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Schöckel L, Woischke C, Surendran SA, Michl M, Schiergens T, Hölscher A, Glass F, Kreissl P, Klauschen F, Günther M, Ormanns S, Neumann J. PPARG activation promotes the proliferation of colorectal cancer cell lines and enhances the antiproliferative effect of 5-fluorouracil. BMC Cancer 2024; 24:234. [PMID: 38378472 PMCID: PMC10877928 DOI: 10.1186/s12885-024-11985-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/08/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Peroxisome proliferator-activated receptor gamma (PPARG) is a member of the nuclear receptor family. It is involved in the regulation of adipogenesis, lipid metabolism, insulin sensitivity, vascular homeostasis and inflammation. In addition, PPARG agonists, known as thiazolidinediones, are well established in the treatment of type 2 diabetes mellitus. PPARGs role in cancer is a matter of debate, as pro- and anti-tumour properties have been described in various tumour entities. Currently, the specific role of PPARG in patients with colorectal cancer (CRC) is not fully understood. MATERIAL AND METHODS The prognostic impact of PPARG expression was investigated by immunohistochemistry in a case-control study using a matched pair selection of CRC tumours (n = 246) with either distant metastases to the liver (n = 82), lung (n = 82) or without distant metastases (n = 82). Its effect on proliferation as well as the sensitivity to the chemotherapeutic drug 5-fluorouracil (5-FU) was examined after activation, inhibition, and transient gene knockdown of PPARG in the CRC cell lines SW403 and HT29. RESULTS High PPARG expression was significantly associated with pulmonary metastasis (p = 0.019). Patients without distant metastases had a significantly longer overall survival with low PPARG expression in their tumours compared to patients with high PPARG expression (p = 0.045). In the pulmonary metastasis cohort instead, a trend towards longer survival was observed for patients with high PPARG expression in their tumour (p = 0.059). Activation of PPARG by pioglitazone and rosiglitazone resulted in a significant dose-dependent increase in proliferation of CRC cell lines. Inhibition of PPARG by its specific inhibitor GW9662 and siRNA-mediated knockdown of PPARG significantly decreased proliferation. Activating PPARG significantly increased the CRC cell lines sensitivity to 5-FU while its inhibition decreased it. CONCLUSION The prognostic effect of PPARG expression depends on the metastasis localization in advanced CRC patients. Activation of PPARG increased malignancy associated traits such as proliferation in CRC cell lines but also increases sensitivity towards the chemotherapeutic agent 5-FU. Based on this finding, a combination therapy of PPARG agonists and 5-FU-based chemotherapy constitutes a promising strategy which should be further investigated.
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Affiliation(s)
- Leah Schöckel
- Institute of Pathology, Ludwig-Maximilians-University (LMU) München, Munich, Germany
| | - Christine Woischke
- Institute of Pathology, Ludwig-Maximilians-University (LMU) München, Munich, Germany
| | - Sai Agash Surendran
- Institute of Pathology, Ludwig-Maximilians-University (LMU) München, Munich, Germany
| | - Marlies Michl
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Tobias Schiergens
- Department of General, Visceral and Transplantation Surgery, University Hospital, LMU Munich, Munich, Germany
| | | | | | | | - Frederick Klauschen
- Institute of Pathology, Ludwig-Maximilians-University (LMU) München, Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich, a partnership between DKFZ and LMU Munich Germany, Munich, Germany
| | - Michael Günther
- Institute of Pathology, Ludwig-Maximilians-University (LMU) München, Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich, a partnership between DKFZ and LMU Munich Germany, Munich, Germany
- Innpath Institute for Pathology GmbH, Tirol Kliniken, Innsbruck, Austria
| | - Steffen Ormanns
- Institute of Pathology, Ludwig-Maximilians-University (LMU) München, Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich, a partnership between DKFZ and LMU Munich Germany, Munich, Germany
- Innpath Institute for Pathology GmbH, Tirol Kliniken, Innsbruck, Austria
| | - Jens Neumann
- Institute of Pathology, Ludwig-Maximilians-University (LMU) München, Munich, Germany.
- German Cancer Consortium (DKTK), partner site Munich, a partnership between DKFZ and LMU Munich Germany, Munich, Germany.
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Chang Y, Yang Y, Li C, Chan M, Lu M, Chen M, Chen C, Hsiao M. RAB31 drives extracellular vesicle fusion and cancer-associated fibroblast formation leading to oxaliplatin resistance in colorectal cancer. JOURNAL OF EXTRACELLULAR BIOLOGY 2024; 3:e141. [PMID: 38939899 PMCID: PMC11080812 DOI: 10.1002/jex2.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/14/2023] [Accepted: 01/06/2024] [Indexed: 06/29/2024]
Abstract
Epithelial-mesenchymal transition (EMT) is associated with tumorigenesis and drug resistance. The Rab superfamily of small G-proteins plays a role in regulating cell cytoskeleton and vesicle transport. However, it is not yet clear how the Rab family contributes to cancer progression by participating in EMT. By analysing various in silico datasets, we identified a statistically significant increase in RAB31 expression in the oxaliplatin-resistant group compared to that in the parental or other chemotherapy drug groups. Our findings highlight RAB31's powerful effect on colorectal cancer cell lines when compared with other family members. In a study that analysed multiple online meta-databases, RAB31 RNA levels were continually detected in colorectal tissue arrays. Additionally, RAB31 protein levels were correlated with various clinical parameters in clinical databases and were associated with negative prognoses for patients. RAB31 expression levels in all three probes were calculated using a computer algorithm and were found to be positively correlated with EMT scores. The expression of the epithelial-type marker CDH1 was suppressed in RAB31 overexpression models, whereas the expression of the mesenchymal-type markers SNAI1 and SNAI2 increased. Notably, RAB31-induced EMT and drug resistance are dependent on extracellular vesicle (EV) secretion. Interactome analysis confirmed that RAB31/AGR2 axis-mediated exocytosis was responsible for maintaining colorectal cell resistance to oxaliplatin. Our study concluded that RAB31 alters the sensitivity of oxaliplatin, a supplementary chemotherapy approach, and is an independent prognostic factor that can be used in the treatment of colorectal cancer.
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Affiliation(s)
- Yu‐Chan Chang
- Department of Biomedical Imaging and Radiological SciencesNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Yi‐Fang Yang
- Department of Medical Education and ResearchKaohsiung Veterans General HospitalKaohsiungTaiwan
| | | | - Ming‐Hsien Chan
- Department of Biomedical Imaging and Radiological SciencesNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Meng‐Lun Lu
- Department of OncologyTaipei Veterans General HospitalTaipeiTaiwan
| | - Ming‐Huang Chen
- Department of OncologyTaipei Veterans General HospitalTaipeiTaiwan
- School of MedicineNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
- Center of Immuno‐Oncology, Department of OncologyTaipei Veterans General HospitalTaipeiTaiwan
| | - Chi‐Long Chen
- Department of PathologyTaipei Medical University Hospital, Taipei Medical UniversityTaipeiTaiwan
- Department of Pathology, College of MedicineTaipei Medical UniversityTaipeiTaiwan
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3
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Long F, Tian B, Li L, Ma M, Chen Z, Tan G, Yin N, Zhong C, Yu B, Guo Y, Chen M, Hu G. CircPOFUT1 fosters colorectal cancer metastasis and chemoresistance via decoying miR-653-5p/E2F7/WDR66 axis and stabilizing BMI1. iScience 2024; 27:108729. [PMID: 38230259 PMCID: PMC10790033 DOI: 10.1016/j.isci.2023.108729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 10/31/2023] [Accepted: 12/11/2023] [Indexed: 01/18/2024] Open
Abstract
CircRNAs are implicated in colorectal cancer (CRC) development and progression. Protein O-fucosyltransferase 1 (POFUT1) plays an oncogenic role via activating Notch1 signaling in CRC. However, the roles of circPOFUT1, which is originated from POFUT1, have not been investigated. Our study showed circPOFUT1 was highly expressed in CRC tissues and cells. CircPOFUT1 enhanced the proliferation, migration and invasion of CRC cells, and promoted tumor growth and liver metastasis in vivo. It also reinforced stemness and chemoresistance of CRC cells. Mechanistically, circPOFUT1 regulated the function of E2F7 via sponging miR-653-5p, thereby transcriptionally inducing WDR66 expression and further promoting metastasis in CRC. On the other hand, circPOFUT1 promoted stemness and chemoresistance of CRC cells via stabilizing BMI1 in an IGF2BP1-dependent manner. In conclusion, circPOFUT1 fosters CRC metastasis and chemoresistance via decoying miR-653-5p/E2F7/WDR66 axis and stabilizing BMI1.
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Affiliation(s)
- Fei Long
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
- Postdoctoral Station of Basic Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Buning Tian
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Liang Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Min Ma
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Zhijian Chen
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Guojiang Tan
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Ning Yin
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Chonglei Zhong
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Bowen Yu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Yihang Guo
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Miao Chen
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Gui Hu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
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Li C, Cui X, Li Y, Guo D, He S. Identification of ferroptosis and drug resistance related hub genes to predict the prognosis in Hepatocellular Carcinoma. Sci Rep 2023; 13:8681. [PMID: 37248280 DOI: 10.1038/s41598-023-35796-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 05/24/2023] [Indexed: 05/31/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. Currently, overcoming the drug resistance in HCC is a critical challenge and ferroptosis has emerged as a promising therapeutic option for cancer. We aim to construct a new gene signature related to ferroptosis and drug resistance to predict the prognosis in HCC. The RNA-seq data of HCC patients was obtained from the Cancer Genome Atlas database. Using least absolute shrinkage and selection operator cox regression, Kaplan-Meier analysis, and differential analysis, we constructed a prognostic model consisting of six hub genes (TOP2A, BIRC5, VEGFA, HIF1A, FTH1, ACSL3) related to ferroptosis and drug resistance in HCC. Functional enrichment, pathway enrichment and GSEA analysis were performed to investigate the potential molecular mechanism, and construction of PPI, mRNA-miRNA, mRNA-RBP, mRNA-TF and mRNA-drugs interaction networks to predict its interaction with different molecules. Clinical prognostic characteristics were revealed by univariate, multivariate cox regression analysis and nomogram. We also analyzed the relationship between the signature, immune checkpoints, and drug sensitivity. The expression of the gene signature was detected in HCC cell lines and HPA database. Our prognostic model classified patients into high and low-risk groups based on the risk scores and found the expression level of the genes was higher in the high-risk group than the low-risk group, demonstrating that high expression of the hub genes was associated with poor prognosis in HCC. ROC analysis revealed its high diagnostic efficacy in both HCC and normal tissues. The proportional hazards model and calibration analysis confirmed that the model's prediction was most accurate for 1- and 3-years survival. QRT-PCR showed the high expression level of the gene signature in HCC. Our study built a novel gene signature with good potential to predict the prognosis of HCC, which may provide new therapeutic targets and molecular mechanism for HCC diagnosis and treatment.
