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cancer transcriptome

Yuqing Yang, Renyi Wu, Davit Sargsyan, Ran Yin, Hsiao-Chen Kuo, Irene Yang, Lujing Wang, David Cheng, Chao Wang, Shanyi Li, Rasika Hudlikar, Yaoping Lu, Ah-Ng Kong
Exposure to ultraviolet B (UVB) irradiation results in multitude of cellular responses including generation of reactive oxygen species and DNA damage and is responsible for non-melanoma skin cancers (NMSCs). Although genetic mutation is well documented, the epi-mutation, the alteration in epigenetics, remains elusive. In this study, we utilized CpG Methyl-seq to identify a genome-wide DNA CpG methylation, to profile the DNA methylation in UVB-irradiated SKH-1 mouse skin epidermis and non-melanoma skin papillomas at various stages...
February 13, 2019: Cancer Letters
Patrycja Przygodzka, Izabela Papiewska-Pająk, Helena Bogusz-Koziarska, Ewelina Sochacka, Joanna Boncela, M Anna Kowalska
Epithelial-to-mesenchymal transition (EMT) in cancer cells, represents early stages of metastasis and is a promising target in colorectal cancer (CRC) therapy. There have been many attempts to identify markers and key pathways induced throughout EMT but the process is complex and depends on the cancer type and tumour microenvironment. Here we used the colon cancer cell line HT29, which stably overexpressed Snail, the key transcription factor in early EMT, as a model for colorectal adenocarcinoma cells with a pro-metastatic phenotype...
February 15, 2019: Scientific Reports
Haonan Lu, Mubarik Arshad, Andrew Thornton, Giacomo Avesani, Paula Cunnea, Ed Curry, Fahdi Kanavati, Jack Liang, Katherine Nixon, Sophie T Williams, Mona Ali Hassan, David D L Bowtell, Hani Gabra, Christina Fotopoulou, Andrea Rockall, Eric O Aboagye
The five-year survival rate of epithelial ovarian cancer (EOC) is approximately 35-40% despite maximal treatment efforts, highlighting a need for stratification biomarkers for personalized treatment. Here we extract 657 quantitative mathematical descriptors from the preoperative CT images of 364 EOC patients at their initial presentation. Using machine learning, we derive a non-invasive summary-statistic of the primary ovarian tumor based on 4 descriptors, which we name "Radiomic Prognostic Vector" (RPV)...
February 15, 2019: Nature Communications
Anbang Wang, Yi Bao, Zhenjie Wu, Tangliang Zhao, Dong Wang, Jiazi Shi, Bing Liu, Shuhan Sun, Fu Yang, Linhui Wang, Le Qu
Long noncoding RNAs (lncRNAs) are implicated in renal cell carcinoma (RCC), but remain largely unclear. Using publicly available transcriptome sequencing data from renal cancer (n = 703) and integrating bioinformatics analyses, we screened and identified a valuable lncRNA, EGFR-AS1. In our validation cohort (n = 204), EGFR-AS1 was significantly upregulated in RCC tissues (P < 0.001). Gain-of-function and loss-of-function studies showed that EGFR-AS1 promoted cell proliferation and invasion in vitro and in vivo...
February 15, 2019: Cell Death & Disease
Bastien Nguyen, David Venet, Matteo Lambertini, Christine Desmedt, Roberto Salgado, Hugo Mark Horlings, Françoise Rothé, Christos Sotiriou
BACKGROUND: Although parity and age at first pregnancy are among the most known extrinsic factors that modulate breast cancer risk, their impact on the biology of subsequent breast cancer has never been explored in depth. Recent data suggest that pregnancy-induced tumor protection is different according to breast cancer subtypes, with parity and young age at first pregnancy being associated with a marked reduction in the risk of developing luminal subtype but not triple negative breast cancer...
February 15, 2019: Breast Cancer Research: BCR
Andrew E Blum, Srividya Venkitachalam, Durgadevi Ravillah, Aruna K Chelluboyina, Ann Marie Kieber-Emmons, Lakshmeswari Ravi, Adam Kresak, Apoorva K Chandar, Sanford D Markowitz, Marcia I Canto, Jean S Wang, Nicholas J Shaheen, Yan Guo, Yu Shyr, Joseph E Willis, Amitabh Chak, Vinay Varadan, Kishore Guda
BACKGROUND & AIMS: Esophageal adenocarcinoma (EAC) is resistant to standard chemoradiation treatments and few targeted therapies are available. We used large-scale tissue profiling and pharmacogenetic analyses to identify deregulated signaling pathways in EAC tissues that might be targeted to slow tumor growth or progression. METHODS: We collected 397 biopsy specimens from patients with EAC and non-malignant Barrett's esophagus (BE), with or without dysplasia...
