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Krushkal J, Zhao Y, Roney K, Zhu W, Brooks A, Wilsker D, Parchment RE, McShane LM, Doroshow JH. Association of changes in expression of HDAC and SIRT genes after drug treatment with cancer cell line sensitivity to kinase inhibitors. Epigenetics 2024; 19:2309824. [PMID: 38369747 PMCID: PMC10878021 DOI: 10.1080/15592294.2024.2309824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/14/2024] [Indexed: 02/20/2024] Open
Abstract
Histone deacetylases (HDACs) and sirtuins (SIRTs) are important epigenetic regulators of cancer pathways. There is a limited understanding of how transcriptional regulation of their genes is affected by chemotherapeutic agents, and how such transcriptional changes affect tumour sensitivity to drug treatment. We investigated the concerted transcriptional response of HDAC and SIRT genes to 15 approved antitumor agents in the NCI-60 cancer cell line panel. Antitumor agents with diverse mechanisms of action induced upregulation or downregulation of multiple HDAC and SIRT genes. HDAC5 was upregulated by dasatinib and erlotinib in the majority of the cell lines. Tumour cell line sensitivity to kinase inhibitors was associated with upregulation of HDAC5, HDAC1, and several SIRT genes. We confirmed changes in HDAC and SIRT expression in independent datasets. We also experimentally validated the upregulation of HDAC5 mRNA and protein expression by dasatinib in the highly sensitive IGROV1 cell line. HDAC5 was not upregulated in the UACC-257 cell line resistant to dasatinib. The effects of cancer drug treatment on expression of HDAC and SIRT genes may influence chemosensitivity and may need to be considered during chemotherapy.
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Affiliation(s)
- Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Kyle Roney
- Department of Biostatistics and Bioinformatics, George Washington University, Washington, DC, USA
| | - Weimin Zhu
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Alan Brooks
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Deborah Wilsker
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ralph E. Parchment
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lisa M. McShane
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - James H. Doroshow
- Division of Cancer Treatment and Diagnosis and Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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Zheng R, Su R, Fan Y, Xing F, Huang K, Yan F, Chen H, Liu B, Fang L, Du Y, Zhou F, Wang D, Feng S. Machine Learning-Based Integrated Multiomics Characterization of Colorectal Cancer Reveals Distinctive Metabolic Signatures. Anal Chem 2024; 96:8772-8781. [PMID: 38743842 DOI: 10.1021/acs.analchem.4c01171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The metabolic signature identification of colorectal cancer is critical for its early diagnosis and therapeutic approaches that will significantly block cancer progression and improve patient survival. Here, we combined an untargeted metabolic analysis strategy based on internal extractive electrospray ionization mass spectrometry and the machine learning approach to analyze metabolites in 173 pairs of cancer samples and matched normal tissue samples to build robust metabolic signature models for diagnostic purposes. Screening and independent validation of metabolic signatures from colorectal cancers via machine learning methods (Logistic Regression_L1 for feature selection and eXtreme Gradient Boosting for classification) was performed to generate a panel of seven signatures with good diagnostic performance (the accuracy of 87.74%, sensitivity of 85.82%, and specificity of 89.66%). Moreover, seven signatures were evaluated according to their ability to distinguish between cancer and normal tissues, with the metabolic molecule PC (30:0) showing good diagnostic performance. In addition, genes associated with PC (30:0) were identified by multiomics analysis (combining metabolic data with transcriptomic data analysis) and our results showed that PC (30:0) could promote the proliferation of colorectal cancer cell SW480, revealing the correlation between genetic changes and metabolic dysregulation in cancer. Overall, our results reveal potential determinants affecting metabolite dysregulation, paving the way for a mechanistic understanding of altered tissue metabolites in colorectal cancer and design interventions for manipulating the levels of circulating metabolites.