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Affiliation(s)
- Chengjun Li
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Xiaomeng Cui
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Yarui Li
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Dan Guo
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Shuixiang He
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
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Horaira MA, Islam MA, Kibria MK, Alam MJ, Kabir SR, Mollah MNH. Bioinformatics screening of colorectal-cancer causing molecular signatures through gene expression profiles to discover therapeutic targets and candidate agents. BMC Med Genomics 2023; 16:64. [PMID: 36991484 PMCID: PMC10053149 DOI: 10.1186/s12920-023-01488-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND Detection of appropriate receptor proteins and drug agents are equally important in the case of drug discovery and development for any disease. In this study, an attempt was made to explore colorectal cancer (CRC) causing molecular signatures as receptors and drug agents as inhibitors by using integrated statistics and bioinformatics approaches. METHODS To identify the important genes that are involved in the initiation and progression of CRC, four microarray datasets (GSE9348, GSE110224, GSE23878, and GSE35279) and an RNA_Seq profiles (GSE50760) were downloaded from the Gene Expression Omnibus database. The datasets were analyzed by a statistical r-package of LIMMA to identify common differentially expressed genes (cDEGs). The key genes (KGs) of cDEGs were detected by using the five topological measures in the protein-protein interaction network analysis. Then we performed in-silico validation for CRC-causing KGs by using different web-tools and independent databases. We also disclosed the transcriptional and post-transcriptional regulatory factors of KGs by interaction network analysis of KGs with transcription factors (TFs) and micro-RNAs. Finally, we suggested our proposed KGs-guided computationally more effective candidate drug molecules compared to other published drugs by cross-validation with the state-of-the-art alternatives of top-ranked independent receptor proteins. RESULTS We identified 50 common differentially expressed genes (cDEGs) from five gene expression profile datasets, where 31 cDEGs were downregulated, and the rest 19 were up-regulated. Then we identified 11 cDEGs (CXCL8, CEMIP, MMP7, CA4, ADH1C, GUCA2A, GUCA2B, ZG16, CLCA4, MS4A12 and CLDN1) as the KGs. Different pertinent bioinformatic analyses (box plot, survival probability curves, DNA methylation, correlation with immune infiltration levels, diseases-KGs interaction, GO and KEGG pathways) based on independent databases directly or indirectly showed that these KGs are significantly associated with CRC progression. We also detected four TFs proteins (FOXC1, YY1, GATA2 and NFKB) and eight microRNAs (hsa-mir-16-5p, hsa-mir-195-5p, hsa-mir-203a-3p, hsa-mir-34a-5p, hsa-mir-107, hsa-mir-27a-3p, hsa-mir-429, and hsa-mir-335-5p) as the key transcriptional and post-transcriptional regulators of KGs. Finally, our proposed 15 molecular signatures including 11 KGs and 4 key TFs-proteins guided 9 small molecules (Cyclosporin A, Manzamine A, Cardidigin, Staurosporine, Benzo[A]Pyrene, Sitosterol, Nocardiopsis Sp, Troglitazone, and Riccardin D) were recommended as the top-ranked candidate therapeutic agents for the treatment against CRC. CONCLUSION The findings of this study recommended that our proposed target proteins and agents might be considered as the potential diagnostic, prognostic and therapeutic signatures for CRC.
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Affiliation(s)
- Md Abu Horaira
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Ariful Islam
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Kaderi Kibria
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Jahangir Alam
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Syed Rashel Kabir
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh.
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Park H, Imoto S, Miyano S. Gene Regulatory Network-Classifier: Gene Regulatory Network-Based Classifier and Its Applications to Gastric Cancer Drug (5-Fluorouracil) Marker Identification. J Comput Biol 2023; 30:223-243. [PMID: 36450117 DOI: 10.1089/cmb.2022.0181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
The complex mechanisms of diseases involve the disturbance of the molecular network, rather than disorder in a single gene, implying that single gene-based analysis is insufficient to understand these mechanisms. Gene regulatory networks (GRNs) have attracted a lot of interest and various approaches have been developed for their statistical inference and gene network-based analysis. Although various computational methods have been developed, relatively little attention has been paid to incorporation of biological knowledge into the computational approaches. Furthermore, existing studies on network-based analysis perform prediction/classification of status of cell lines based on preconstructed GRNs, implying that we cannot extract prediction/classification-specific gene networks, leading to difficulty in interpretation of biological mechanisms and marker identification related to the status of cancer cell lines. We developed a novel strategy to build a GRN-based classifier, called a GRN-classifier. The proposed GRN-classifier estimates GRNs and classifies cell lines simultaneously, where the gene network is estimated to minimize error in gene network estimation and the negative log-likelihood for classifying cell lines. Thus, we can identify biological status-specific gene regulatory systems, enabling us to achieve biologically reliable interpretation of the classification. We also propose an algorithm to implement the GRN-classifier based on coordinate descent update. Monte Carlo simulations were conducted to examine performance of the GRN-classifier. Results: Our strategy provides effective results in feature selection in the classification model and edge selection in gene network estimation. The GRN-classifier also shows outstanding classification accuracy. We apply the GRN-classifier to classify cancer cell lines into anticancer drug-related status, that is, 5-fluorouracil (5-FU)-sensitive/resistant and 5-FU target/nontarget cancer cell lines. We then identified 5-FU markers based on 5-FU-related status classification-specific gene networks. The mechanisms of the identified markers were verified through literature survey. Our results suggest that the molecular interplay between MYOF and AHNAK2 may play a crucial role in drug resistance and can provide information on the chemotherapy efficiency of 5-FU. It is also suggested that suppression of the identified 5-FU markers, including MYOF/AHNAK2 and AKR1C1/AKR1C3 may improve 5-FU resistance of cancer cell lines.
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Affiliation(s)
- Heewon Park
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Seiya Imoto
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan.,Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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7
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Chen L, Tian B, Liu W, Liang H, You Y, Liu W. Molecular Biomarker of Drug Resistance Developed From Patient-Derived Organoids Predicts Survival of Colorectal Cancer Patients. Front Oncol 2022; 12:855674. [PMID: 35425715 PMCID: PMC9004628 DOI: 10.3389/fonc.2022.855674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/10/2022] [Indexed: 12/24/2022] Open
Abstract
The drug 5-fluorouracil (5-Fu) is the critical composition of colorectal cancer (CRC) treatments. Prognostic and predictive molecular biomarkers for CRC patients (CRCpts) treated with 5-Fu-based chemotherapy can provide assistance for tailoring treatment approach. Here, we established a molecular biomarker of 5-Fu resistance derived from colorectal cancer organoids (CRCOs) for predicting the survival of CRCpts. Forty-one CRCO cultures were generated from 50 CRC tumor tissues after surgery (82%). The following experiments revealed a great diversity in drug sensitivity for 10 μM 5-Fu treatment tested by using organoid size change. Fourteen cases (34.1%) were 5-Fu sensitive and the other 27 (65.9%) were resistant. Then, differentially expressed genes (DEGs) associated with 5-Fu resistance were outputted by transcriptome sequencing. In particular, DEGs were generated in two comparison groups: 1) 5-Fu sensitive and resistant untreated CRCOs; 2) CRCOs before 5-Fu treatment and surviving CRCOs after 5-Fu treatment. Some molecules and most of the pathways that have been reported to be involved in 5-Fu resistance were identified in the current research. By using DEGs correlated with 5-Fu resistance and survival of CRCpts, the gene signature and drug-resistant score model (DRSM) containing five molecules were established in The Cancer Genome Atlas (TCGA)-CRC cohort by least absolute shrinkage and selection operator (LASSO) regression analysis and 5-fold cross-validation. Multivariate analysis revealed that drug-resistant score (DRS) was an independent prognostic factor for overall survival (OS) in CRCpts in TCGA-CRC cohort (P < 0.001). Further validation results from four Gene Expression Omnibus (GEO) cohorts elucidated that the DRSM based on five genes related to 5-Fu chemosensitivity and developed from patient-derived organoids can predict survival of CRCpts. Meanwhile, our model could predict the survival of CRCpts in different subgroups. Besides, the difference of molecular pathways, tumor mutational burden (TMB), immune response-related pathways, immune score, stromal score, and immune cell proportion were dissected between DRS-high and DRS-low patients in TCGA-CRC cohort.
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Affiliation(s)
- Lifeng Chen
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Tian
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wen Liu
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haitao Liang
- Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University, Health Science Center), Shenzhen, China
| | - Yong You
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weizhen Liu
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Sbirkov Y, Molander D, Milet C, Bodurov I, Atanasov B, Penkov R, Belev N, Forraz N, McGuckin C, Sarafian V. A Colorectal Cancer 3D Bioprinting Workflow as a Platform for Disease Modeling and Chemotherapeutic Screening. Front Bioeng Biotechnol 2021; 9:755563. [PMID: 34869264 PMCID: PMC8638705 DOI: 10.3389/fbioe.2021.755563] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/20/2021] [Indexed: 12/23/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common malignancy and has recently moved up to the second leading cause of death among carcinomas. Prognosis, especially for advanced diseases or certain molecular subtypes of CRC, remains poor, which highlights the urgent need for better therapeutic strategies. However, currently, as little as 0.1% of all drugs make it from bench to bedside because of the inherently high false-positive and false-negative rates of current preclinical and clinical drug testing data. Therefore, the success of developing novel treatment agents lies in the introduction of improved preclinical disease models which resemble in vivo carcinomas closer, possess higher predictive properties, and offer opportunities for individualized therapies. Aiming to address these needs, we have established an affordable, flexible, and highly reproducible 3D bioprinted CRC model. The histological assessment of Caco-2 cells in 3D bioprints revealed the formation of glandular-like structures which show greater pathomorphological resemblance to tumors than monolayer cultures do. RNA expression profiles in 3D bioprinted cells were marked by upregulation of genes involved in cell adhesion, hypoxia, EGFR/KRAS signaling, and downregulation of cell cycle programs. Testing this 3D experimental platform with three of the most commonly used chemotherapeutics in CRC (5-fluoruracil, oxaliplatin, and irinotecan) revealed overall increased resistance compared to 2D cell cultures. Last, we demonstrate that our workflow can be successfully extended to primary CRC samples. Thereby, we describe a novel accessible platform for disease modeling and drug testing, which may present an innovative opportunity for personalized therapeutic screening.
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Affiliation(s)
- Yordan Sbirkov
- Department of Medical Biology, Medical University of Plovdiv, Plovdiv, Bulgaria
- Research Institute at Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Diana Molander
- Department of Medical Biology, Medical University of Plovdiv, Plovdiv, Bulgaria
- Research Institute at Medical University of Plovdiv, Plovdiv, Bulgaria
| | | | - Ilia Bodurov
- UMHAT-Eurohospital, Clinical Pathology Department, Plovdiv, Bulgaria
| | - Boyko Atanasov
- UMHAT-Eurohospital, Surgical Department, Plovdiv, Bulgaria
- Department of Propaedeutics of Surgical Diseases, Medical University of Plovdiv, Plovdiv, Bulgaria
| | | | - Nikolay Belev
- Research Institute at Medical University of Plovdiv, Plovdiv, Bulgaria
- UMHAT-Eurohospital, Surgical Department, Plovdiv, Bulgaria
- Medical Simulation Training Centre, Medical University of Plovdiv, Plovdiv, Bulgaria
| | | | | | - Victoria Sarafian
- Department of Medical Biology, Medical University of Plovdiv, Plovdiv, Bulgaria
- Research Institute at Medical University of Plovdiv, Plovdiv, Bulgaria
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9
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Roy JW, Taylor CA, Beauregard AP, Dhadi SR, Ayre DC, Fry S, Chacko S, Wajnberg G, Joy AP, Mai-Thi NN, Crapoulet N, Barnett DA, Ghosh A, Lewis SM, Ouellette RJ. A multiparametric extraction method for Vn96-isolated plasma extracellular vesicles and cell-free DNA that enables multi-omic profiling. Sci Rep 2021; 11:8085. [PMID: 33850235 PMCID: PMC8044196 DOI: 10.1038/s41598-021-87526-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EVs) have been recognized as a rich material for the analysis of DNA, RNA, and protein biomarkers. A remaining challenge for the deployment of EV-based diagnostic and prognostic assays in liquid biopsy testing is the development of an EV isolation method that is amenable to a clinical diagnostic lab setting and is compatible with multiple types of biomarker analyses. We have previously designed a synthetic peptide, known as Vn96 (ME kit), which efficiently isolates EVs from multiple biofluids in a short timeframe without the use of specialized lab equipment. Moreover, it has recently been shown that Vn96 also facilitates the co-isolation of cell-free DNA (cfDNA) along with EVs. Herein we describe an optimized method for Vn96 affinity-based EV and cfDNA isolation from plasma samples and have developed a multiparametric extraction protocol for the sequential isolation of DNA, RNA, and protein from the same plasma EV and cfDNA sample. We are able to isolate sufficient material by the multiparametric extraction protocol for use in downstream analyses, including ddPCR (DNA) and ‘omic profiling by both small RNA sequencing (RNA) and mass spectrometry (protein), from a minimum volume (4 mL) of plasma. This multiparametric extraction protocol should improve the ability to analyse multiple biomarker materials (DNA, RNA and protein) from the same limited starting material, which may improve the sensitivity and specificity of liquid biopsy tests that exploit EV-based and cfDNA biomarkers for disease detection and monitoring.
