A literature mining-based approach for identification of cellular pathways associated with chemoresistance in cancer

Chemoresistance is a major obstacle to the successful treatment of many human cancer types. Increasing evidence has revealed that chemoresistance involves many genes and multiple complex biological mechanisms including cancer stem cells, drug efflux mechanism, autophagy and epithelial-mesenchymal transition. Many studies have been conducted to investigate the possible molecular mechanisms of chemoresistance. However, understanding of the biological mechanisms in chemoresistance still remains limited. We surveyed the literature on chemoresistance-related genes and pathways of multiple cancer types. We then used a curated pathway database to investigate significant chemoresistance-related biological pathways. In addition, to investigate the importance of chemoresistance-related markers in protein-protein interaction networks identified using the curated database, we used a gene-ranking algorithm designed based on a graph-based scoring function in our previous study. Our comprehensive survey and analysis provide a systems biology-based overview of the underlying mechanisms of chemoresistance.

[1]  Q. Cao,et al.  Estrogen and progestin regulate metastasis through the PI3K/AKT pathway in human ovarian cancer. , 2008, International journal of oncology.

[2]  J. Ajani,et al.  Sonic Hedgehog promotes multiple drug resistance by regulation of drug transport , 2007, Oncogene.

[3]  W. Hahn,et al.  Maintenance of tumor initiating cells of defined genetic composition by nucleostemin , 2011, Proceedings of the National Academy of Sciences.

[4]  Steven Elliott,et al.  Targeting NFĸB mediated breast cancer chemoresistance through selective inhibition of sphingosine kinase-2 , 2011, Cancer biology & therapy.

[5]  Z. Duan,et al.  Inhibition of ABCB 1 ( MDR 1 ) and ABCB 4 ( MDR 3 ) expression by small interfering RNA and reversal of paclitaxel resistance in human ovarian cancer cells , 2004 .

[6]  Andres Kriete,et al.  Computational systems biology of aging , 2011, Wiley interdisciplinary reviews. Systems biology and medicine.

[7]  Paola Lecca,et al.  An integrative network inference approach to predict mechanisms of cancer chemoresistance. , 2013, Integrative biology : quantitative biosciences from nano to macro.

[8]  R. Layfield,et al.  Proteomic profiling of MCF-7 breast cancer cells with chemoresistance to different types of anti-cancer drugs. , 2007, International journal of oncology.

[9]  W. Hsu,et al.  Construction of gene clusters resembling genetic causal mechanisms for common complex disease with an application to young-onset hypertension , 2013, BMC Genomics.

[10]  Werner Dubitzky.  Understanding the computational methodologies of systems biology , 2006, Briefings Bioinform..

[11]  Yu Fan,et al.  Long non‐coding RNA UCA1 increases chemoresistance of bladder cancer cells by regulating Wnt signaling , 2014, The FEBS journal.

[12]  三沢 彩.  AP-1-dependent miR-21 expression contributes to chemoresistance in cancer stem cell-like SP cells , 2010 .

[13]  Toll-like receptor 4 ligation confers chemoresistance to docetaxel on PC-3 human prostate cancer cells , 2012, Cell Biology and Toxicology.

[14]  Jung-Hsien Chiang,et al.  An integrative approach to identifying cancer chemoresistance-associated pathways , 2011, BMC Medical Genomics.

[15]  M. Burow,et al.  Apoptosis, Chemoresistance, and Breast Cancer: Insights From the MCF-7 Cell Model System , 2003, Experimental biology and medicine.

[16]  He-da Zhang,et al.  Ginsenoside Rh2 differentially mediates microRNA expression to prevent chemoresistance of breast cancer. , 2015, Asian Pacific journal of cancer prevention : APJCP.

[17]  Michael Schroeder,et al.  Unraveling Protein Networks with Power Graph Analysis , 2008, PLoS Comput. Biol..

[18]  Kewei Xu,et al.  NOTCH1 signaling promotes chemoresistance via regulating ABCC1 expression in prostate cancer stem cells , 2014, Molecular and Cellular Biochemistry.

[19]  M. Gleave,et al.  The mechanism of DAB 2 IP in chemo-resistance of prostate cancer cells , 2013 .