February 12, 2019: Gastroenterology
Sarah C Pyfrom, Hong Luo, Jacqueline E Payton
BACKGROUND: Long non-coding RNAs (lncRNAs) exhibit remarkable cell-type specificity and disease association. LncRNA's functional versatility includes epigenetic modification, nuclear domain organization, transcriptional control, regulation of RNA splicing and translation, and modulation of protein activity. However, most lncRNAs remain uncharacterized due to a shortage of predictive tools available to guide functional experiments. RESULTS: To address this gap for lymphoma-associated lncRNAs identified in our studies, we developed a new computational method, Predicting LncRNA Activity through Integrative Data-driven 'Omics and Heuristics (PLAIDOH), which has several unique features not found in other methods...
February 15, 2019: BMC Genomics
An-Qi Li, Zhan-Peng Sun, Xu Liu, Jin-Shu Yang, Feng Jin, Lin Zhu, Wen-Huan Jia, Stephanie De Vos, Gilbert Van Stappen, Peter Bossier, Wei-Jun Yang
Cellular quiescence, a reversible state in which growth, proliferation, and other cellular activities are arrested, is important for self-renewal, differentiation, development, re-generation, and stress resistance. However, the physiological mechanisms underlying cellular quiescence remain largely unknown. In the present study, we used embryos of the crustacean Artemia in the diapause stage, in which these embryos remain quiescent for prolonged periods, as a model to explore the relationship between cell membrane potential (Vmem ) and quiescence...
February 14, 2019: Journal of Biological Chemistry
Alba Rodriguez-Meira, Gemma Buck, Sally-Ann Clark, Benjamin J Povinelli, Veronica Alcolea, Eleni Louka, Simon McGowan, Angela Hamblin, Nikolaos Sousos, Nikolaos Barkas, Alice Giustacchini, Bethan Psaila, Sten Eirik W Jacobsen, Supat Thongjuea, Adam J Mead
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for resolving transcriptional heterogeneity. However, its application to studying cancerous tissues is currently hampered by the lack of coverage across key mutation hotspots in the vast majority of cells; this lack of coverage prevents the correlation of genetic and transcriptional readouts from the same single cell. To overcome this, we developed TARGET-seq, a method for the high-sensitivity detection of multiple mutations within single cells from both genomic and coding DNA, in parallel with unbiased whole-transcriptome analysis...
February 11, 2019: Molecular Cell
Boran Pang, Qin Wang, Shipeng Ning, Junqiang Wu, Xingda Zhang, Yanbo Chen, Shouping Xu
BACKGROUND: The landscape and biological functions of tumor suppressor long noncoding RNAs in breast cancer are still unknown. METHODS: Data from whole transcriptome sequencing of 33 breast specimens in the Harbin Medical University Cancer Center cohort and The Cancer Genome Atlas was applied to identify and validate the landscape of tumor suppressor long noncoding RNAs, which was further validated by The Cancer Genome Atlas pancancer data including 33 cancer types and 12,839 patients...
February 14, 2019: Journal of Experimental & Clinical Cancer Research: CR
Stefan Zimmerman, Arundhati Das, Shuhang Wang, Ricklie Julian, Leena Gandhi, Juergen Wolf
Small cell lung cancer remains an aggressive, deadly cancer with only modest effect on survival from standard chemotherapy. However, with the advent of immunotherapy and comprehensive genomic and transcriptomic profiling, multiple new targets are showing promise in the clinical arena, and just recently PD-L1 inhibition has been shown to improve the efficacy of standard chemotherapy in extended disease SCLC. Our increasing understanding of the interactions between different pathways will enable more tailored immuno- as well as targeted therapies based on specific biomarkers and rational combinations...
February 11, 2019: Journal of Thoracic Oncology
G-H Zhang, Q-Y Zhong, X-X Gou, E-X Fan, Y Shuai, M-N Wu, G-J Yue
PURPOSE: Glioma is a common malignant tumor of the central nervous system, which is characterized by a low cure rate, high morbidity, and high recurrence rate. Consequently, it is imperative to explore some indicators for prognostic prediction in glioma. METHODS: We obtained glioma data from The Cancer Genome Atlas (TCGA). Differentially expressed genes (DEGs) were obtained by R software from TCGA data sets. Through Cox regression analysis, risk scores were obtained to assess the weighted gene-expression levels, which could predict the prognosis of patients with glioma...
February 14, 2019: Clinical & Translational Oncology
Lazar Vujanovic, Christopher Chuckran, Yan Lin, Fei Ding, Cindy A Sander, Patricia M Santos, Joel Lohr, Afshin Mashadi-Hossein, Sarah Warren, Andy White, Alan Huang, John M Kirkwood, Lisa H Butterfield
Natural killer (NK) cells are innate cytotoxic and immunoregulatory lymphocytes that have a central role in anti-tumor immunity and play a critical role in mediating cellular immunity in advanced cancer immunotherapies, such as dendritic cell (DC) vaccines. Our group recently tested a novel recombinant adenovirus-transduced autologous DC-based vaccine that simultaneously induces T cell responses against three melanoma-associated antigens for advanced melanoma patients. Here, we examine the impact of this vaccine as well as the subsequent systemic delivery of high-dose interferon-α2b (HDI) on the circulatory NK cell profile in melanoma patients...