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Affiliation(s)
- Jeremy W Roy
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
| | - Catherine A Taylor
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
| | - Annie P Beauregard
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada.,Fisheries and Oceans Canada, Aquatic Animal Health, Moncton, NB, Canada
| | - Surendar R Dhadi
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
| | - D Craig Ayre
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada.,Immunology, Genetics and Molecular Sciences, University of Medicine and Health Sciences, Basseterre, St. Kitts and Nevis
| | - Sheena Fry
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada.,Specialized Health Services Directorate, Health Canada, Ottawa, ON, Canada
| | - Simi Chacko
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
| | - Gabriel Wajnberg
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
| | - Andrew P Joy
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
| | - Ngoc-Nu Mai-Thi
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
| | - Nicolas Crapoulet
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
| | - David A Barnett
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
| | - Anirban Ghosh
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada.,Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada
| | - Stephen M Lewis
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada.,Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada.,Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Rodney J Ouellette
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada. .,Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada.
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10
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Caro D, Rivera D, Ocampo Y, Müller K, Franco LA. A promising naphthoquinone [8-hydroxy-2-(2-thienylcarbonyl)naphtho[2,3-b]thiophene-4,9-dione] exerts anti-colorectal cancer activity through ferroptosis and inhibition of MAPK signaling pathway based on RNA sequencing. OPEN CHEM 2020. [DOI: 10.1515/chem-2020-0170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
AbstractNaphthoquinones are naturally occurring metabolites with recognized anti-cancer potential but limited clinical application. This study investigated the molecular mechanism of 8-hydroxy-2-(2-thenoyl)naphtho[2,3-b]thiophene-4,9-dione (1), a new candidate for colorectal cancer (CRC) treatment, using different experimental settings: MTT, clonogenic, wound healing, and cell cycle assays; as well as RNA sequencing. Naphthoquinone 1 selectively reduced the viability and migration of HT-29 cells by G2/M arrest and changes in their transcriptome signature with significant effect on cellular survival, proliferation, angiogenesis, response to interferon, oxidative stress, and immune response. Impact analysis identified ferroptosis and MAPK pathways as significantly affected. In summary, our results suggest that 1 induces the selective death of CRC cells by inducing oxidative stress, ferroptosis, and MAPK inhibition.
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Affiliation(s)
- Daneiva Caro
- Biological Evaluation of Promising Substances Group, Department of Pharmaceutical Sciences, University of Cartagena, Carrera 50 No. 29-11, Cartagena, 130014, Colombia
| | - David Rivera
- Biological Evaluation of Promising Substances Group, Department of Pharmaceutical Sciences, University of Cartagena, Carrera 50 No. 29-11, Cartagena, 130014, Colombia
| | - Yanet Ocampo
- Biological Evaluation of Promising Substances Group, Department of Pharmaceutical Sciences, University of Cartagena, Carrera 50 No. 29-11, Cartagena, 130014, Colombia
| | - Klaus Müller
- Institute of Pharmaceutical and Medicinal Chemistry, PharmaCampus, Westphalian Wilhelms University, Corrensstraße 48, D-48149, Münster, Germany
| | - Luis A. Franco
- Biological Evaluation of Promising Substances Group, Department of Pharmaceutical Sciences, University of Cartagena, Carrera 50 No. 29-11, Cartagena, 130014, Colombia
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11
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Xie J, Chen P, Xie H, Sun Y, Huang Z, Wei R, Miao Z, Wang Q, Zhang SD, Wong KH, Lin Y, Huang C, Kwok HF. Exploration of gastric neuroendocrine carcinoma (GNEC) specific signaling pathways involved in chemoresistance via transcriptome and in vitro analysis. Comput Struct Biotechnol J 2020; 18:2610-2620. [PMID: 33033581 PMCID: PMC7530231 DOI: 10.1016/j.csbj.2020.09.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/22/2022] Open
Abstract
Gastric neuroendocrine carcinoma (GNEC) is rare cancer detected in the stomach. Previously, we demonstrated that the poorer prognosis of GNEC patients compared with gastric adenocarcinoma (GAC) patients was probably due to the lack of response to chemotherapy. Thus, it is crucial to study the specific GNEC gene expression pattern and investigate chemoresistance mechanism of GNEC. The transcriptome of GNEC patients was compared with that of GAC patients using RNA-seq. The KEGG analysis was employed to explore the specific differential expression gene function enrichment pattern. In addition, the transcriptomes of two GNEC cell lines, ECC10 and ECC12, were also compared with those of two GAC cell lines, MGC-803 and AGS, using RNA-seq. Comparing patient samples and cell lines transcriptome data, we try to uncover the potential targets and pathways which may affect the chemoresistance of GNEC. By combing all transcriptome data, we identified 22 key genes that were specifically up-regulated in GNEC. This panel of genes probably involves in the chemoresistance of GNEC. From our current experimental data, NeuroD1, one of the 22 genes, is associated with the prognosis of GNEC patients. Knockdown of NeuroD1 enhanced the sensitivity to irinotecan of GNEC cell lines. Our research sheds light in identifying a panel of novel therapeutic target specifically for GNEC clinical treatment which has not been reported before.
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Affiliation(s)
- Jianwei Xie
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian 350000, PR China
| | - Pengchen Chen
- Cancer Centre, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR
| | - Hongteng Xie
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian 350000, PR China
| | - Yuqin Sun
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian 350000, PR China.,Department of General Surgery, Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou 363000, PR China
| | - Zhen Huang
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350000, PR China
| | - Ran Wei
- Cancer Centre, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR
| | - Zhengqiang Miao
- Cancer Centre, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR
| | - Qingshui Wang
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350000, PR China
| | - Shu-Dong Zhang
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, Londonderry BT47, United Kingdom
| | - Koon Ho Wong
- Cancer Centre, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR
| | - Yao Lin
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350000, PR China.,Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Normal University, Fuzhou, Fujian 350000, PR China
| | - Changming Huang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian 350000, PR China
| | - Hang Fai Kwok
- Cancer Centre, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR
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12
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Identification and Characterization of the Copy Number Dosage-Sensitive Genes in Colorectal Cancer. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 18:501-510. [PMID: 32775488 PMCID: PMC7390836 DOI: 10.1016/j.omtm.2020.06.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 06/22/2020] [Indexed: 02/07/2023]
Abstract
Dosage effect is one of the common mechanisms of somatic copy number alteration in the development of colorectal cancer, yet the roles of dosage-sensitive genes (DSGs) in colorectal cancer (CRC) remain to be characterized more deeply. In this study, we developed a five-step pipeline to identify DSGs and analyzed their characterization in CRC. Results showed that our pipeline performed better than existing methods, and the result was significantly overlapped between solid tumor and cell line. We also found that the top five DSGs (PSMF1, RAF1, PTPRA, MKRN2, and ELP3) were associated with the progression of CRC. By analyzing the characterization, DSGs were enriched in driver genes and they drove sub-pathways of CRC. In addition, immune-related DSGs are associated with CRC progression. Our results also showed that the CRC samples affected by high microsatellites have fewer DSGs, but a higher overlap with DSGs in microsatellite low instability and microsatellite stable samples. In addition, we applied DSGs to identify potential drug targets, with the results showing that 22 amplified DSGs were more sensitive to four drugs. In conclusion, DSGs play an important role in CRC, and our pipeline is effective to identify them.
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13
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Ekanem TI, Tsai WL, Lin YH, Tan WQ, Chang HY, Huang TC, Chen HY, Lee KH. Identification of the Effects of Aspirin and Sulindac Sulfide on the Inhibition of HMGA2-Mediated Oncogenic Capacities in Colorectal Cancer. Molecules 2020; 25:molecules25173826. [PMID: 32842685 PMCID: PMC7504004 DOI: 10.3390/molecules25173826] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/17/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022] Open
Abstract
Distant metastatic colorectal cancer (CRC) is present in approximately 25% of patients at initial diagnosis, and eventually half of CRC patients will develop metastatic disease. The 5-year survival rate for patients with metastatic CRC is a mere 12.5%; thus, there is an urgent need to investigate the molecular mechanisms of cancer progression in CRC. High expression of human high-mobility group A2 (HMGA2) is related to tumor progression, a poor prognosis, and a poor response to therapy for CRC. Therefore, HMGA2 is an attractive target for cancer therapy. In this study, we identified aspirin and sulindac sulfide as novel potential inhibitors of HMGA2 using a genome-wide mRNA signature-based approach. In addition, aspirin and sulindac sulfide induced cytotoxicity of CRC cells stably expressing HMGA2 by inhibiting cell proliferation and migration. Moreover, a gene set enrichment analysis (GSEA) revealed that gene sets related to inflammation were positively correlated with HMGA2 and that the main molecular function of these genes was categorized as a G-protein-coupled receptor (GPCR) activity event. Collectively, this is the first study to report that aspirin and sulindac sulfide are novel potential inhibitors of HMGA2, which can induce cytotoxicity of CRC cells stably expressing HMGA2 by inhibiting cell proliferation and migration through influencing inflammatory-response genes, the majority of which are involved in GPCR signaling.
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Affiliation(s)
- Titus Ime Ekanem
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan;
- Department of Hematology, University of Uyo, Uyo 520271, Nigeria
| | - Wei-Lun Tsai
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (W.-L.T.); (W.-Q.T.); (T.-C.H.)
| | - Yi-Hsuan Lin
- Nutrition and Health Sciences, College of Nutrition, Taipei Medical University, Taipei 11031, Taiwan;
| | - Wan-Qian Tan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (W.-L.T.); (W.-Q.T.); (T.-C.H.)
| | - Hsin-Yi Chang
- Graduate Institute of Metabolism and Obesity Sciences, College of Nutrition, Taipei Medical University, Taipei 11031, Taiwan;
| | - Tsui-Chin Huang
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (W.-L.T.); (W.-Q.T.); (T.-C.H.)
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Hsin-Yi Chen
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (W.-L.T.); (W.-Q.T.); (T.-C.H.)
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Correspondence: (H.-Y.C.); (K.-H.L.); Tel.: +886-2-26972035 (H.-Y.C.); +886-2-26972035 (K.-H.L.); Fax: +886-2-66387537 (H.-Y.C.); +886-2-66387537 (K.-H.L.)
| | - Kuen-Haur Lee
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (W.-L.T.); (W.-Q.T.); (T.-C.H.)