[20]  G. Hortobagyi,et al.  Activation of FOXO3a is sufficient to reverse mitogen-activated protein/extracellular signal-regulated kinase kinase inhibitor chemoresistance in human cancer. , 2010, Cancer research.

[21]  Geng-Hung Liu,et al.  Downregulation of BMP6 enhances cell proliferation and chemoresistance via activation of the ERK signaling pathway in breast cancer. , 2013, Oncology reports.

[22]  Xiaobo Song,et al.  Modification of Sialylation Mediates the Invasive Properties and Chemosensitivity of Human Hepatocellular Carcinoma* , 2013, Molecular & Cellular Proteomics.

[23]  H-l Chen,et al.  Activation of Akt and ERK signalling pathways induced by etoposide confer chemoresistance in gastric cancer cells. , 2006, Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver.

[24]  Yiling Lu,et al.  Exploiting the PI3K/AKT Pathway for Cancer Drug Discovery , 2005, Nature Reviews Drug Discovery.

[25]  M. Okada,et al.  JNK suppression of chemotherapeutic agents-induced ROS confers chemoresistance on pancreatic cancer stem cells , 2014, Oncotarget.

[26]  Zhenghong Qin,et al.  The role of autophagy in sensitizing malignant glioma cells to radiation therapy. , 2009, Acta biochimica et biophysica Sinica.

[27]  Yanqin Sun,et al.  Overexpression of secretagogin inhibits cell apoptosis and induces chemoresistance in small cell lung cancer under the regulation of miR-494 , 2014, Oncotarget.

[28]  S. Lam,et al.  Elevated Expression of BIRC6 Protein in Non–Small-Cell Lung Cancers is Associated with Cancer Recurrence and Chemoresistance , 2013, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[29]  Honggang Yu,et al.  Chemoresistance to doxorubicin induces epithelial-mesenchymal transition via upregulation of transforming growth factor β signaling in HCT116 colon cancer cells , 2015, Molecular medicine reports.

[30]  Jingde Zhu,et al.  MiR-193a-3p promotes the multi-chemoresistance of bladder cancer by targeting the HOXC9 gene. , 2015, Cancer letters.

[31]  Jie Huang,et al.  Downregulation of HOXA1 gene affects small cell lung cancer cell survival and chemoresistance under the regulation of miR-100. , 2014, European journal of cancer.

[32]  Enrique Casado,et al.  PI3K/Akt signalling pathway and cancer. , 2004, Cancer treatment reviews.

[33]  J. Eliaou,et al.  IL-17A is produced by breast cancer TILs and promotes chemoresistance and proliferation through ERK1/2 , 2013, Scientific Reports.

[34]  M. Gleave,et al.  The Mechanism of DAB2IP in Chemoresistance of Prostate Cancer Cells , 2013, Clinical Cancer Research.

[35]  Kwunmin Chen,et al.  Elevated p53 and p21waf1 mRNA expression in blood lymphocytes from lung cancer patients with chemoresistance. , 2007, Cancer detection and prevention.

[36]  G. Nolan,et al.  Computational solutions to large-scale data management and analysis , 2010, Nature Reviews Genetics.

[37]  Chunhua Xu,et al.  Expression of the enhancer of zeste homolog 2 in biopsy specimen predicts chemoresistance and survival in advanced non-small cell lung cancer receiving first-line platinum-based chemotherapy. , 2014, Lung cancer.

[38]  E. Yi,et al.  Proteomic analysis reveals that CD147/EMMPRIN confers chemoresistance in cancer stem cell‐like cells , 2013, Proteomics.

[39]  Gang Li,et al.  Cancer chemoresistance: The relationship between p53 and multidrug transporters , 2002, International journal of cancer.

[40]  M. Saleem,et al.  CANCER STEM CELLS Concise Review: Role of BMI1, a Stem Cell Factor, in Cancer Recurrence and Chemoresistance: Preclinical and Clinical Evidences , 2012 .

[41]  A. Gasbarrini,et al.  Tumor Initiating Cells and Chemoresistance: Which Is the Best Strategy to Target Colon Cancer Stem Cells? , 2014, BioMed research international.

[42]  S. Asuthkar,et al.  Multifunctional roles of urokinase plasminogen activator (uPA) in cancer stemness and chemoresistance of pancreatic cancer , 2013, Molecular biology of the cell.

