Integrated Transcriptomic Analysis Revealed Hub Genes and Pathways Involved in Sorafenib Resistance in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC), a high mortality malignancy, has become a worldwide public health concern. Acquired resistance to the multikinase inhibitor sorafenib challenges its clinical efficacy and the survival benefits it provides to patients with advanced HCC. This study aimed to identify critical genes and pathways associated with sorafenib resistance in HCC using integrated bioinformatics analysis. Differentially expressed genes (DEGs) were identified using four HCC gene expression profiles (including 34 sorafenib-resistant and 29 sorafenib-sensitive samples) based on the robust rank aggregation method and R software. Gene ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool. A protein–protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes (STRING), and small molecules reversing sorafenib resistance were searched for using the connectivity map (CMAP) database. Pearson correlation and survival analyses of hub genes were performed using cBioPortal and Gene Expression Profiling and Interactive Analysis (GEPIA). Finally, the expression levels of hub genes in sorafenib-resistant HCC cells were verified using quantitative polymerase chain reaction (q-PCR). A total of 165 integrated DEGs (66 upregulated and 99 downregulated in sorafenib resistant samples compared sorafenib sensitive ones) primarily enriched in negative regulation of endopeptidase activity, extracellular exosome, and protease binding were identified. Some pathways were commonly shared between the integrated DEGs. Seven promising therapeutic agents and 13 hub genes were identified. These findings provide a strategy and theoretical basis for overcoming sorafenib resistance in HCC patients.

[1]  Yongquan Zheng,et al.  Extracellular Matrix: Emerging Roles and Potential Therapeutic Targets for Breast Cancer , 2021, Frontiers in Oncology.

[2]  D. Schuppan,et al.  Targeting Cancer Associated Fibroblasts in Liver Fibrosis and Liver Cancer Using Nanocarriers , 2020, Cells.

[3]  Kai Liu,et al.  Upregulation of secreted phosphoprotein 1 affects malignant progression, prognosis, and resistance to cetuximab via the KRAS/MEK pathway in head and neck cancer. , 2020, Molecular carcinogenesis.

[4]  S. Xie,et al.  LncRNA CRNDE facilitates epigenetic suppression of CELF2 and LATS2 to promote proliferation, migration and chemoresistance in hepatocellular carcinoma , 2020, Cell Death & Disease.

[5]  W. Dai,et al.  Emerging roles and the regulation of aerobic glycolysis in hepatocellular carcinoma , 2020, Journal of Experimental & Clinical Cancer Research.

[6]  Erratum: Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. , 2020, CA: a cancer journal for clinicians.

[7]  T. Singh,et al.  Identification and differential expression of serotransferrin and apolipoprotein A-I in the plasma of HIV-1 patients treated with first-line antiretroviral therapy , 2020, BMC Infectious Diseases.

[8]  E. D. De Toni,et al.  The mechanisms of sorafenib resistance in hepatocellular carcinoma: theoretical basis and therapeutic aspects , 2020, Signal Transduction and Targeted Therapy.

[9]  Yinting Chen,et al.  TIMP1 down-regulation enhances gemcitabine sensitivity and reverses chemoresistance in pancreatic cancer. , 2020, Biochemical pharmacology.

[10]  H. Carter,et al.  IRE1α and IGF signaling predict resistance to an endoplasmic reticulum stress-inducing drug in glioblastoma cells , 2020, Scientific Reports.

[11]  Haoming Lin,et al.  Comprehensive network analysis of the molecular mechanisms associated with sorafenib resistance in hepatocellular carcinoma. , 2020, Cancer genetics.

[12]  Yan Zheng,et al.  IGFBP-1 Expression Promotes Tamoxifen Resistance in Breast Cancer Cells via Erk Pathway Activation , 2020, Frontiers in Endocrinology.

[13]  Hongyang Wang,et al.  CCL22 signaling contributes to sorafenib resistance in hepatitis B virus-associated hepatocellular carcinoma. , 2020, Pharmacological research.

[14]  Yanping Tang,et al.  Identification and validation of potential key long noncoding RNAs in sorafenib-resistant hepatocellular carcinoma cells , 2020, PeerJ.

[15]  Chi‐Huey Wong,et al.  Multiple Growth Factor Targeting by Engineered Insulin-like Growth Factor Binding Protein-3 Augments EGF Receptor Tyrosine Kinase Inhibitor Efficacy , 2020, Scientific Reports.