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Cancer Center, Wan Fang Hospital, Taipei Medical University 11696, Taipei, Taiwan
- Correspondence: (H.-Y.C.); (K.-H.L.); Tel.: +886-2-26972035 (H.-Y.C.); +886-2-26972035 (K.-H.L.); Fax: +886-2-66387537 (H.-Y.C.); +886-2-66387537 (K.-H.L.)
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14
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Kotelevets L, Chastre E. Rac1 Signaling: From Intestinal Homeostasis to Colorectal Cancer Metastasis. Cancers (Basel) 2020; 12:cancers12030665. [PMID: 32178475 PMCID: PMC7140047 DOI: 10.3390/cancers12030665] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/06/2020] [Accepted: 03/08/2020] [Indexed: 12/14/2022] Open
Abstract
The small GTPase Rac1 has been implicated in a variety of dynamic cell biological processes, including cell proliferation, cell survival, cell-cell contacts, epithelial mesenchymal transition (EMT), cell motility, and invasiveness. These processes are orchestrated through the fine tuning of Rac1 activity by upstream cell surface receptors and effectors that regulate the cycling Rac1-GDP (off state)/Rac1-GTP (on state), but also through the tuning of Rac1 accumulation, activity, and subcellular localization by post translational modifications or recruitment into molecular scaffolds. Another level of regulation involves Rac1 transcripts stability and splicing. Downstream, Rac1 initiates a series of signaling networks, including regulatory complex of actin cytoskeleton remodeling, activation of protein kinases (PAKs, MAPKs) and transcription factors (NFkB, Wnt/β-catenin/TCF, STAT3, Snail), production of reactive oxygen species (NADPH oxidase holoenzymes, mitochondrial ROS). Thus, this GTPase, its regulators, and effector systems might be involved at different steps of the neoplastic progression from dysplasia to the metastatic cascade. After briefly placing Rac1 and its effector systems in the more general context of intestinal homeostasis and in wound healing after intestinal injury, the present review mainly focuses on the several levels of Rac1 signaling pathway dysregulation in colorectal carcinogenesis, their biological significance, and their clinical impact.
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Affiliation(s)
- Larissa Kotelevets
- Institut National de la Santé et de la Recherche Médicale, UMR S 938, Centre de Recherche Saint-Antoine, 75012 Paris, France
- Sorbonne Université, Hôpital Saint-Antoine, Site Bâtiment Kourilsky, 75012 Paris, France
- Correspondence: (L.K.); (E.C.)
| | - Eric Chastre
- Institut National de la Santé et de la Recherche Médicale, UMR S 938, Centre de Recherche Saint-Antoine, 75012 Paris, France
- Sorbonne Université, Hôpital Saint-Antoine, Site Bâtiment Kourilsky, 75012 Paris, France
- Correspondence: (L.K.); (E.C.)
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15
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Chen Q, Gao P, Song Y, Huang X, Xiao Q, Chen X, Lv X, Wang Z. Predicting the effect of 5-fluorouracil-based adjuvant chemotherapy on colorectal cancer recurrence: A model using gene expression profiles. Cancer Med 2020; 9:3043-3056. [PMID: 32150672 PMCID: PMC7196071 DOI: 10.1002/cam4.2952] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 02/08/2020] [Accepted: 02/16/2020] [Indexed: 12/21/2022] Open
Abstract
It is critical to identify patients with stage II and III colorectal cancer (CRC) who will benefit from adjuvant chemotherapy (ACT) after curative surgery, while the only use of clinical factors is insufficient to predict this beneficial effect. In this study, we performed genetic algorithm (GA) to select ACT candidate genes, and built a predictive model of support vector machine (SVM) using gene expression profiles from the Gene Expression Omnibus database. The model contained four ACT candidate genes (EDEM1, MVD, SEMA5B, and WWP2) and TNM stage (stage II or III). After using Subpopulation Treatment Effect Pattern Plot to determine the optimal cutoff value of predictive scores, the validated patients from The Cancer Genome Atlas database can be divided into the predictive ACT-benefit/-futile groups. Patients in the predictive ACT-benefit group with 5-fluorouracil (5-Fu)-based ACT had significantly longer relapse-free survival (RFS) compared to those without ACT (P = .015); However, the difference in RFS in the predictive ACT-futile group was insignificant (P = .596). The multivariable analysis found that the predictive groups were significantly associated with the effect of ACT (Pinteraction = .011). Consequently, we developed a predictive model based on the SVM and GA algorithm which was further validated to define patients who benefit from ACT on recurrence.
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Affiliation(s)
- Quan Chen
- Department of Surgical Oncology and General SurgeryKey Laboratory of Precision Diagnosis and Treatment of Gastrointestinal TumorsMinistry of EducationThe First Affiliated Hospital of China Medical UniversityShenyang CityChina
| | - Peng Gao
- Department of Surgical Oncology and General SurgeryKey Laboratory of Precision Diagnosis and Treatment of Gastrointestinal TumorsMinistry of EducationThe First Affiliated Hospital of China Medical UniversityShenyang CityChina
| | - Yongxi Song
- Department of Surgical Oncology and General SurgeryKey Laboratory of Precision Diagnosis and Treatment of Gastrointestinal TumorsMinistry of EducationThe First Affiliated Hospital of China Medical UniversityShenyang CityChina
| | - Xuanzhang Huang
- Department of Surgical Oncology and General SurgeryKey Laboratory of Precision Diagnosis and Treatment of Gastrointestinal TumorsMinistry of EducationThe First Affiliated Hospital of China Medical UniversityShenyang CityChina
| | - Qiong Xiao
- Department of Surgical Oncology and General SurgeryKey Laboratory of Precision Diagnosis and Treatment of Gastrointestinal TumorsMinistry of EducationThe First Affiliated Hospital of China Medical UniversityShenyang CityChina
| | - Xiaowan Chen
- Department of Surgical Oncology and General SurgeryKey Laboratory of Precision Diagnosis and Treatment of Gastrointestinal TumorsMinistry of EducationThe First Affiliated Hospital of China Medical UniversityShenyang CityChina
| | - Xinger Lv
- Department of Surgical Oncology and General SurgeryKey Laboratory of Precision Diagnosis and Treatment of Gastrointestinal TumorsMinistry of EducationThe First Affiliated Hospital of China Medical UniversityShenyang CityChina
| | - Zhenning Wang
- Department of Surgical Oncology and General SurgeryKey Laboratory of Precision Diagnosis and Treatment of Gastrointestinal TumorsMinistry of EducationThe First Affiliated Hospital of China Medical UniversityShenyang CityChina
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16
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Liu R, Sun M, Zhang G, Lan Y, Yang Z. Towards early monitoring of chemotherapy-induced drug resistance based on single cell metabolomics: Combining single-probe mass spectrometry with machine learning. Anal Chim Acta 2019; 1092:42-48. [PMID: 31708031 PMCID: PMC6878984 DOI: 10.1016/j.aca.2019.09.065] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/30/2019] [Accepted: 09/23/2019] [Indexed: 01/22/2023]
Abstract
Despite the presence of methods evaluating drug resistance during chemotherapies, techniques, which allow for monitoring the degree of drug resistance in early chemotherapeutic stage from single cells in their native microenvironment, are still absent. Herein, we report an analytical approach that combines single cell mass spectrometry (SCMS) based metabolomics with machine learning (ML) models to address the existing challenges. Metabolomic profiles of live cancer cells (HCT-116) with different levels (i.e., no, low, and high) of chemotherapy-induced drug resistance were measured using the Single-probe SCMS technique. A series of ML models, including random forest (RF), artificial neural network (ANN), and penalized logistic regression (LR), were constructed to predict the degrees of drug resistance of individual cells. A systematic comparison of performance was conducted among multiple models, and the method validation was carried out experimentally. Our results indicate that these ML models, especially the RF model constructed on the obtained SCMS datasets, can rapidly and accurately predict different degrees of drug resistance of live single cells. With such rapid and reliable assessment of drug resistance demonstrated at the single cell level, our method can be potentially employed to evaluate chemotherapeutic efficacy in the clinic.
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Affiliation(s)
- Renmeng Liu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Mei Sun
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Genwei Zhang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Yunpeng Lan
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
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17
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Machine learning and data mining frameworks for predicting drug response in cancer: An overview and a novel in silico screening process based on association rule mining. Pharmacol Ther 2019; 203:107395. [DOI: 10.1016/j.pharmthera.2019.107395] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/11/2019] [Indexed: 12/20/2022]
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18
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Meng Q, Wang S, Zhou S, Liu H, Ma X, Zhou X, Liu H, Xu C, Jiang W. Dissecting the m6A methylation affection on afatinib resistance in non-small cell lung cancer. THE PHARMACOGENOMICS JOURNAL 2019; 20:227-234. [DOI: 10.1038/s41397-019-0110-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 09/11/2019] [Accepted: 10/03/2019] [Indexed: 12/22/2022]
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19
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Zhu Q, Tian G, Gao J. Construction of prognostic risk prediction model of oral squamous cell carcinoma based on co-methylated genes. Int J Mol Med 2019; 44:787-796. [PMID: 31198983 PMCID: PMC6657967 DOI: 10.3892/ijmm.2019.4243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 05/14/2019] [Indexed: 12/21/2022] Open
Abstract
This study aimed to identify DNA methylation markers in oral squamous cell carcinoma (OSCC) and to construct a prognostic prediction model of OSCC. For this purpose, the methylation data of patients with OSCC downloaded from The Cancer Genome Atlas were considered as a training dataset. The methylation profiles of GSE37745 for OSCC samples were downloaded from Gene Expression Omnibus and considered as validation dataset. Differentially methylated genes (DMGs) were screened from the TCGA training dataset, followed by co-methylation analysis using weighted correlation network analysis (WGCNA). Subsequently, the methylation and gene expression levels of DMGs involved in key modules were extracted for correlation analysis. Prognosis-related methylated genes were screened using the univariate Cox regression analysis. Finally, the risk prediction model was constructed and validated through GSE52793. The results revealed that a total of 948 DMGs with CpGs were screened out. Co-methylation gene analysis obtained 2 (brown and turquoise) modules involving 380 DMGs. Correlation analysis revealed that the methylation levels of 132 genes negatively correlated with the gene expression levels. By combining with the clinical survival prognosis of samples, 5 optimized prognostic genes [centromere protein V (CENPV), Tubby bipartite transcription factor (TUB), synaptotagmin like 2 (SYTL2), occludin (OCLN) and CAS1 domain containing 1 (CASD1)] were selected for constructing a risk prediction model. It was consistent in the training dataset and GSE52793 that low-risk samples had a better survival prognosis. On the whole, this study indicates that the constructed risk prediction model based on CENPV, SYTL2, OCLN, CASD1, and TUB may have the potential to be used for predicting the survival prognosis of patients with OSCC.