[43]  F. Crea,et al.  Cancer stem cell epigenetics and chemoresistance. , 2009, Epigenomics.

[44]  O. Stoeltzing,et al.  Overexpression of neuropilin-1 promotes constitutive MAPK signalling and chemoresistance in pancreatic cancer cells , 2005, British Journal of Cancer.

[45]  I. Pastan,et al.  Expression of a multidrug-resistance gene in human tumors and tissues. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[46]  Y. Doki,et al.  Mesenchymal phenotype after chemotherapy is associated with chemoresistance and poor clinical outcome in esophageal cancer. , 2014, Oncology reports.

[47]  Xianwei Wang,et al.  Autophagy of cancer stem cells is involved with chemoresistance of colon cancer cells. , 2013, Biochemical and biophysical research communications.

[48]  Zhiming He,et al.  Up-regulation of breast cancer resistance protein plays a role in HER2-mediated chemoresistance through PI3K/Akt and nuclear factor-kappa B signaling pathways in MCF7 breast cancer cells. , 2011, Acta biochimica et biophysica Sinica.

[49]  Haizhu Song,et al.  MicroRNA-mediated autophagic signaling networks and cancer chemoresistance. , 2013, Cancer biotherapy & radiopharmaceuticals.

[50]  Alfonso Bellacosa,et al.  Epithelial–mesenchymal transition in development and cancer: role of phosphatidylinositol 3′ kinase/AKT pathways , 2005, Oncogene.

[51]  P. Lønning.  Genes causing inherited cancer as beacons to identify the mechanisms of chemoresistance. , 2004, Trends in molecular medicine.

[52]  W. Ongkeko,et al.  ABCG2: the key to chemoresistance in cancer stem cells? , 2009, Expert opinion on drug metabolism & toxicology.

[53]  J. Niu,et al.  The β6-integrin-ERK/MAP kinase pathway contributes to chemo resistance in colon cancer. , 2013, Cancer letters.

[54]  O. Eremin,et al.  Breast cancer chemoresistance: emerging importance of cancer stem cells. , 2010, Surgical oncology.

[55]  H. Ishii,et al.  Epithelial-mesenchymal transition with expression of SNAI1-induced chemoresistance in colorectal cancer. , 2009, Biochemical and biophysical research communications.

[56]  Lichuan Zhang,et al.  Upregulation of GRP78 and GRP94 and Its Function in Chemotherapy Resistance to VP-16 in Human Lung Cancer Cell Line SK-MES-1 , 2009, Cancer investigation.

[57]  M. Gnant,et al.  TP53 mutation and p53 overexpression for prediction of response to neoadjuvant treatment in breast cancer patients. , 2000, Clinical cancer research : an official journal of the American Association for Cancer Research.

[58]  Jin Huang,et al.  Upregulation of Autophagy-Related Gene-5 (ATG-5) Is Associated with Chemoresistance in Human Gastric Cancer , 2014, PloS one.

[59]  J. Rathmell,et al.  Metabolic stress in autophagy and cell death pathways. , 2012, Cold Spring Harbor perspectives in biology.

[60]  Joseph O. Deasy,et al.  A Bioinformatics Filtering Strategy for Identifying Radiation Response Biomarker Candidates , 2012, PloS one.

[61]  L. Meng,et al.  Activation of fibronectin/PI-3K/Akt2 leads to chemoresistance to docetaxel by regulating survivin protein expression in ovarian and breast cancer cells. , 2008, Cancer letters.

[62]  Lixin Wei,et al.  Increased p38-MAPK is responsible for chemotherapy resistance in human gastric cancer cells , 2008, BMC Cancer.

[63]  E. Sabo,et al.  Multidrug resistance-related phenotype and apoptosis-related protein expression in ovarian serous carcinomas. , 2006, Gynecologic oncology.

[64]  Ke Li,et al.  Increased expression and function of P-glycoprotein in peripheral blood CD56+ cells is associated with the chemoresistance of non-small-cell lung cancer , 2012, Cancer Chemotherapy and Pharmacology.

[65]  Z. Huang,et al.  Autophagy and chemotherapy resistance: a promising therapeutic target for cancer treatment , 2013, Cell Death and Disease.

