53 or p53-null background, and RNA sequence analysis of breast invasive carcinoma. Here, we unveil ten novel p53 target candidates that are up-regulated after the induction of p53 in wild-type cells. Their expressions are also high in breast invasive carcinoma tissues with wild-type p53. The GO analysis identified epidermis development and ectoderm development, which COL17A1 participates, as significantly up-regulated by wild-type p53...
June 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28622514/landscape-of-infiltrating-t-cells-in-liver-cancer-revealed-by-single-cell-sequencing
#9
Chunhong Zheng, Liangtao Zheng, Jae-Kwang Yoo, Huahu Guo, Yuanyuan Zhang, Xinyi Guo, Boxi Kang, Ruozhen Hu, Julie Y Huang, Qiming Zhang, Zhouzerui Liu, Minghui Dong, Xueda Hu, Wenjun Ouyang, Jirun Peng, Zemin Zhang
Systematic interrogation of tumor-infiltrating lymphocytes is key to the development of immunotherapies and the prediction of their clinical responses in cancers. Here, we perform deep single-cell RNA sequencing on 5,063 single T cells isolated from peripheral blood, tumor, and adjacent normal tissues from six hepatocellular carcinoma patients. The transcriptional profiles of these individual cells, coupled with assembled T cell receptor (TCR) sequences, enable us to identify 11 T cell subsets based on their molecular and functional properties and delineate their developmental trajectory...
June 15, 2017: Cell
https://www.readbyqxmd.com/read/28622513/comprehensive-and-integrative-genomic-characterization-of-hepatocellular-carcinoma
#10
(no author information available yet)
Liver cancer has the second highest worldwide cancer mortality rate and has limited therapeutic options. We analyzed 363 hepatocellular carcinoma (HCC) cases by whole-exome sequencing and DNA copy number analyses, and we analyzed 196 HCC cases by DNA methylation, RNA, miRNA, and proteomic expression also. DNA sequencing and mutation analysis identified significantly mutated genes, including LZTR1, EEF1A1, SF3B1, and SMARCA4. Significant alterations by mutation or downregulation by hypermethylation in genes likely to result in HCC metabolic reprogramming (ALB, APOB, and CPS1) were observed...
June 15, 2017: Cell
https://www.readbyqxmd.com/read/28621736/a-panel-of-micrornas-as-diagnostic-biomarkers-for-the-identification-of-prostate-cancer
#11
Rhonda Daniel, Qianni Wu, Vernell Williams, Gene Clark, Georgi Guruli, Zendra Zehner
Prostate cancer is the most common non-cutaneous cancer among men; yet, current diagnostic methods are insufficient, and more reliable diagnostic markers need to be developed. One answer that can bridge this gap may lie in microRNAs. These small RNA molecules impact protein expression at the translational level, regulating important cellular pathways, the dysregulation of which can exert tumorigenic effects contributing to cancer. In this study, high throughput sequencing of small RNAs extracted from blood from 28 prostate cancer patients at initial stages of diagnosis and prior to treatment was used to identify microRNAs that could be utilized as diagnostic biomarkers for prostate cancer compared to 12 healthy controls...