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Affiliation(s)
- Qiang Zhu
- Department of Stomatolgy, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Gang Tian
- Department of Stomatolgy, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Jianyong Gao
- Department of Stomatolgy, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
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20
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The Phenolic compound Kaempferol overcomes 5-fluorouracil resistance in human resistant LS174 colon cancer cells. Sci Rep 2019; 9:195. [PMID: 30655588 PMCID: PMC6336835 DOI: 10.1038/s41598-018-36808-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/23/2018] [Indexed: 02/06/2023] Open
Abstract
Resistance to 5-Fluorouracil chemotherapy is a major cause of therapeutic failure in colon cancer cure. Development of combined therapies constitutes an effective strategy to inhibit cancer cells and prevent the emergence of drug resistance. For this purpose, we investigated the anti-tumoral effect of thirteen phenolic compounds, from the Tunisian quince Cydonia oblonga Miller, alone or combined to 5-FU, on the human 5-FU-resistant LS174-R colon cancer cells in comparison to parental cells. Our results showed that only Kaempferol was able to chemo-sensitize 5-FU-resistant LS174-R cells. This phenolic compound combined with 5-FU exerted synergistic inhibitory effect on cell viability. This combination enhanced the apoptosis and induced cell cycle arrest of both chemo-resistant and sensitive cells through impacting the expression levels of different cellular effectors. Kaempferol also blocked the production of reactive oxygen species (ROS) and modulated the expression of JAK/STAT3, MAPK, PI3K/AKT and NF-κB. In silico docking analysis suggested that the potent anti-tumoral effect of Kaempferol, compared to its two analogs (Kaempferol 3-O-glucoside and Kampferol 3-O-rutinoside), can be explained by the absence of glucosyl groups. Overall, our data propose Kaempferol as a potential chemotherapeutic agent to be used alone or in combination with 5-FU to overcome colon cancer drug resistance.
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21
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Jiang S, Miao D, Wang M, Lv J, Wang Y, Tong J. MiR-30-5p suppresses cell chemoresistance and stemness in colorectal cancer through USP22/Wnt/β-catenin signaling axis. J Cell Mol Med 2018; 23:630-640. [PMID: 30338942 PMCID: PMC6307779 DOI: 10.1111/jcmm.13968] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/06/2018] [Accepted: 09/23/2018] [Indexed: 12/15/2022] Open
Abstract
Colorectal cancer (CRC) remains both common and fatal, and its successful treatment is greatly limited by the development of stem cell‐like characteristics (stemness) and chemoresistance. MiR‐30‐5p has been shown to function as a tumor suppressor by targeting the Wnt/β‐catenin signaling pathway, but its activity in CRC has never been assessed. We hypothesized that miR‐30‐5p exerts anti‐oncogenic effects in CRC by regulating the USP22/Wnt/β‐catenin signaling axis. In the present study, we demonstrate that tissues from CRC patients and human CRC cell lines show significantly decreased miR‐30‐5p family expression. After identifying the 3’UTR of USP22 as a potential binding site of miR‐30‐5p, we constructed a luciferase reporter containing the potential miR‐30‐5p binding site and measured the effects on USP22 expression. Western blot assays showed that miR‐30‐5p decreased USP22 protein expression in HEK293 and Caco2 CRC cells. To evaluate the effects of miR‐30‐5p on CRC cell stemness, we isolated CD133 + CRC cells (Caco2 and HCT15). We then determined that, while miR‐30‐5p is normally decreased in CD133 + CRC cells, miR‐30‐5p overexpression significantly reduces expression of stem cell markers CD133 and Sox2, sphere formation, and cell proliferation. Similarly, we found that miR‐30‐5p expression is normally reduced in 5‐fluorouracil (5‐FU) resistant CRC cells, whereas miR‐30‐5p overexpression in 5‐FU resistant cells reduces sphere formation and cell viability. Inhibition of miR‐30‐5p reversed the process. Finally, we determined that miR‐30‐5p attenuates the expression of Wnt/β‐catenin signaling target genes (Axin2 and MYC), Wnt luciferase activity, and β‐catenin protein levels in CRC stem cells.
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Affiliation(s)
- Shixiong Jiang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Dazhuang Miao
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Muhong Wang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jiachen Lv
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yihui Wang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jinxue Tong
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
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22
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Aversa I, Chirillo R, Chiarella E, Zolea F, Di Sanzo M, Biamonte F, Palmieri C, Costanzo F. Chemoresistance in H-Ferritin Silenced Cells: The Role of NF-κB. Int J Mol Sci 2018; 19:ijms19102969. [PMID: 30274235 PMCID: PMC6213748 DOI: 10.3390/ijms19102969] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/21/2018] [Accepted: 09/26/2018] [Indexed: 02/06/2023] Open
Abstract
Nuclear Factor-κB (NF-κB) is frequently activated in tumor cells contributing to aggressive tumor growth and resistance to chemotherapy. Here we demonstrate that Ferritin Heavy Chain (FHC) protein expression inversely correlates with NF-κB activation in cancer cell lines. In fact, FHC silencing in K562 and SKOV3 cancer cell lines induced p65 nuclear accumulation, whereas FHC overexpression correlated with p65 nuclear depletion in the same cell lines. In FHC-silenced cells, the p65 nuclear accumulation was reverted by treatment with the reactive oxygen species (ROS) scavenger, indicating that NF-κB activation was an indirect effect of FHC on redox metabolism. Finally, FHC knock-down in K562 and SKOV3 cancer cell lines resulted in an improved cell viability following doxorubicin or cisplatin treatment, being counteracted by the transient expression of inhibitory of NF-κB, IκBα. Our results provide an additional layer of information on the complex interplay of FHC with cellular metabolism, and highlight a novel scenario of NF-κB-mediated chemoresistance triggered by the downregulation of FHC with potential therapeutic implications.
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Affiliation(s)
- Ilenia Aversa
- Research Center of Biochemistry and Advanced Molecular Biology, Department of Experimental and Clinical Medicine, "Magna Græcia" University of Catanzaro, Campus Salvatore Venuta-Viale Europa, 88100 Catanzaro, Italy.
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, Campus Salvatore Venuta-Viale Europa, 88100 Catanzaro, Italy.
| | - Roberta Chirillo
- Research Center of Biochemistry and Advanced Molecular Biology, Department of Experimental and Clinical Medicine, "Magna Græcia" University of Catanzaro, Campus Salvatore Venuta-Viale Europa, 88100 Catanzaro, Italy.
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, Campus Salvatore Venuta-Viale Europa, 88100 Catanzaro, Italy.
| | - Emanuela Chiarella
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, Campus Salvatore Venuta-Viale Europa, 88100 Catanzaro, Italy.
| | - Fabiana Zolea
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, Campus Salvatore Venuta-Viale Europa, 88100 Catanzaro, Italy.
| | - Maddalena Di Sanzo
- Research Center of Biochemistry and Advanced Molecular Biology, Department of Experimental and Clinical Medicine, "Magna Græcia" University of Catanzaro, Campus Salvatore Venuta-Viale Europa, 88100 Catanzaro, Italy.
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, Campus Salvatore Venuta-Viale Europa, 88100 Catanzaro, Italy.
| | - Flavia Biamonte
- Research Center of Biochemistry and Advanced Molecular Biology, Department of Experimental and Clinical Medicine, "Magna Græcia" University of Catanzaro, Campus Salvatore Venuta-Viale Europa, 88100 Catanzaro, Italy.
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, Campus Salvatore Venuta-Viale Europa, 88100 Catanzaro, Italy.
| | - Camillo Palmieri
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, Campus Salvatore Venuta-Viale Europa, 88100 Catanzaro, Italy.
| | - Francesco Costanzo
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, Campus Salvatore Venuta-Viale Europa, 88100 Catanzaro, Italy.
- Interdepartmental Center of Services (CIS), University Magna Graecia of Catanzaro, Campus Salvatore Venuta-Viale Europa, 88100 Catanzaro, Italy.
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23
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Zhang Y, Li X, Zhou D, Zhi H, Wang P, Gao Y, Guo M, Yue M, Wang Y, Shen W, Ning S, Li Y, Li X. Inferences of individual drug responses across diverse cancer types using a novel competing endogenous RNA network. Mol Oncol 2018; 12:1429-1446. [PMID: 29464864 PMCID: PMC6120231 DOI: 10.1002/1878-0261.12181] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/23/2018] [Accepted: 02/07/2018] [Indexed: 12/19/2022] Open
Abstract
Differences in individual drug responses are an obstacle to progression in cancer treatment, and predicting responses would help to plan treatment. The accumulation of cancer molecular profiling and drug response data provides opportunities and challenges to identify novel molecular signatures and mechanisms of tumor responsiveness to drugs. This study evaluated drug responses with a competing endogenous RNA (ceRNA) system that depended on competition between diverse RNA species. We identified drug response‐related ceRNA (DRCEs) by combining the sequence and expression data of long noncoding RNA (lncRNA), microRNA (miRNA), and messenger RNA (mRNA), and the survival data of cancer patients treated with drugs. We constructed a patient–drug two‐layer integrated network and used a linear weighting method to predict individual drug responses. DRCEs were found to be significantly enriched in known cancer and drug‐associated data resources, involved in biological processes known to mediate drug responses, and correlated to drug activity in cancer cell lines. The dysregulation of DRCE expression influenced drug response‐associated functions and pathways, suggesting DRCEs as potential therapeutic targets affecting drug responses. A further case study in breast invasive carcinoma (BRCA) found that DRCE expression was consistent with the drug response pattern and the aberrant expression of the two NEAT1‐related DRCEs may lead to poor response to tamoxifen therapy for patients with TP53 mutations. In summary, this study provides a framework for ceRNA‐based evaluation of clinical drug responses across multiple cancer types. Understanding the underlying molecular mechanisms of drug responses will allow improved response to chemotherapy and outcomes of cancer treatment.
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Affiliation(s)
- Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Xin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Dianshuang Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Maoni Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Ming Yue
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Yanxia Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Weitao Shen
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Yixue Li
- College of Bioinformatics Science and Technology, Harbin Medical University, China.,Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, China
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24
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Schrank Z, Chhabra G, Lin L, Iderzorig T, Osude C, Khan N, Kuckovic A, Singh S, Miller RJ, Puri N. Current Molecular-Targeted Therapies in NSCLC and Their Mechanism of Resistance. Cancers (Basel) 2018; 10:E224. [PMID: 29973561 PMCID: PMC6071023 DOI: 10.3390/cancers10070224] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 12/20/2022] Open
Abstract
Lung cancer is treated with many conventional therapies, such as surgery, radiation, and chemotherapy. However, these therapies have multiple undesirable side effects. To bypass the side effects elicited by these conventional treatments, molecularly-targeted therapies are currently in use or under development. Current molecularly-targeted therapies effectively target specific biomarkers, which are commonly overexpressed in lung cancers and can cause increased tumorigenicity. Unfortunately, several molecularly-targeted therapies are associated with initial dramatic responses followed by acquired resistance due to spontaneous mutations or activation of signaling pathways. Acquired resistance to molecularly targeted therapies presents a major clinical challenge in the treatment of lung cancer. Therefore, to address this clinical challenge and to improve lung cancer patient prognosis, we need to understand the mechanism of acquired resistance to current therapies and develop additional novel therapies. This review concentrates on various lung cancer biomarkers, including EGFR, ALK, and BRAF, as well as their potential mechanisms of drug resistance.
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Affiliation(s)
- Zachary Schrank
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA.
| | - Gagan Chhabra
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA.
| | - Leo Lin
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA.
| | - Tsatsral Iderzorig
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA.
| | - Chike Osude
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA.
| | - Nabiha Khan
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA.
| | - Adijan Kuckovic
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA.
| | - Sanjana Singh
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA.
| | - Rachel J Miller
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA.
| | - Neelu Puri
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA.