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Affiliation(s)
- Ran Zheng
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130021, China
| | - Rui Su
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130021, China
| | - Yusi Fan
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Software, Jilin University, Changchun 130021, China
| | - Fan Xing
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130021, China
| | - Keke Huang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130021, China
| | - Fei Yan
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130021, China
| | - Huanwen Chen
- School of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang 330004, China
| | - Botong Liu
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130021, China
| | - Laiping Fang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130021, China
| | - Yechao Du
- Department of General Surgery Center, First Hospital of Jilin University, 1 Xinmin Street Changchun, Jilin 130012, China
| | - Fengfeng Zhou
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Software, Jilin University, Changchun 130021, China
| | - Daguang Wang
- Department of Gastric Colorectal and Anal Surgery, First Hospital of Jilin University, 1 Xinmin Street Changchun, Jilin 130012, China
| | - Shouhua Feng
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130021, China
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Tang C, Ke M, Yu X, Sun S, Luo X, Liu X, Zhou Y, Wang Z, Cui X, Gu C, Yang Y. GART Functions as a Novel Methyltransferase in the RUVBL1/β-Catenin Signaling Pathway to Promote Tumor Stemness in Colorectal Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301264. [PMID: 37439412 PMCID: PMC10477903 DOI: 10.1002/advs.202301264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/30/2023] [Indexed: 07/14/2023]
Abstract
Tumor stemness is associated with the recurrence and incurability of colorectal cancer (CRC), which lacks effective therapeutic targets and drugs. Glycinamide ribonucleotide transformylase (GART) fulfills an important role in numerous types of malignancies. The present study aims to identify the underlying mechanism through which GART may promote CRC stemness, as to developing novel therapeutic methods. An elevated level of GART is associated with poor outcomes in CRC patients and promotes the proliferation and migration of CRC cells. CD133+ cells with increased GART expression possess higher tumorigenic and proliferative capabilities both in vitro and in vivo. GART is identified to have a novel methyltransferase function, whose enzymatic activity center is located at the E948 site. GART also enhances the stability of RuvB-like AAA ATPase 1 (RUVBL1) through methylating its K7 site, which consequently aberrantly activates the Wnt/β-catenin signaling pathway to induce tumor stemness. Pemetrexed (PEM), a compound targeting GART, combined with other chemotherapy drugs greatly suppresses tumor growth both in a PDX model and in CRC patients. The present study demonstrates a novel methyltransferase function of GART and the role of the GART/RUVBL1/β-catenin signaling axis in promoting CRC stemness. PEM may be a promising therapeutic agent for the treatment of CRC.
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Affiliation(s)
- Chao Tang
- Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western MedicineNanjing University of Chinese MedicineNanjing210008China
- School of Medicine & Holistic Integrative MedicineNanjing University of Chinese MedicineNanjing210046China
| | - Mengying Ke
- School of Medicine & Holistic Integrative MedicineNanjing University of Chinese MedicineNanjing210046China
| | - Xichao Yu
- School of Medicine & Holistic Integrative MedicineNanjing University of Chinese MedicineNanjing210046China
| | - Shanliang Sun
- School of PharmacyNanjing University of Chinese MedicineNanjing210046China
| | - Xian Luo
- School of Medicine & Holistic Integrative MedicineNanjing University of Chinese MedicineNanjing210046China
| | - Xin Liu
- School of Medicine & Holistic Integrative MedicineNanjing University of Chinese MedicineNanjing210046China
| | - Yanyan Zhou
- School of Medicine & Holistic Integrative MedicineNanjing University of Chinese MedicineNanjing210046China
| | - Ze Wang
- School of Medicine & Holistic Integrative MedicineNanjing University of Chinese MedicineNanjing210046China
| | - Xing Cui
- Department of Hematology and OncologyThe Second Affiliated Hospital of Shandong University of Traditional Chinese MedicineJinan250001China
| | - Chunyan Gu
- Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western MedicineNanjing University of Chinese MedicineNanjing210008China
- School of Medicine & Holistic Integrative MedicineNanjing University of Chinese MedicineNanjing210046China
| | - Ye Yang
- School of Medicine & Holistic Integrative MedicineNanjing University of Chinese MedicineNanjing210046China
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Lin C, Liu P, Shi C, Qiu L, Shang D, Lu Z, Tu Z, Liu H. Therapeutic targeting of DNA damage repair pathways guided by homologous recombination deficiency scoring in ovarian cancers. Fundam Clin Pharmacol 2023; 37:194-214. [PMID: 36130021 DOI: 10.1111/fcp.12834] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 07/23/2022] [Accepted: 09/20/2022] [Indexed: 12/01/2022]
Abstract
The susceptibility of cells to DNA damage and their DNA repair ability are crucial for cancer therapy. Homologous recombination is one of the major repairing mechanisms for DNA double-strand breaks. Approximately half of ovarian cancer (OvCa) cells harbor homologous recombination deficiency (HRD). Considering that HRD is a major hallmark of OvCas, scholars proposed HRD scoring to evaluate the HRD degree and guide the choice of therapeutic strategies for OvCas. In the last decade, synthetic lethal strategy by targeting poly (ADP-ribose) polymerase (PARP) in HR-deficient OvCas has attracted considerable attention in view of its favorable clinical effort. We therefore suggested that the uses of other DNA damage/repair-targeted drugs in HR-deficient OvCas might also offer better clinical outcome. Here, we reviewed the current small molecule compounds that targeted DNA damage/repair pathways and discussed the HRD scoring system to guide their clinical uses.