[16]  W. Dai,et al.  Simvastatin re-sensitizes hepatocellular carcinoma cells to sorafenib by inhibiting HIF-1α/PPAR-γ/PKM2-mediated glycolysis , 2020, Journal of Experimental & Clinical Cancer Research.

[17]  Stephen R. Piccolo,et al.  Functional and transcriptomic characterization of cisplatin-resistant AGS and MKN-28 gastric cancer cell lines , 2020, PloS one.

[18]  M. Nicoloso,et al.  TIMP-1 Is Overexpressed and Secreted by Platinum Resistant Epithelial Ovarian Cancer Cells , 2019, Cells.

[19]  Xiaofei Xu,et al.  MiR-181a Promotes Apoptosis and Reduces Cisplatin Resistance by Inhibiting Osteopontin in Cervical Cancer Cells. , 2019, Cancer biotherapy & radiopharmaceuticals.

[20]  Z. Zou,et al.  Cullin7 Enhances Resistance to Trastuzumab Therapy in Her2 Positive Breast Cancer via Degrading IRS-1 and Downregulating IGFBP-3 to Activate the PI3K/AKT Pathway. , 2019, Cancer letters.

[21]  Xiaocong Pang,et al.  Identification of SPP1 as an Extracellular Matrix Signature for Metastatic Castration-Resistant Prostate Cancer , 2019, Front. Oncol..

[22]  Yih-Leong Chang,et al.  Acquired resistance to EGFR tyrosine kinase inhibitors is mediated by the reactivation of STC2/JUN/AXL signaling in lung cancer , 2019, International journal of cancer.

[23]  S. Xie,et al.  Low‐intensity pulsed ultrasound promotes the proliferation of human bone mesenchymal stem cells by activating PI3K/AKt signaling pathways , 2019, Journal of cellular biochemistry.

[24]  Xinwen Wang,et al.  Secreted Phosphoprotein 1 (SPP1) Contributes to Second-Generation EGFR Tyrosine Kinase Inhibitor Resistance in Non-Small Cell Lung Cancer , 2019, Oncology research.

[25]  S. Xie,et al.  Identification of significant gene and pathways involved in HBV-related hepatocellular carcinoma by bioinformatics analysis , 2019, PeerJ.

[26]  Guangchun Sun,et al.  Bioinformatics analysis revealed hub genes and pathways involved in sorafenib resistance in hepatocellular carcinoma. , 2019, Mathematical biosciences and engineering : MBE.

[27]  B. Zhai,et al.  LncRNA SNHG1 contributes to sorafenib resistance by activating the Akt pathway and is positively regulated by miR-21 in hepatocellular carcinoma cells , 2019, Journal of Experimental & Clinical Cancer Research.

[28]  A. Aref,et al.  Exosomes: composition, biogenesis, and mechanisms in cancer metastasis and drug resistance , 2019, Molecular Cancer.

[29]  J. Ross,et al.  Dual Targeting of EGFR and IGF1R in the TNFAIP8 Knockdown Non–Small Cell Lung Cancer Cells , 2019, Molecular Cancer Research.

[30]  D. Xiong,et al.  SPP1 inhibition improves the cisplatin chemo-sensitivity of cervical cancer cell lines , 2019, Cancer Chemotherapy and Pharmacology.

[31]  Yongchun Yu,et al.  Exosomes in hepatocellular carcinoma: a new horizon , 2019, Cell Communication and Signaling.

[32]  Yajin Chen,et al.  TNF-α is a potential therapeutic target to overcome sorafenib resistance in hepatocellular carcinoma , 2018, EBioMedicine.

[33]  T. Hielscher,et al.  Targeting Resistance against the MDM2 Inhibitor RG7388 in Glioblastoma Cells by the MEK Inhibitor Trametinib , 2018, Clinical Cancer Research.

[34]  A. Jemal,et al.  Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries , 2018, CA: a cancer journal for clinicians.

[35]  A. Schneeweiss,et al.  Stress signaling in breast cancer cells induces matrix components that promote chemoresistant metastasis , 2018, EMBO molecular medicine.

[36]  Hanmin Li,et al.  Identification of key pathways and biomarkers in sorafenib-resistant hepatocellular carcinoma using bioinformatics analysis , 2018, Experimental and therapeutic medicine.

[37]  M. Ferrer,et al.  High-throughput screening identified selective inhibitors of exosome biogenesis and secretion: A drug repurposing strategy for advanced cancer , 2018, Scientific Reports.

[38]  L. Paavolainen,et al.  Association of tamoxifen resistance and lipid reprogramming in breast cancer , 2018, BMC Cancer.