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25
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Feng C, Zhang L, Sun Y, Li X, Zhan L, Lou Y, Wang Y, Liu L, Zhang Y. GDPD5, a target of miR-195-5p, is associated with metastasis and chemoresistance in colorectal cancer. Biomed Pharmacother 2018; 101:945-952. [DOI: 10.1016/j.biopha.2018.03.028] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/06/2018] [Accepted: 03/06/2018] [Indexed: 12/12/2022] Open
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26
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Azuaje F. Computational models for predicting drug responses in cancer research. Brief Bioinform 2017; 18:820-829. [PMID: 27444372 PMCID: PMC5862310 DOI: 10.1093/bib/bbw065] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Indexed: 02/06/2023] Open
Abstract
The computational prediction of drug responses based on the analysis of multiple types of genome-wide molecular data is vital for accomplishing the promise of precision medicine in oncology. This will benefit cancer patients by matching their tumor characteristics to the most effective therapy available. As larger and more diverse layers of patient-related data become available, further demands for new bioinformatics approaches and expertise will arise. This article reviews key strategies, resources and techniques for the prediction of drug sensitivity in cell lines and patient-derived samples. It discusses major advances and challenges associated with the different model development steps. This review highlights major trends in this area, and will assist researchers in the assessment of recent progress and in the selection of approaches to emerging applications in oncology.
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Affiliation(s)
- Francisco Azuaje
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg
- Corresponding author: Francisco Azuaje, NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg L-1526, Luxembourg. Tel.: +352-26970875; Fax: +352-26970396; E-mail:
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27
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The toxin BjussuLAAO-II induces oxidative stress and DNA damage, upregulates the inflammatory cytokine genes TNF and IL6, and downregulates the apoptotic-related genes BAX, BCL2 and RELA in human Caco-2 cells. Int J Biol Macromol 2017; 109:212-219. [PMID: 29222016 DOI: 10.1016/j.ijbiomac.2017.12.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 12/01/2017] [Accepted: 12/04/2017] [Indexed: 12/21/2022]
Abstract
Colorectal carcinoma is one of the most common cancers in adults. As chemotherapy, the first-choice treatment for colorectal carcinoma, is often infeasible due to acquired tumor resistance and several adverse effects, it is important to discover and explore new molecules with better therapeutic action. Snake venom toxins have shown promising results with high cytotoxicity against tumor cells, but their mechanisms of action remain unclear. Here we examined how BjussuLAAO-II, an L-amino acid oxidase isolated from Bothrops jararacussu snake venom, exerts cytotoxicity towards colorectal adenocarcinoma human cells (Caco-2) and human umbilical vein endothelial cell line (HUVEC). A 24-h treatment with BjussuLAAO-II at 0.25 - 5.00 μg/mL diminished cell viability by decreasing (i) mitochondrial activity, assessed by reduction of 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide and resazurin; (ii) the activity of acid phosphatases; and (iii) lysosomal function, assessed by neutral red uptake. BjussuLAAO-II also increased intracellular levels of reactive oxygen species and DNA damage, as assessed by fluorescence and the comet assay, respectively. BjussuLAAO-II altered the expression of cell proliferation-related genes, as determined by RT-qPCR: it elevated the expression of the inflammatory cytokine genes TNF and IL6, and lowered the expression of the apoptotic-related genes BAX, BCL2, and RELA. Therefore, BjussuLAAO-II induces Caco-2 cells death by acting on multiple intracellular targets, providing important data for further studies to assess whether these effects are seen in both tumor and normal cells, with the aim of selecting this drug for possible therapeutic purposes in the future.
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28
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Qiao Z, Shiozawa K, Kondo T. Proteomic approach toward determining the molecular background of pazopanib resistance in synovial sarcoma. Oncotarget 2017; 8:109587-109595. [PMID: 29312631 PMCID: PMC5752544 DOI: 10.18632/oncotarget.22730] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/28/2017] [Indexed: 12/13/2022] Open
Abstract
Pazopanib, a multitarget tyrosine kinase (TK) inhibitor, has been approved for treatment of soft tissue sarcoma. Elucidation of the molecular background of pazopanib resistance should lead to improved clinical outcomes in sarcomas; accordingly, we investigated this in synovial sarcoma using a proteomic approach. Pazopanib sensitivity was examined in four synovial sarcoma cell lines: SYO-1, HS-SYII, 1273/99, and YaFuSS. The 1273/99 cell line showed significantly higher IC50 values than the others for pazopanib. Expression levels of 90 TKs in the cell lines were examined by western blotting. Among these, the levels of PDGFRB, DDR1, AXL, MET, and PYK2 were higher, and those of FGFR1 and VEGFR3 were lower in the 1273/99 cell line than the other cell lines. Gene silencing analysis of the TKs upregulated in 1273/99 cells showed differing effects on cell growth: PDGFRB, MET, and PYK2 knockdown induced cell growth inhibition, whereas DDR1 and AXL knockdown did not influence cell growth. Using the PamChip peptide microarray, we found that 18 peptide substrates were highly phosphorylated in the 1273/99 cell line compared with other cell lines. Using the PhosphoNet database, we found that kinases FGFR3, RET, VEGFR1, EPHA2, EPHA4, TRKA, and SRC phosphorylated these 18 peptide substrates. Moreover, the results for overexpressed and aberrantly activated TKs in pazopanib-resistant cells showed no overlap. Taken together, our study indicates that identification of comprehensive TK profiles represents an essential approach to determining the molecular background of pazopanib resistance in synovial sarcoma.
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Affiliation(s)
- Zhiwei Qiao
- Division of Rare Cancer Research, National Cancer Center Research Institute, Chuo-ku, Tokyo 104-0045, Japan
| | - Kumiko Shiozawa
- Division of Rare Cancer Research, National Cancer Center Research Institute, Chuo-ku, Tokyo 104-0045, Japan
| | - Tadashi Kondo
- Division of Rare Cancer Research, National Cancer Center Research Institute, Chuo-ku, Tokyo 104-0045, Japan
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29
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Meisenberg C, Ashour ME, El-Shafie L, Liao C, Hodgson A, Pilborough A, Khurram SA, Downs JA, Ward SE, El-Khamisy SF. Epigenetic changes in histone acetylation underpin resistance to the topoisomerase I inhibitor irinotecan. Nucleic Acids Res 2017; 45:1159-1176. [PMID: 28180300 PMCID: PMC5388393 DOI: 10.1093/nar/gkw1026] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 10/08/2016] [Accepted: 10/18/2016] [Indexed: 02/06/2023] Open
Abstract
The topoisomerase I (TOP1) inhibitor irinotecan triggers cell death by trapping TOP1 on DNA, generating cytotoxic protein-linked DNA breaks (PDBs). Despite its wide application in a variety of solid tumors, the mechanisms of cancer cell resistance to irinotecan remains poorly understood. Here, we generated colorectal cancer (CRC) cell models for irinotecan resistance and report that resistance is neither due to downregulation of the main cellular target of irinotecan TOP1 nor upregulation of the key TOP1 PDB repair factor TDP1. Instead, the faster repair of PDBs underlies resistance, which is associated with perturbed histone H4K16 acetylation. Subsequent treatment of irinotecan-resistant, but not parental, CRC cells with histone deacetylase (HDAC) inhibitors can effectively overcome resistance. Immunohistochemical analyses of CRC tissues further corroborate the importance of histone H4K16 acetylation in CRC. Finally, the resistant clones exhibit cross-resistance with oxaliplatin but not with ionising radiation or 5-fluoruracil, suggesting that the latter two could be employed following loss of irinotecan response. These findings identify perturbed chromatin acetylation in irinotecan resistance and establish HDAC inhibitors as potential therapeutic means to overcome resistance.
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Affiliation(s)
- Cornelia Meisenberg
- Mammalian Genome Stability Group, Krebs and Sheffield Institute for Nucleic Acids, University of Sheffield, Western Bank, Sheffield, UK.,The Wellcome Trust DNA Repair Group, University of Sussex, Brighton, UK
| | - Mohamed E Ashour
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City for Science and Technology, Giza, Egypt.,Mammalian Genome Stability Group, Krebs and Sheffield Institute for Nucleic Acids, University of Sheffield, Western Bank, Sheffield, UK
| | - Lamia El-Shafie
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City for Science and Technology, Giza, Egypt
| | - Chunyan Liao
- Mammalian Genome Stability Group, Krebs and Sheffield Institute for Nucleic Acids, University of Sheffield, Western Bank, Sheffield, UK
| | - Adam Hodgson
- Mammalian Genome Stability Group, Krebs and Sheffield Institute for Nucleic Acids, University of Sheffield, Western Bank, Sheffield, UK
| | - Alice Pilborough
- Unit of Oral and Maxillofacial Pathology, School of Clinical Dentistry, University of Sheffield, UK
| | - Syed A Khurram
- Unit of Oral and Maxillofacial Pathology, School of Clinical Dentistry, University of Sheffield, UK
| | - Jessica A Downs
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Simon E Ward
- Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK
| | - Sherif F El-Khamisy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City for Science and Technology, Giza, Egypt.,Mammalian Genome Stability Group, Krebs and Sheffield Institute for Nucleic Acids, University of Sheffield, Western Bank, Sheffield, UK.,The Wellcome Trust DNA Repair Group, University of Sussex, Brighton, UK
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30
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Peng J, Lu J, Shang X, Chen J. Identifying consistent disease subnetworks using DNet. Methods 2017; 131:104-110. [PMID: 28807723 DOI: 10.1016/j.ymeth.2017.07.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 12/12/2022] Open
Abstract
It is critical to identify disease-specific subnetworks from the vastly available genome-wide gene expression data for elucidating how genes perform high-level biological functions together. Various algorithms have been developed for disease gene identification. However, the topological structure of the disease networks (or even the fraction of the networks) has been left largely unexplored. In this article, we present DNet, a method for the identification of significant disease subnetworks by integrating both the network structure and gene expression information. Our work will lead to the identification of missing key disease genes, which are be highly expressed in a disease-specific gene expression dataset. The experimental evaluation of our method on both the Leukemia and the Duchenne Muscular Dystrophy gene expression datasets show that DNet performs better than the existing state-of-the-art methods. In addition, literature supports were found for the discovered disease subnetworks in a case study.
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Affiliation(s)
- Jiajie Peng
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China.
| | - Junya Lu
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China.
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China.
| | - Jin Chen
- Institute for Biomedical Informatics, University of Kentucky, Lexington, USA; Department of Internal Medicine, University of Kentucky, Lexington, USA; Department of Computer Science, University of Kentucky, Lexington, USA.
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31
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Sonowal H, Pal PB, Wen JJ, Awasthi S, Ramana KV, Srivastava SK. Aldose reductase inhibitor increases doxorubicin-sensitivity of colon cancer cells and decreases cardiotoxicity. Sci Rep 2017; 7:3182. [PMID: 28600556 PMCID: PMC5466629 DOI: 10.1038/s41598-017-03284-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/25/2017] [Indexed: 01/01/2023] Open
Abstract
Anthracycline drugs such as doxorubicin (DOX) and daunorubicin remain some of the most active wide-spectrum and cost-effective drugs in cancer therapy. However, colorectal cancer (CRC) cells are inherently resistant to anthracyclines which at higher doses cause cardiotoxicity. Our recent studies indicate that aldose reductase (AR) inhibitors such as fidarestat inhibit CRC growth in vitro and in vivo. Here, we show that treatment of CRC cells with fidarestat increases the efficacy of DOX-induced death in HT-29 and SW480 cells and in nude mice xenografts. AR inhibition also results in higher intracellular accumulation of DOX and decreases the expression of drug transporter proteins MDR1, MRP1, and ABCG2. Further, fidarestat also inhibits DOX-induced increase in troponin-I and various inflammatory markers in the serum and heart and restores cardiac function in mice. These results suggest that fidarestat could be used as adjuvant therapy to enhance DOX sensitivity of CRC cells and to reduce DOX-associated cardiotoxicity.
