Autophagy in Cancer Cells vs. Cancer Tissues: Two Different Stories
Autophagy has been considered strongly associated with cancer development and possibly playing important roles in cancer progression. Here we present a computational study of transcriptomic data of cancer tissues, totaling 6317 tissue samples of 11 cancer
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Autophagy in Cancer Cells vs. Cancer Tissues: Two Different Stories Chi Zhang, Tao Sheng, Sha Cao, Samira Issa-Boube, Tongyu Tang, Xiwen Zhu, Ning Dong, Wei Du, and Ying Xu Abstract Autophagy has been considered strongly associated with cancer development and possibly playing important roles in cancer progression. Here we present a computational study of transcriptomic data of cancer tissues, totaling 6317 tissue samples of 11 cancer types along with tissues of inflammatory diseases and cell line based experiments for comparative purposes. Our study clearly revealed that some widely held beliefs and speculations regarding autophagy in cancer may not be well founded, knowing that many of the previous observations were made on cancer cells cultured in man-made environments rather than actual cancer tissues. Our major findings include: (i) the widely used assumption that cancer tissue cells are nutrient depleted is not supported by our tissue-based gene-expression data analysis; (ii) the 11 cancer types studied fall into 2 distinct groups: those with low macro-autophagy (LM) activities and those with high lysosome (HL) activities but induced by C. Zhang • T. Sheng • S. Cao • S. Issa-Boube Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, The University of Georgia, Athens, GA, USA T. Tang Department of Gastroenterology, First hospital of Jilin University, Changchun, China X. Zhu Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China N. Dong Emergency Department, First hospital of Jilin University, Changchun, China W. Du Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, The University of Georgia, Athens, GA, USA College of Computer Science and Technology, Jilin University, Changchun, Jilin, China Y. Xu (*) Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, The University of Georgia, Athens, GA, USA College of Computer Science and Technology, Jilin University, Changchun, Jilin, China School of Public Health, First hospital of Jilin University, Changchun, China e-mail: [email protected] © Springer International Publishing Switzerland 2016 J.-M. Yang (ed.), Targeting Autophagy in Cancer Therapy, Current Cancer Research, DOI 10.1007/978-3-319-42740-9_2
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icro-autophagy and chaperon-mediated autophagy; (ii) co-reduction in autophagy m and apoptosis are widely observed in cancer tissues; (iii) down-regulated autophagy strongly correlates with up-regulated cell-cycle progression genes across all cancer types, with one possible functional link detected that repressed autophagosome formation may reduce the degradation of cellular organelles that are essential to cytokinesis, hence contributing to cell cycle progression; (iv) significant correlation is observed between autophagy and immune activities; (v) the down-regulated macro- autophagy gene
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