[39]  Haiyang Xie,et al.  Genome-wide CRISPR screen reveals SGOL1 as a druggable target of sorafenib-treated hepatocellular carcinoma , 2018, Laboratory Investigation.

[40]  Hongwei Cheng,et al.  Overcoming STC2 mediated drug resistance through drug and gene co-delivery by PHB-PDMAEMA cationic polyester in liver cancer cells. , 2018, Materials science & engineering. C, Materials for biological applications.

[41]  Xiaoming Fan,et al.  By inhibiting PFKFB3, aspirin overcomes sorafenib resistance in hepatocellular carcinoma , 2017, International journal of cancer.

[42]  E. O’Neill,et al.  Gemcitabine-Induced TIMP1 Attenuates Therapy Response and Promotes Tumor Growth and Liver Metastasis in Pancreatic Cancer. , 2017, Cancer research.

[43]  Xinyu Zheng,et al.  Osteopontin and vasculogenic mimicry formation are associated with response to neoadjuvant chemotherapy in advanced breast cancer , 2017, OncoTargets and therapy.

[44]  In-kyu Lee,et al.  PPARδ Reprograms Glutamine Metabolism in Sorafenib-Resistant HCC , 2017, Molecular Cancer Research.

[45]  K. Alimoghaddam,et al.  Osteopontin b and c isoforms: Molecular Candidates Associated with Leukemic Stem Cell Chemoresistance in Acute Myeloid Leukemia , 2017, Asian Pacific journal of cancer prevention : APJCP.

[46]  M. Nowicki,et al.  Microarray-based detection and expression analysis of new genes associated with drug resistance in ovarian cancer cell lines , 2017, Oncotarget.

[47]  Cheng Li,et al.  GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses , 2017, Nucleic Acids Res..

[48]  Bo Zhu,et al.  Identification and characterization of biomarkers and their functions for Lapatinib-resistant breast cancer , 2017, Medical Oncology.

[49]  Lei Chen,et al.  New knowledge of the mechanisms of sorafenib resistance in liver cancer , 2017, Acta Pharmacologica Sinica.

[50]  T. Yeatman,et al.  Three-dimensional culture system identifies a new mode of cetuximab resistance and disease-relevant genes in colorectal cancer , 2017, Proceedings of the National Academy of Sciences.

[51]  M. Ohba,et al.  Distinct Afatinib Resistance Mechanisms Identified in Lung Adenocarcinoma Harboring an EGFR Mutation , 2017, Molecular Cancer Research.

[52]  K. Gu,et al.  Dysregulation of mRNA profile in cisplatin-resistant gastric cancer cell line SGC7901 , 2017, World journal of gastroenterology.

[53]  Yan Zheng,et al.  IGF-1 Receptor Modulates FoxO1-Mediated Tamoxifen Response in Breast Cancer Cells , 2017, Molecular Cancer Research.

[54]  Thumuluru Kavitha Madhuri,et al.  Proteomics Analysis of Ovarian Cancer Cell Lines and Tissues Reveals Drug Resistance-associated Proteins. , 2017, Cancer genomics & proteomics.

[55]  Jian Zhao,et al.  Osteopontin induces autophagy to promote chemo-resistance in human hepatocellular carcinoma cells. , 2016, Cancer letters.

[56]  H. Gabra,et al.  Identification of proteomic and metabolic signatures associated with chemoresistance of human epithelial ovarian cancer. , 2016, International journal of oncology.

[57]  T. Pawlik,et al.  Hepatocellular carcinoma: From diagnosis to treatment. , 2016, Surgical oncology.

[58]  B. De Moor,et al.  A Global Risk Score (GRS) to Simultaneously Predict Early and Late Tumor Recurrence Risk after Resection of Hepatocellular Carcinoma1 , 2016, Translational oncology.

[59]  D. Gao,et al.  Galectin-1 induces hepatocellular carcinoma EMT and sorafenib resistance by activating FAK/PI3K/AKT signaling , 2016, Cell Death and Disease.

[60]  Q. Wang,et al.  Stanniocalcin 2 induces oxaliplatin resistance in colorectal cancer cells by upregulating P-glycoprotein. , 2016, Canadian journal of physiology and pharmacology.

[61]  J. Llovet,et al.  Tumour initiating cells and IGF/FGF signalling contribute to sorafenib resistance in hepatocellular carcinoma , 2015, Gut.

[62]  Guichun Yang,et al.  Stanniocalcin 2 promotes cell proliferation and cisplatin resistance in cervical cancer. , 2015, Biochemical and biophysical research communications.