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Affiliation(s)
- Himangshu Sonowal
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX-77555, USA
| | - Pabitra B Pal
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX-77555, USA
| | - Jian-Jun Wen
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX-77555, USA
| | - Sanjay Awasthi
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX-79430, USA
| | - Kota V Ramana
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX-77555, USA
| | - Satish K Srivastava
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX-77555, USA.
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32
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Bommer UA, Vine KL, Puri P, Engel M, Belfiore L, Fildes K, Batterham M, Lochhead A, Aghmesheh M. Translationally controlled tumour protein TCTP is induced early in human colorectal tumours and contributes to the resistance of HCT116 colon cancer cells to 5-FU and oxaliplatin. Cell Commun Signal 2017; 15:9. [PMID: 28143584 PMCID: PMC5286767 DOI: 10.1186/s12964-017-0164-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/23/2017] [Indexed: 12/22/2022] Open
Abstract
Background Translationally controlled tumour protein TCTP is an anti-apoptotic protein frequently overexpressed in cancers, where high levels are often associated with poor patient outcome. TCTP may be involved in protecting cancer cells against the cytotoxic action of anti-cancer drugs. Here we study the early increase of TCTP levels in human colorectal cancer (CRC) and the regulation of TCTP expression in HCT116 colon cancer cells, in response to treatment with the anti-cancer drugs 5-FU and oxaliplatin. Methods Using immunohistochemistry, we assessed TCTP levels in surgical samples from adenomas and adenocarcinomas of the colon, compared to normal colon tissue. We also studied the regulation of TCTP in HCT116 colon cancer cells in response to 5-FU and oxaliplatin by western blotting. TCTP mRNA levels were assessed by RT-qPCR. We used mTOR kinase inhibitors to demonstrate mTOR-dependent translational regulation of TCTP under these conditions. Employing the Real-Time Cell Analysis (RTCA) System and the MTS assay, we investigated the effect of TCTP-knockdown on the sensitivity of HCT116 cells to the anti-cancer drugs 5-FU and oxaliplatin. Results 1. TCTP levels are significantly increased in colon adenomas and adenocarcinomas, compared to normal colon tissue. 2. TCTP protein levels are about 4-fold upregulated in HCT116 colon cancer cells, in response to 5-FU and oxaliplatin treatment, whereas TCTP mRNA levels are down regulated. 3. mTOR kinase inhibitors prevented the up-regulation of TCTP protein, indicating that TCTP is translationally regulated through the mTOR complex 1 signalling pathway under these conditions. 4. Using two cellular assay systems, we demonstrated that TCTP-knockdown sensitises HCT116 cells to the cytotoxicity caused by 5-FU and oxaliplatin. Conclusions Our results demonstrate that TCTP levels increase significantly in the early stages of CRC development. In colon cancer cells, expression of this protein is largely upregulated during treatment with the DNA-damaging anti-cancer drugs 5-FU and oxaliplatin, as part of the cellular stress response. TCTP may thus contribute to the development of anti-cancer drug resistance. These findings indicate that TCTP might be suitable as a biomarker and that combinatorial treatment using 5-FU/oxaliplatin, together with mTOR kinase inhibitors, could be a route to preventing the development of resistance to these drugs. Electronic supplementary material The online version of this article (doi:10.1186/s12964-017-0164-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ulrich-Axel Bommer
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia. .,Graduate School of Medicine, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia.
| | - Kara L Vine
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia.,School of Biological Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, 2522, NSW, Australia
| | - Prianka Puri
- Graduate School of Medicine, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia.,Present address: Southeast Sydney Illawarra Area Health Services, Sydney, NSW, Australia
| | - Martin Engel
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia.,School of Biological Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, 2522, NSW, Australia
| | - Lisa Belfiore
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia.,School of Biological Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, 2522, NSW, Australia
| | - Karen Fildes
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia.,Graduate School of Medicine, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Marijka Batterham
- School of Mathematics and Applied Statistics, Faculty of Engineering and Information Sciences University of Wollongong, Wollongong, 2522, NSW, Australia
| | - Alistair Lochhead
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia.,Southern IML Pathology Wollongong, 2500, Wollongong, NSW, Australia.,Present address: Syd-Path, St. Vincent's Hospital Darlinghurst, Sydney, 2010, NSW, Australia
| | - Morteza Aghmesheh
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia.,Illawarra Cancer Care Centre, The Wollongong Hospital, Wollongong, 2500, NSW, Australia
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Zhao W, Chen B, Guo X, Wang R, Chang Z, Dong Y, Song K, Wang W, Qi L, Gu Y, Wang C, Yang D, Guo Z. A rank-based transcriptional signature for predicting relapse risk of stage II colorectal cancer identified with proper data sources. Oncotarget 2017; 7:19060-71. [PMID: 26967049 PMCID: PMC4951352 DOI: 10.18632/oncotarget.7956] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/25/2016] [Indexed: 01/02/2023] Open
Abstract
The irreproducibility problem seriously hinders the studies on transcriptional signatures for predicting relapse risk of early stage colorectal cancer (CRC) patients. Through reviewing recently published 34 literatures for the development of CRC prognostic signatures based on gene expression profiles, we revealed a surprising phenomenon that 33 of these studies analyzed CRC samples with and without adjuvant chemotherapy together in the training and/or validation datasets. This data misuse problem could be partially attributed to the unclear and incomplete data annotation in public data sources. Furthermore, all the signatures proposed by these studies were based on risk scores summarized from gene expression levels, which are sensitive to experimental batch effects and risk compositions of the samples analyzed together. To avoid the above-mentioned problems, we carefully selected three qualified large datasets to develop and validate a signature consisting of three pairs of genes. The within-sample relative expression orderings of these gene pairs could robustly predict relapse risk of stage II CRC samples assessed in different laboratories. The transcriptional and functional analyses provided clear evidence that the high risk patients predicted by the proposed signature represent patients with micro-metastases.
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Affiliation(s)
- Wenyuan Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Beibei Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xin Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ruiping Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhiqiang Chang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yu Dong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Kai Song
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wen Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Lishuang Qi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yunyan Gu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Chenguang Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Da Yang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, USA.,Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA.,Department of Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zheng Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
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34
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Kotelevets L, Chastre E, Desmaële D, Couvreur P. Nanotechnologies for the treatment of colon cancer: From old drugs to new hope. Int J Pharm 2016; 514:24-40. [DOI: 10.1016/j.ijpharm.2016.06.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/03/2016] [Accepted: 06/04/2016] [Indexed: 12/15/2022]
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35
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Identifying clinically relevant drug resistance genes in drug-induced resistant cancer cell lines and post-chemotherapy tissues. Oncotarget 2016; 6:41216-27. [PMID: 26515599 PMCID: PMC4747401 DOI: 10.18632/oncotarget.5649] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/12/2015] [Indexed: 12/13/2022] Open
Abstract
Until recently, few molecular signatures of drug resistance identified in drug-induced resistant cancer cell models can be translated into clinical practice. Here, we defined differentially expressed genes (DEGs) between pre-chemotherapy colorectal cancer (CRC) tissue samples of non-responders and responders for 5-fluorouracil and oxaliplatin-based therapy as clinically relevant drug resistance genes (CRG5-FU/L-OHP). Taking CRG5-FU/L-OHP as reference, we evaluated the clinical relevance of several types of genes derived from HCT116 CRC cells with resistance to 5-fluorouracil and oxaliplatin, respectively. The results revealed that DEGs between parental and resistant cells, when both were treated with the corresponding drug for a certain time, were significantly consistent with the CRG5-FU/L-OHP as well as the DEGs between the post-chemotherapy CRC specimens of responders and non-responders. This study suggests a novel strategy to extract clinically relevant drug resistance genes from both drug-induced resistant cell models and post-chemotherapy cancer tissue specimens.
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36
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Tong M, Zheng W, Li H, Li X, Ao L, Shen Y, Liang Q, Li J, Hong G, Yan H, Cai H, Li M, Guan Q, Guo Z. Multi-omics landscapes of colorectal cancer subtypes discriminated by an individualized prognostic signature for 5-fluorouracil-based chemotherapy. Oncogenesis 2016; 5:e242. [PMID: 27429074 PMCID: PMC5399173 DOI: 10.1038/oncsis.2016.51] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/27/2016] [Accepted: 06/17/2016] [Indexed: 12/11/2022] Open
Abstract
Until recently, few prognostic signatures for colorectal cancer (CRC) patients receiving 5-fluorouracil (5-FU)-based chemotherapy could be used in clinical practice. Here, using transcriptional profiles for a panel of cancer cell lines and three cohorts of CRC patients, we developed a prognostic signature based on within-sample relative expression orderings (REOs) of six gene pairs for stage II-III CRC patients receiving 5-FU-based chemotherapy. This REO-based signature had the unique advantage of being insensitive to experimental batch effects and free of the impractical data normalization requirement. After stratifying 184 CRC samples with multi-omics data from The Cancer Genome Atlas into two prognostic groups using the REO-based signature, we further revealed that patients with high recurrence risk were characterized by frequent gene copy number aberrations reducing 5-FU efficacy and DNA methylation aberrations inducing distinct transcriptional alternations to confer 5-FU resistance. In contrast, patients with low recurrence risk exhibited deficient mismatch repair and carried frequent gene mutations suppressing cell adhesion. These results reveal the multi-omics landscapes determining prognoses of stage II-III CRC patients receiving 5-FU-based chemotherapy.
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Affiliation(s)
- M Tong
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - W Zheng
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - H Li
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - X Li
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - L Ao
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Y Shen
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Q Liang
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - J Li
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - G Hong
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - H Yan
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - H Cai
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - M Li
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Q Guan
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Z Guo
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
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Peritoneal expression of Matrilysin helps identify early post-operative recurrence of colorectal cancer. Oncotarget 2016; 6:13402-15. [PMID: 25596746 PMCID: PMC4537023 DOI: 10.18632/oncotarget.2830] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 11/27/2014] [Indexed: 12/20/2022] Open
Abstract
Recurrence of colorectal cancer (CRC) following a potentially curative resection is a challenging clinical problem. Matrix metalloproteinase-7 (MMP-7) is over-expressed by CRC cells and supposed to play a major role in CRC cell diffusion and metastasis. MMP-7 RNA expression was assessed by real-time PCR using specific primers in peritoneal washing fluid obtained during surgical procedure. After surgery, patients underwent a regular follow up for assessing recurrence. transcripts for MMP-7 were detected in 31/57 samples (54%). Patients were followed-up (range 20-48 months) for recurrence prevention. Recurrence was diagnosed in 6 out of 55 patients (11%) and two patients eventually died because of this. Notably, all the six patients who had relapsed were positive for MMP-7. Sensitivity and specificity of the test were 100% and 49% respectively. Data from patients have also been corroborated by computational approaches. Public available coloncarcinoma datasets have been employed to confirm MMP7 clinical impact on the disease. Interestingly, MMP-7 expression appeared correlated to Tgfb-1, and correlation of the two factors represented a poor prognostic factor. This study proposes positivity of MMP-7 in peritoneal cavity as a novel biomarker for predicting disease recurrence in patients with CRC.