[66]  A. Letai,et al.  UvA-DARE ( Digital Academic Repository ) Targeting cancer stem cells : Modulating apoptosis and stemness Çolak , 2016 .

[67]  M. Oshimura,et al.  PI3K-Akt pathway: Its functions and alterations in human cancer , 2004, Apoptosis.

[68]  H. Riedel,et al.  PSP94 contributes to chemoresistance and its peptide derivative PCK3145 represses tumor growth in ovarian cancer , 2014, Oncogene.

[69]  H. Coley.  Mechanisms and strategies to overcome chemotherapy resistance in metastatic breast cancer. , 2008, Cancer treatment reviews.

[70]  Jingde Zhu,et al.  The miR-193a-3p regulated PSEN1 gene suppresses the multi-chemoresistance of bladder cancer. , 2015, Biochimica et biophysica acta.

[71]  Hae-June Lee,et al.  CD44 Expression Denotes a Subpopulation of Gastric Cancer Cells in Which Hedgehog Signaling Promotes Chemotherapy Resistance , 2014, Clinical Cancer Research.

[72]  Z. Duan,et al.  Inhibition of ABCB1 (MDR1) and ABCB4 (MDR3) expression by small interfering RNA and reversal of paclitaxel resistance in human ovarian cancer cells. , 2004, Molecular cancer therapeutics.

[73]  P. Lønning,et al.  P53 and its molecular basis to chemoresistance in breast cancer , 2012, Expert opinion on therapeutic targets.

[74]  L. Wang,et al.  The DNA methylation-regulated miR-193a-3p dictates the multi-chemoresistance of bladder cancer via repression of SRSF2/PLAU/HIC2 expression , 2014, Cell Death and Disease.

[75]  Ke Chen,et al.  Understanding and targeting cancer stem cells: therapeutic implications and challenges , 2013, Acta Pharmacologica Sinica.

[76]  P. Krammer,et al.  Upregulation of bcl‐2 is involved in the mediation of chemotherapy resistance in human small cell lung cancer cell lines , 2002, International journal of cancer.

[77]  M. Kuo,et al.  Roles of multidrug resistance genes in breast cancer chemoresistance. , 2007, Advances in experimental medicine and biology.

[78]  David Gomez-Cabrero,et al.  Data integration in the era of omics: current and future challenges , 2014, BMC Systems Biology.

[79]  T. Crook,et al.  p53 family members and chemoresistance in cancer: what we know and what we need to know. , 2003, Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy.

[80]  H. Friess,et al.  Mitogen-activated protein kinases and chemoresistance in pancreatic cancer cells. , 2006, The Journal of surgical research.

[81]  Ai-min Wang,et al.  Periostin induces chemoresistance in colon cancer cells through activation of the PI3K/Akt/survivin pathway , 2015, Biotechnology and applied biochemistry.

[82]  Liping Wang,et al.  Epigenetic regulation of CD271, a potential cancer stem cell marker associated with chemoresistance and metastatic capacity , 2014, Oncology reports.

[83]  J. Panyam,et al.  Nanoparticle-mediated simultaneous and targeted delivery of paclitaxel and tariquidar overcomes tumor drug resistance. , 2009, Journal of controlled release : official journal of the Controlled Release Society.

[84]  Guojun Wu,et al.  PDGFRα and β play critical roles in mediating Foxq1-driven breast cancer stemness and chemoresistance. , 2015, Cancer research.

[85]  J. Fueyo,et al.  Autophagy regulation in cancer development and therapy. , 2011, American journal of cancer research.

[86]  H. Su,et al.  Epigenetic silencing of SFRP5 is related to malignant phenotype and chemoresistance of ovarian cancer through Wnt signaling pathway , 2010, International journal of cancer.

[87]  C. Ricciardelli,et al.  Chemotherapy-induced hyaluronan production: a novel chemoresistance mechanism in ovarian cancer , 2013, BMC Cancer.

[88]  M. Gnant,et al.  TP 53 Mutation and p 53 Overexpression for Prediction of Response to Neoadjuvant Treatment in Breast Cancer Patients 1 , 2000 .