[63]  R. Cabrera,et al.  Current and future treatments for hepatocellular carcinoma. , 2015, World journal of gastroenterology.

[64]  F. Bertucci,et al.  Decreased expression of ABAT and STC2 hallmarks ER‐positive inflammatory breast cancer and endocrine therapy resistance in advanced disease , 2015, Molecular oncology.

[65]  R. Dummer,et al.  Versican upregulation in Sézary cells alters growth, motility and resistance to chemotherapy , 2015, Leukemia.

[66]  Tim Beißbarth,et al.  mRNA Profiling Reveals Determinants of Trastuzumab Efficiency in HER2-Positive Breast Cancer , 2015, PloS one.

[67]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[68]  G. Semenza,et al.  Hypoxia-inducible factors are required for chemotherapy resistance of breast cancer stem cells , 2014, Proceedings of the National Academy of Sciences.

[69]  Davide Heller,et al.  STRING v10: protein–protein interaction networks, integrated over the tree of life , 2014, Nucleic Acids Res..

[70]  M. Kitagawa,et al.  Anti‐VEGF antibody therapy induces tumor hypoxia and stanniocalcin 2 expression and potentiates growth of human colon cancer xenografts , 2014, International journal of cancer.

[71]  E. Meiyanto,et al.  Hesperidin as a preventive resistance agent in MCF-7 breast cancer cells line resistance to doxorubicin. , 2014, Asian Pacific journal of tropical biomedicine.

[72]  M. Kudo,et al.  Sunitinib versus sorafenib in advanced hepatocellular cancer: results of a randomized phase III trial. , 2013, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[73]  Y. Zhao,et al.  Recombinant TIMP-1-GPI inhibits growth of fibrosarcoma and enhances tumor sensitivity to doxorubicin , 2013, Targeted Oncology.

[74]  H. Nielsen,et al.  TIMP1 overexpression mediates resistance of MCF-7 human breast cancer cells to fulvestrant and down-regulates progesterone receptor expression , 2013, Tumor Biology.

[75]  M. Madonna,et al.  Differential effect of long-term drug selection with doxorubicin and vorinostat on neuroblastoma cells with cancer stem cell characteristics , 2013, Cell Death and Disease.

[76]  W. Fu,et al.  Upregulation of Drug Transporter Expression by Osteopontin in Prostate Cancer Cells , 2013, Molecular Pharmacology.

[77]  V. Nitti,et al.  Results of a randomized phase III trial of mirabegron in patients with overactive bladder. , 2013, The Journal of urology.

[78]  J. Dufour,et al.  Intermediate hepatocellular carcinoma: current treatments and future perspectives. , 2013, Annals of oncology : official journal of the European Society for Medical Oncology.

[79]  Frederik Nevens,et al.  Long-term exposure to sorafenib of liver cancer cells induces resistance with epithelial-to-mesenchymal transition, increased invasion and risk of rebound growth. , 2013, Cancer letters.

[80]  Chao Li,et al.  IGFBP-3 sensitizes antiestrogen-resistant breast cancer cells through interaction with GRP78. , 2012, Cancer letters.

[81]  Anna Tesei,et al.  Specific Biomarkers Are Associated with Docetaxeland Gemcitabine-Resistant NSCLC Cell Lines. , 2012, Translational oncology.

[82]  J. McCubrey,et al.  Molecular mechanisms of sorafenib action in liver cancer cells , 2012, Cell cycle.

[83]  H. El‐Serag,et al.  Epidemiology of viral hepatitis and hepatocellular carcinoma. , 2012, Gastroenterology.

[84]  Yan Pan,et al.  Atorvastatin sensitizes human non-small cell lung carcinomas to carboplatin via suppression of AKT activation and upregulation of TIMP-1. , 2012, The international journal of biochemistry & cell biology.

[85]  Yujie Sun,et al.  High expression of TIMP-1 in human breast cancer tissues is a predictive of resistance to paclitaxel-based chemotherapy , 2012, Medical Oncology.

[86]  Wei Liu,et al.  A genome-wide RNAi screen identifies novel targets of neratinib resistance leading to identification of potential drug resistant genetic markers. , 2012, Molecular bioSystems.

[87]  Sven Laur,et al.  Robust rank aggregation for gene list integration and meta-analysis , 2012, Bioinform..

[88]  Ruedi Aebersold,et al.  A Serum Protein Profile Predictive of the Resistance to Neoadjuvant Chemotherapy in Advanced Breast Cancers* , 2011, Molecular & Cellular Proteomics.