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Shi M, He J. SNRFCB: sub-network based random forest classifier for predicting chemotherapy benefit on survival for cancer treatment. MOLECULAR BIOSYSTEMS 2016; 12:1214-23. [PMID: 26864276 DOI: 10.1039/c5mb00399g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Adjuvant chemotherapy (CTX) should be individualized to provide potential survival benefit and avoid potential harm to cancer patients. Our goal was to establish a computational approach for making personalized estimates of the survival benefit from adjuvant CTX. We developed Sub-Network based Random Forest classifier for predicting Chemotherapy Benefit (SNRFCB) based gene expression datasets of lung cancer. The SNRFCB approach was then validated in independent test cohorts for identifying chemotherapy responder cohorts and chemotherapy non-responder cohorts. SNRFCB involved the pre-selection of gene sub-network signatures based on the mutations and on protein-protein interaction data as well as the application of the random forest algorithm to gene expression datasets. Adjuvant CTX was significantly associated with the prolonged overall survival of lung cancer patients in the chemotherapy responder group (P = 0.008), but it was not beneficial to patients in the chemotherapy non-responder group (P = 0.657). Adjuvant CTX was significantly associated with the prolonged overall survival of lung cancer squamous cell carcinoma (SQCC) subtype patients in the chemotherapy responder cohorts (P = 0.024), but it was not beneficial to patients in the chemotherapy non-responder cohorts (P = 0.383). SNRFCB improved prediction performance as compared to the machine learning method, support vector machine (SVM). To test the general applicability of the predictive model, we further applied the SNRFCB approach to human breast cancer datasets and also observed superior performance. SNRFCB could provide recurrent probability for individual patients and identify which patients may benefit from adjuvant CTX in clinical trials.
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Affiliation(s)
- Mingguang Shi
- School of Electric Engineering and Automation, Hefei University of Technology, Hefei, Anhui 230009, China.
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39
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Bounaix Morand du Puch C, Nouaille M, Giraud S, Labrunie A, Luce S, Preux PM, Labrousse F, Gainant A, Tubiana-Mathieu N, Le Brun-Ly V, Valleix D, Guillaudeau A, Mesturoux L, Coulibaly B, Lautrette C, Mathonnet M. Chemotherapy outcome predictive effectiveness by the Oncogramme: pilot trial on stage-IV colorectal cancer. J Transl Med 2016; 14:10. [PMID: 26791256 PMCID: PMC4721000 DOI: 10.1186/s12967-016-0765-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 12/28/2015] [Indexed: 12/25/2022] Open
Abstract
Background Colorectal cancer (CRC) remains a major public concern. While conventional chemotherapeutic regimens have proved useful against advanced/metastatic diseases, progresses are to be made to effectively cure the large portion of patients not benefiting from these treatments. One direction to improve response rates is to develop chemosensitivity and resistance assays (CSRAs) efficiently assisting clinicians in treatment selection process, an already long preoccupation of oncologists and researchers. Several methods have been described to this day, none achieving yet sufficient reliability for recommended use in the clinical routine. Methods
We led a pilot study on 19 metastatic CRC patients evaluating capacity of the Oncogramme, a standardized process using tumor ex vivo models, to provide chemosensitivity profiles and predict clinical outcome of patients receiving standard CRC chemotherapeutics. Oncogramme responses were categorized according to the method of percentiles to assess sensitivity, specificity and concordance. Results We report from a primary analysis a success rate of 97.4 %, a very good sensitivity (84.6 %), a below-average specificity (33.3 %), along with a global agreement of 63.6 % and a concordance between Oncogramme results and patients’ responses (Kappa coefficient) of 0.193. A supplementary analysis, focusing on CRC patients with no treatment switch over a longer time course, demonstrated improvement in specificity and concordance. Conclusions Results establish feasibility and usefulness of the Oncogramme, prelude to a larger-scale trial. Advantages and drawbacks of the procedure are discussed, as well as the place of CSRAs within the future arsenal of methods available to clinicians to individualize treatments and improve patient prognosis. Trial registration: ClinicalTrials.gov database, registration number: NCT02305368 Electronic supplementary material The online version of this article (doi:10.1186/s12967-016-0765-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Michelle Nouaille
- Centre d'Investigation Clinique, INSERM 1435, Centre hospitalier régional universitaire de Limoges Dupuytren, 2 avenue Martin Luther King, 87042, Limoges Cedex, France.
| | - Stéphanie Giraud
- Oncomedics SAS, ESTER technopole, 1 avenue d'Ester, 87069, Limoges, France.
| | - Anaïs Labrunie
- Centre d'Épidémiologie, de Biostatistique et de Méthodologie de la Recherche, Centre hospitalier régional universitaire de Limoges Dupuytren, 2 rue du Dr Marcland, 87025, Limoges Cedex, France.
| | - Sandrine Luce
- Centre d'Épidémiologie, de Biostatistique et de Méthodologie de la Recherche, Centre hospitalier régional universitaire de Limoges Dupuytren, 2 rue du Dr Marcland, 87025, Limoges Cedex, France.
| | - Pierre-Marie Preux
- Centre d'Épidémiologie, de Biostatistique et de Méthodologie de la Recherche, Centre hospitalier régional universitaire de Limoges Dupuytren, 2 rue du Dr Marcland, 87025, Limoges Cedex, France.
| | - François Labrousse
- Centre hospitalier régional universitaire de Limoges Dupuytren, service d'anatomopathologie, 2 avenue Martin Luther King, 87042, Limoges Cedex, France.
| | - Alain Gainant
- Centre hospitalier régional universitaire de Limoges Dupuytren, service de chirurgie digestive, 2 rue du Dr Marcland, 87025, Limoges, France.
| | - Nicole Tubiana-Mathieu
- Centre hospitalier régional universitaire de Limoges Dupuytren, service d'oncologie médicale, 2 avenue Martin Luther King, 87042, Limoges Cedex, France.
| | - Valérie Le Brun-Ly
- Centre hospitalier régional universitaire de Limoges Dupuytren, service d'oncologie médicale, 2 avenue Martin Luther King, 87042, Limoges Cedex, France.
| | - Denis Valleix
- Centre hospitalier régional universitaire de Limoges Dupuytren, service de chirurgie viscérale, 2 avenue Martin Luther King, 87042, Limoges Cedex, France.
| | - Angélique Guillaudeau
- Centre hospitalier régional universitaire de Limoges Dupuytren, service d'anatomopathologie, 2 avenue Martin Luther King, 87042, Limoges Cedex, France.
| | - Laura Mesturoux
- Centre hospitalier régional universitaire de Limoges Dupuytren, service d'anatomopathologie, 2 avenue Martin Luther King, 87042, Limoges Cedex, France.
| | - Béma Coulibaly
- Centre hospitalier régional universitaire de Limoges Dupuytren, service d'anatomopathologie, 2 avenue Martin Luther King, 87042, Limoges Cedex, France.
| | | | - Muriel Mathonnet
- Centre hospitalier régional universitaire de Limoges Dupuytren, service de chirurgie digestive générale et endocrinienne, 2 avenue Martin Luther King, 87042, Limoges Cedex, France. .,Université de Limoges, Institut 145 GEIST, EA 3842 "Homéostasie cellulaire et pathologies", Facultés de médecine et de pharmacie, 2 rue du Dr Marcland, 87025, Limoges Cedex, France.
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Sarkar FH. Novel Holistic Approaches for Overcoming Therapy Resistance in Pancreatic and Colon Cancers. Med Princ Pract 2016; 25 Suppl 2:3-10. [PMID: 26228733 PMCID: PMC5588517 DOI: 10.1159/000435814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 06/08/2015] [Indexed: 12/12/2022] Open
Abstract
Gastrointestinal (GI) cancers, such as of the colon and pancreas, are highly resistant to both standard and targeted therapeutics. Therapy-resistant and heterogeneous GI cancers harbor highly complex signaling networks (the resistome) that resist apoptotic programming. Commonly used gemcitabine or platinum-based regimens fail to induce meaningful (i.e. disease-reversing) perturbations in the resistome, resulting in high rates of treatment failure. The GI cancer resistance networks are, in part, due to interactions between parallel signaling and aberrantly expressed microRNAs (miRNAs) that collectively promote the development and survival of drug-resistant cancer stem cells with epithelial-to-mesenchymal transition (EMT) characteristics. The lack of understanding of the resistance networks associated with this subpopulation of cells as well as reductionist, single protein-/pathway-targeted approaches have made 'effective drug design' a difficult task. We propose that the successful design of novel therapeutic regimens to target drug-resistant GI tumors is only possible if network-based drug avenues and agents, in particular 'natural agents' with no known toxicity, are correctly identified. Natural agents (dietary agents or their synthetic derivatives) can individually alter miRNA profiles, suppress EMT pathways and eliminate cancer stem-like cells that derive from pancreatic cancer and colon cancer, by partially targeting multiple yet meaningful networks within the GI cancer resistome. However, the efficacy of these agents as combinations (e.g. consumed in the diet) against this resistome has never been studied. This short review article provides an overview of the different challenges involved in the understanding of the GI resistome, and how novel computational biology can help in the design of effective therapies to overcome resistance.
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Affiliation(s)
- Fazlul H. Sarkar
- *Fazlul H. Sarkar, PhD, Departments of Pathology and Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, 4100 John R, 740 HWCRC, Detroit, MI 48201 (USA), E-Mail
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Abstract
Neuroendocrine tumors (NETs) of the gastrointestinal (GI) tract have a propensity for producing hepatic metastases. Most GI NETs arise from the foregut or midgut, are malignant, and can cause severe debilitating symptoms adversely affecting quality of life. Aggressive treatments to reduce symptoms have an important role in therapy. Patients with GI NETs usually present with inoperable metastatic disease and severe symptoms from a variety of hormones and biogenic amines. This article describes intra-arterial hepatic-directed therapies for metastases from NETs, a group of treatments in which the therapeutic and/or embolic agents are released intra-arterially in specific hepatic vessels to target tumors.
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Affiliation(s)
- Andrew S Kennedy
- Radiation Oncology Research, Sarah Cannon Research Institute, Nashville, TN, USA; Department of Biomedical Engineering, Department of Mechanical and Aerospace Engineering, North Carolina State University, Raleigh, NC, USA.
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Jin X, Tan X, Zhang X, Han M, Zhao Y. In vitro and in vivo anticancer effects of singly protonated dehydronorcantharidin silver coordination polymer in CT-26 murine colon carcinoma model. Bioorg Med Chem Lett 2015; 25:4477-80. [DOI: 10.1016/j.bmcl.2015.08.078] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 08/25/2015] [Accepted: 08/28/2015] [Indexed: 02/08/2023]
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Long Noncoding RNAs in Digestive System Malignancies: A Novel Class of Cancer Biomarkers and Therapeutic Targets? Gastroenterol Res Pract 2015; 2015:319861. [PMID: 26064090 PMCID: PMC4429197 DOI: 10.1155/2015/319861] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 04/20/2015] [Indexed: 01/17/2023] Open
Abstract
High throughput methodologies have revealed the existence of an unexpectedly large number of long noncoding RNAs (lncRNAs). The unconventional role of lncRNAs in gene expression regulation and their broad implication in oncogenic and tumor suppressive pathways have introduced lncRNAs as novel biological tumor markers. The most prominent example of lncRNAs application in routine clinical practice is PCA3, a FDA-approved biomarker for prostate cancer. Regarding digestive system malignancies, the oncogenic HOTAIR is one of the most widely studied lncRNAs in the preclinical level and has already been identified as a potent prognostic marker for major malignancies of the gastrointestinal tract. Here, we provide an overview of recent findings regarding the emerging role of lncRNAs not only as key regulators of cancer initiation and progression in colon, stomach, pancreatic, liver, and esophageal cancers, but also as reliable tumor markers and therapeutic tools. lncRNAs can be easily, rapidly, and cost-effectively determined in tissues, serum, and gastric juice, making them highly versatile analytes. Taking also into consideration the largely unmet clinical need for early diagnosis and more accurate prognostic/predictive markers for gastrointestinal cancer patients, we comment upon the perspectives of lncRNAs as efficient molecular tools that could aid in the clinical management.
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