2019: Frontiers in Immunology
Nahyeon Kang, Su Yeon Choi, Bit Na Kim, Chang Dong Yeo, Chan Kwon Park, Young Kyoon Kim, Tae-Jung Kim, Seong-Beom Lee, Sug Hyung Lee, Jong Y Park, Mi Sun Park, Hyeon Woo Yim, Seung Joon Kim
BACKGROUND: A hypoxic microenvironment leads to an increase in the invasiveness and the metastatic potential of cancer cells within tumors via the epithelial-mesenchymal transition (EMT) and cancer stemness acquisition. However, hypoxia-induced changes in the expression and function of candidate stem cell markers and their possible molecular mechanism is still not understood. METHODS: Lung cell lines were analyzed in normoxic or hypoxic conditions. For screening among the stem cell markers, a transcriptome analysis using next-generation sequencing was performed...
February 13, 2019: BMC Cancer
Hao Cai, Xiangyu Li, Jun He, Wenbin Zhou, Kai Song, You Guo, Huaping Liu, Qingzhou Guan, Haidan Yan, Xianlong Wang, Zheng Guo
BACKGROUND: The amount of RNA per cell, namely the transcriptome size, may vary under many biological conditions including tumor. If the transcriptome size of two cells is different, direct comparison of the expression measurements on the same amount of total RNA for two samples can only identify genes with changes in the relative mRNA abundances, i.e., cellular mRNA concentration, rather than genes with changes in the absolute mRNA abundances. RESULTS: Our recently proposed RankCompV2 algorithm identify differentially expressed genes (DEGs) through comparing the relative expression orderings (REOs) of disease samples with that of normal samples...
February 13, 2019: BMC Genomics
Su-Kyeong Jang, Byung-Ha Yoon, Seung Min Kang, Yeo-Gha Yoon, Seon-Young Kim, Wankyu Kim
Understanding the mechanisms of cancer drug resistance is a critical challenge in cancer therapy. For many cancer drugs, various resistance mechanisms have been identified such as target alteration, alternative signaling pathways, epithelial-mesenchymal transition, and epigenetic modulation. Resistance may arise via multiple mechanisms even for a single drug, making it necessary to investigate multiple independent models for comprehensive understanding and therapeutic application. In particular, we hypothesize that different resistance processes result in distinct gene expression changes...
February 12, 2019: Molecules and Cells
Anthony Atala
No abstract text is available yet for this article.
March 2019: Journal of Urology
Jennifer Beauvarlet, Paul Bensadoun, Elodie Darbo, Gaelle Labrunie, Benoît Rousseau, Elodie Richard, Irena Draskovic, Arturo Londono-Vallejo, Jean-William Dupuy, Rabindra Nath Das, Aurore Guédin, Guillaume Robert, Francois Orange, Sabrina Croce, Valerie Valesco, Pierre Soubeyran, Kevin M Ryan, Jean-Louis Mergny, Mojgan Djavaheri-Mergny
G-quadruplex ligands exert their antiproliferative effects through telomere-dependent and telomere-independent mechanisms, but the inter-relationships among autophagy, cell growth arrest and cell death induced by these ligands remain largely unexplored. Here, we demonstrate that the G-quadruplex ligand 20A causes growth arrest of cancer cells in culture and in a HeLa cell xenografted mouse model. This response is associated with the induction of senescence and apoptosis. Transcriptomic analysis of 20A treated cells reveals a significant functional enrichment of biological pathways related to growth arrest, DNA damage response and the lysosomal pathway...
February 13, 2019: Nucleic Acids Research
Chris H Wendt, Brian J Sandri, Laia Masvidal, Carl Murie, Margarita Bartish, Svetlana Avdulov, LeeAnn Higgins, Todd Markowski, Mark Peterson, Jonas Bergh, Ping Yang, Charlotte Rolny, Andrew H Limper, Timothy J Griffin, Peter B Bitterman, Ola Larsson
RATIONALE: Chronic obstructive pulmonary disease (COPD) is an independent risk factor for lung cancer, but the underlying molecular mechanisms are unknown. We hypothesized that stromal cells comprising the COPD lung contain pathological gene expression programs supporting oncogenesis. OBJECTIVES: To identify molecular mechanisms operating in the lung stroma that support the development of lung cancer. METHODS: Study subjects included patients with COPD with (n = 30) or without (n = 30) lung cancer across a spectrum of COPD severity...
December 2018: Annals of the American Thoracic Society
Patricia Dauer, Nikita S Sharma, Vineet K Gupta, Brittany Durden, Roey Hadad, Santanu Banerjee, Vikas Dudeja, Ashok Saluja, Sulagna Banerjee
Endoplasmic reticulum (ER) stress and the unfolded protein response (UPR) signaling have been shown to be dysregulated in multiple cancer types. Glucose regulatory protein 78 (GRP78), the master regulator of the UPR, plays a role in proliferation, invasion, and metastasis in cancer. Cancer stem cells (CSCs) make up a crucial component of the tumor heterogeneity in pancreatic cancer, as well as other cancers. "Stemness" in pancreatic cancer defines a population of cells within the tumor that have increased therapeutic resistance as well as survival advantage...
February 12, 2019: Cell Death & Disease
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