June 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28618937/37lrp-induces-invasion-in-hypoxic-lung-adenocarcinoma-cancer-cells-a549-through-the-jnk-erk-c-jun-signaling-cascade
#12
Yongan Zhou, Yafang Wang, Zhengwei Zhao, Yanxia Wang, Ning Zhang, Helong Zhang, Lili Liu
We previously reported that 37-kDa laminin receptor precursor involved in metastasis of lung adenocarcinoma cancer cells. In this study, we further revealed that hypoxia induced 37-kDa laminin receptor precursor expression and activation of extracellular signal-regulated protein kinase, c-Jun N-terminal kinase, and p38 mitogen-activated protein kinase in lung adenocarcinoma cancer cells. In addition, we further demonstrated that the c-Jun N-terminal kinase inhibitor SP600125 and extracellular signal-regulated protein kinase inhibitor U0126 blocked the c-Jun activity and abolished hypoxia-induced 37-kDa laminin receptor precursor expression and promoter activity in a concentration-dependent manner...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28618934/identification-of-curcumin-inhibited-extracellular-matrix-receptors-in-non-small-cell-lung-cancer-a549-cells-by-rna-sequencing
#13
Huiping Li, Hongjin Wu, Hongfang Zhang, Ying Li, Shuang Li, Qiang Hou, Shixiu Wu, Shuan-Ying Yang
Curcumin is a potent anti-cancer drug in several types of human cancers. Despite of several preclinical and clinical studies of curcumin, the precise mechanism of curcumin in cancer prevention has remained unclear. In our study, we for the first time investigated whole transcriptome alteration in A549 non-small cell lung cancer (NSCLC) cell lines after treatment with curcumin using RNA sequencing. We found that lots of genes and signaling pathways were significantly altered after curcumin treatment in A549 cells...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28618399/rna-sequencing-investigation-identifies-an-effective-risk-score-generated-by-three-novel-lncrnas-for-the-survival-of-papillary-thyroid-cancer-patients
#14
Yi-Huan Luo, Liang Liang, Rong-Quan He, Dong-Yue Wen, Guo-Fei Deng, Hong Yang, Yun He, Wei Ma, Xiao-Yong Cai, Jun-Qiang Chen, Gang Chen
Scholars are striving to apply molecular biology involving long non-coding RNA (lncRNA) in the prognostication of papillary thyroid cancer (PTC). However, the clinical role of lncRNAs in the prognostic setting of PTC is still unclear. Herein, a comprehensive inquiry was performed to screen lncRNA expression profiling with 507 PTC patients from The Cancer Genome Atlas RNA-sequencing datasets. A total of 734 lncRNAs were detected to be aberrantly expressed, among which three novel lncRNAs including AC079630.2, CRNDE and CTD-2171N6...
May 26, 2017: Oncotarget
https://www.readbyqxmd.com/read/28618396/vitamin-d-receptor-binding-site-variants-affect-prostate-cancer-progression
#15
Victor C Lin, Shu-Pin Huang, Huei-Ju Ting, Wen-Lung Ma, Chia-Cheng Yu, Chao-Yuan Huang, Hsin-Ling Yin, Tsung-Yi Huang, Cheng-Hsueh Lee, Ta-Yuan Chang, Te-Ling Lu, Bo-Ying Bao
Vitamin D is an important modulator of cellular proliferation through the vitamin D receptor (VDR) that binds to DNA in the regulatory sequences of target genes. We hypothesized that single nucleotide polymorphisms (SNPs) in VDR-binding sites might affect target gene expression and influence the progression of prostate cancer. Using a genome-wide prediction database, 62 SNPs in VDR-binding sites were selected for genotyping in 515 prostate cancer patients and the findings were replicated in an independent cohort of 411 patients...
May 26, 2017: Oncotarget
https://www.readbyqxmd.com/read/28618162/zeb1-regulated-inflammatory-phenotype-in-breast-cancer-cells
#16
Akihiro Katsura, Yusuke Tamura, Satoshi Hokari, Mayumi Harada, Masato Morikawa, Tsubasa Sakurai, Kei Takahashi, Anna Mizutani, Jun Nishida, Yuichiro Yokoyama, Yasuyuki Morishita, Takashi Murakami, Shogo Ehata, Kohei Miyazono, Daizo Koinuma
Zinc finger E-box binding protein 1 (ZEB1) and ZEB2 induce epithelial-mesenchymal transition (EMT) and enhance cancer progression. However, the global view of transcriptional regulation by ZEB1 and ZEB2 is yet to be elucidated. Here, we identified a ZEB1-regulated inflammatory phenotype in breast cancer cells using chromatin immunoprecipitation-sequencing and RNA sequencing, followed by gene set enrichment analysis (GSEA) of ZEB1-bound genes. Knockdown of ZEB1 and/or ZEB2 resulted in the down-regulation of genes encoding inflammatory cytokines related to poor prognosis in cancer patients, including IL6 and IL8, therefore suggesting that ZEB1 and ZEB2 have similar functions in terms of the regulation of production of inflammatory cytokines...