[89]  N. Lemoine,et al.  Intrinsic Chemoresistance to Gemcitabine Is Associated with Decreased Expression of BNIP3 in Pancreatic Cancer , 2005, Clinical Cancer Research.

[90]  Michael Dean,et al.  Tumour stem cells and drug resistance , 2005, Nature Reviews Cancer.

[91]  Yinmo Yang,et al.  Insulin-Like Growth Factor 1 Receptor Promotes the Growth and Chemoresistance of Pancreatic Cancer , 2013, Digestive Diseases and Sciences.

[92]  G. Dontu,et al.  Stem cells in mammary development and carcinogenesis , 2007, Stem Cell Reviews.

[93]  David S. Wishart,et al.  Computational Systems Biology in Cancer: Modeling Methods and Applications , 2007, Gene regulation and systems biology.

[94]  J. Kigawa,et al.  Multidrug resistance gene-1 is a useful predictor of Paclitaxel-based chemotherapy for patients with ovarian cancer. , 2002, Gynecologic oncology.

[95]  J. Engelman,et al.  The PI3K pathway as drug target in human cancer. , 2010, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[96]  Y. Ba,et al.  Shed Syndecan-1 is involved in chemotherapy resistance via the EGFR pathway in colorectal cancer , 2014, British Journal of Cancer.

[97]  E. Wang,et al.  ADAM10 regulates proliferation, invasion, and chemoresistance of bladder cancer cells , 2014, Tumor Biology.

[98]  Youlong Zhu,et al.  Overexpression of CD133 enhances chemoresistance to 5-fluorouracil by activating the PI3K/Akt/p70S6K pathway in gastric cancer cells. , 2014, Oncology reports.

[99]  C. Cordon-Cardo,et al.  Targeting cancer stem cells to suppress acquired chemotherapy resistance , 2014, Oncogene.

[100]  E. Hirsch,et al.  PI3K/AKT signaling pathway and cancer: an updated review , 2014, Annals of medicine.

[101]  T. K. Ritchie,et al.  Conformational Analysis of Human ATP-binding Cassette Transporter ABCB1 in Lipid Nanodiscs and Inhibition by the Antibodies MRK16 and UIC2* , 2011, The Journal of Biological Chemistry.

[102]  Youlong Zhu,et al.  Overexpression of CD 133 enhances chemoresistance to 5-fluorouracil by activating the PI 3 K / Akt / p 70 S 6 K pathway in gastric cancer cells , 2022 .

[103]  Edward Kai-Hua Chow,et al.  Mechanisms of chemoresistance in cancer stem cells , 2013, Clinical and Translational Medicine.

[104]  H. Gómez,et al.  Chemotherapy resistance in metastatic breast cancer: the evolving role of ixabepilone , 2010, Breast Cancer Research.

[105]  A. Ghanate,et al.  Snail and Slug Mediate Radioresistance and Chemoresistance by Antagonizing p53‐Mediated Apoptosis and Acquiring a Stem‐Like Phenotype in Ovarian Cancer Cells , 2009, Stem cells.

[106]  G. Blandino,et al.  Mutant p53 stimulates chemoresistance of pancreatic adenocarcinoma cells to gemcitabine. , 2015, Biochimica et biophysica acta.

[107]  J. Eliaou,et al.  IL-17 A is produced by breast cancer TILs and promotes chemoresistance and proliferation through ERK 1 / 2 , 2013 .

[108]  Darren J. Wilkinson,et al.  Bayesian methods in bioinformatics and computational systems biology , 2006, Briefings Bioinform..

[109]  Xiao-li Zhang,et al.  Tumorspheres Derived from HCC Cells are Enriched with Cancer Stem Cell-like Cells and Present High Chemoresistance Dependent on the Akt Pathway. , 2015, Anti-Cancer Agents in Medicinal Chemistry.

[110]  Michael Fraser,et al.  Role of X-linked inhibitor of apoptosis protein in chemoresistance in ovarian cancer: possible involvement of the phosphoinositide-3 kinase/Akt pathway. , 2002, Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy.

[111]  Dawei Wang,et al.  Effects of the HIF-1α and NF-κB loop on epithelial-mesenchymal transition and chemoresistance induced by hypoxia in pancreatic cancer cells. , 2014, Oncology reports.