[89]  Kuen-Feng Chen,et al.  Activation of Phosphatidylinositol 3-Kinase/Akt Signaling Pathway Mediates Acquired Resistance to Sorafenib in Hepatocellular Carcinoma Cells , 2011, Journal of Pharmacology and Experimental Therapeutics.

[90]  M. Jeddi-Tehrani,et al.  Inactivation of nuclear factor-κB by citrus flavanone hesperidin contributes to apoptosis and chemo-sensitizing effect in Ramos cells. , 2011, European journal of pharmacology.

[91]  E. Tsilibary,et al.  TIMP-1 interaction with αvβ3 integrin confers resistance to human osteosarcoma cell line MG-63 against TNF-α-induced apoptosis , 2010, Cell and Tissue Research.

[92]  P. Cohen,et al.  Reduced levels of IGF-I mediate differential protection of normal and cancer cells in response to fasting and improve chemotherapeutic index. , 2010, Cancer research.

[93]  Xiongfei Zhang,et al.  Tissue inhibitor of metalloproteinase‐1 protects MCF‐7 breast cancer cells from paclitaxel‐induced apoptosis by decreasing the stability of cyclin B1 , 2010, International journal of cancer.

[94]  N. Sarvilinna,et al.  Gene expression changes during the development of estrogen-independent and antiestrogen-resistant growth in breast cancer cell culture models , 2009, Anti-cancer drugs.

[95]  Dieter Häussinger,et al.  Sorafenib in advanced hepatocellular carcinoma. , 2008, The New England journal of medicine.

[96]  D. Yee,et al.  Acquired resistance to EGFR tyrosine kinase inhibitors in cancer cells is mediated by loss of IGF-binding proteins. , 2008, The Journal of clinical investigation.

[97]  H. Nielsen,et al.  TIMP-1 Is Significantly Associated with Objective Response and Survival in Metastatic Colorectal Cancer Patients Receiving Combination of Irinotecan, 5-Fluorouracil, and Folinic Acid , 2007, Clinical Cancer Research.

[98]  A. Graessmann,et al.  Chemotherapy resistance of mouse WAP-SVT/t breast cancer cells is mediated by osteopontin, inhibiting apoptosis downstream of caspase-3 , 2007, Oncogene.

[99]  N. Brünner,et al.  Primary Tumor Levels of Tissue Inhibitor of Metalloproteinases-1 Are Predictive of Resistance to Chemotherapy in Patients with Metastatic Breast Cancer , 2006, Clinical Cancer Research.

[100]  N. Brünner,et al.  TIMP-1 gene deficiency increases tumour cell sensitivity to chemotherapy-induced apoptosis , 2006, British Journal of Cancer.

[101]  Paul A Clemons,et al.  The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease , 2006, Science.

[102]  J. Smyth,et al.  Altered ErbB receptor signaling and gene expression in cisplatin-resistant ovarian cancer. , 2005, Cancer research.

[103]  Gary D. Bader,et al.  An automated method for finding molecular complexes in large protein interaction networks , 2003, BMC Bioinformatics.

[104]  M. Roh,et al.  Recent progress in the treatment of hepatocellular carcinoma. , 1990, Current opinion in oncology.

[105]  J. Holloman.  A new horizon. , 1966, Journal of the National Medical Association.

[106]  Chi Wang,et al.  Predictive and targeting value of IGFBP-3 in therapeutically resistant prostate cancer. , 2019, American journal of clinical and experimental urology.

[107]  A. Pillai,et al.  Goals and targets for personalized therapy for HCC , 2019, Hepatology International.

[108]  B. Zhai,et al.  LncRNA SNHG1 contributes to sorafenib resistance by activating the Akt pathway and is positively regulated by miR-21 in hepatocellular carcinoma cells , 2019, Journal of Experimental & Clinical Cancer Research.

[109]  Ming Zhou,et al.  Genomic analysis of drug resistant pancreatic cancer cell line by combining long non-coding RNA and mRNA expression profling. , 2015, International journal of clinical and experimental pathology.

[110]  Yoon-Koo Kang,et al.  Efficacy and safety of sorafenib in patients in the Asia-Pacific region with advanced hepatocellular carcinoma: a phase III randomised, double-blind, placebo-controlled trial. , 2009, The Lancet. Oncology.

[111]  Justin Lamb,et al.  The Connectivity Map: a new tool for biomedical research , 2007, Nature Reviews Cancer.

[112]  P. McLaughlin.  Diagnosis treatment. , 2000, British dental journal.