June 15, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28618048/transcriptomic-profiling-in-human-decidua-of-severe-preeclampsia-detected-by-rna-sequencing
#17
Jing Tong, Weixiu Zhao, Hong Lv, Wei-Ping Li, Zi-Jiang Chen, Cong Zhang
Maternal decidua plays a critical role in implantation and placentation. Impaired decidualization causes failed intravascular trophoblast invasion and inadequate placentation and then increases the risk of preeclampsia (PE). RNA sequencing (RNA-Seq) has achieved great advances in the characterization and quantification of transcriptomes, is a powerful tool for new transcript discovery, genome annotation and expression profiling. In the present study, we conducted a RNA-Seq analysis to compare gene expression between decidua of PE (n = 3, early-onset severe PE, EOSPE; n = 3, late-onset severe PE, LOSPE) and normal pregnancies (n = 3)...
June 15, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28615101/-eukaryotic-expression-and-localization-of-human-mterf2-in-cervical-cancer-caski-cells
#18
Meitao Sun, Chenggui Zhang, Wen Mei, Yongqin Yang, Zefang Yang, Xiaojuan Zhang, Wei Xiong
Objective To construct the recombinant eukaryotic expression vector of human mitochondrial transcription termination factor 2 (MTERF2) gene and determine the cellular localization by overexpressing MTERF2 in human Caski cervical cancer cells. Methods The coding sequence of MTERF2 was amplified by reverse transcription-PCR using the total RNA extracted from human cervical cancer Caski cells, and then was inserted into p3×FLAG-CMV-14 vector. After being verified by PCR and DNA sequencing, the positive recombinant plasmid was transiently transfected into Caski cells...
June 2017: Xi Bao Yu Fen Zi Mian Yi Xue za Zhi, Chinese Journal of Cellular and Molecular Immunology
https://www.readbyqxmd.com/read/28612520/regulation-of-itga3-by-the-anti-tumor-mir-199-family-inhibits-cancer-cell-migration-and-invasion-in-head-and-neck-cancer
#19
Keiichi Koshizuka, Toyoyuki Hanazawa, Naoko Kikkawa, Takayuki Arai, Atsushi Okato, Akira Kurozumi, Mayuko Kato, Koji Katada, Yoshitaka Okamoto, Naohiko Seki
For patients with head and neck squamous cell carcinoma (HNSCC), survival rates have not improved due to local recurrence and distant metastasis. Current targeted molecular therapies do not provide a substantial benefit to HNSCC patients. Therefore, it is necessary to use advanced genomic approaches to elucidate the molecular mechanisms underlying the aggressiveness of HNSCC cells. Analysis of our microRNA (miRNA) expression signature by RNA-sequencing showed that the miR-199 family (miR-199a-5p, miR-199a-3p, miR-199b-5p and miR-199b-3p) was significantly reduced in cancer tissues...
June 14, 2017: Cancer Science
https://www.readbyqxmd.com/read/28612394/tumor-associated-with-cd70-expression-is-involved-in-promoting-tumor-migration-and-macrophage-infiltration-in-gbm
#20
Haitao Ge, Luyan Mu, Linchun Jin, Changlin Yang, Yifan Emily Chang, Yu Long, Gabriel De Leon, Loic Deleyrolle, Duane A Mitchell, Paul S Kubilis, Dunyue Lu, Jiping Qi, Yunhe Gu, Zhiguo Lin, Jianping Huang
Tumor migration/metastasis and immunosuppression are major obstacles in effective cancer therapy. Incidentally, these 2 hurdles usually coexist inside tumors, therefore making therapy significantly more complicated, as both oncogenic mechanisms must be addressed for successful therapeutic intervention. Our recent report highlights that the tumor expression of a TNF family member, CD70, is correlated with poor survival for primary gliomas. In this study, we investigated how CD70 expression by GBM affects the characteristics of tumor cells and the tumor microenvironment...
June 13, 2017: International Journal of Cancer. Journal International du Cancer
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