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Affiliation(s)
- Chunxiu Lin
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Peng Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Chaowen Shi
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Lipeng Qiu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Dongsheng Shang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ziwen Lu
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zhigang Tu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Hanqing Liu
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, China
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5
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Moravveji SS, Khoshbakht S, Mokhtari M, Salimi M, Lanjanian H, Nematzadeh S, Torkamanian-Afshar M, Masoudi-Nejad A. Impact of 5HydroxyMethylCytosine (5hmC) on reverse/direct association of cell-cycle, apoptosis, and extracellular matrix pathways in gastrointestinal cancers. BMC Genom Data 2022; 23:49. [PMID: 35768769 PMCID: PMC9241275 DOI: 10.1186/s12863-022-01061-x] [Citation(s) in RCA: 3] [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: 12/09/2021] [Accepted: 06/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aberrant levels of 5-hydroxymethylcytosine (5-hmC) can lead to cancer progression. Identification of 5-hmC-related biological pathways in cancer studies can produce better understanding of gastrointestinal (GI) cancers. We conducted a network-based analysis on 5-hmC levels extracted from circulating free DNAs (cfDNA) in GI cancers including colon, gastric, and pancreatic cancers, and from healthy donors. The co-5-hmC network was reconstructed using the weighted-gene co-expression network method. The cancer-related modules/subnetworks were detected. Preservation of three detected 5-hmC-related modules was assessed in an external dataset. The 5-hmC-related modules were functionally enriched, and biological pathways were identified. The relationship between modules was assessed using the Pearson correlation coefficient (p-value < 0.05). An elastic network classifier was used to assess the potential of the 5-hmC modules in distinguishing cancer patients from healthy individuals. To assess the efficiency of the model, the Area Under the Curve (AUC) was computed using five-fold cross-validation in an external dataset. RESULTS The main biological pathways were the cell cycle, apoptosis, and extracellular matrix (ECM) organization. Direct association between the cell cycle and apoptosis, inverse association between apoptosis and ECM organization, and inverse association between the cell cycle and ECM organization were detected for the 5-hmC modules in GI cancers. An AUC of 92% (0.73-1.00) was observed for the predictive model including 11 genes. CONCLUSION The intricate association between biological pathways of identified modules may reveal the hidden significance of 5-hmC in GI cancers. The identified predictive model and new biomarkers may be beneficial in cancer detection and precision medicine using liquid biopsy in the early stages.
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Affiliation(s)
- Sayyed Sajjad Moravveji
- Laboratory of Systems Biology and Bioinformatics (LBB), Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran
| | - Samane Khoshbakht
- Laboratory of Systems Biology and Bioinformatics (LBB), Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran
| | - Majid Mokhtari
- Laboratory of Systems Biology and Bioinformatics (LBB), Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran
| | - Mahdieh Salimi
- Department of Medical Genetics, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Hossein Lanjanian
- Molecular Biology and Genetics Department, Engineering and Natural Science Faculty, Istinye University, Istanbul, Turkey
| | - Sajjad Nematzadeh
- Computer Engineering Department, Architecture and Engineering Faculty, Nisantasi University, Istanbul, Turkey
| | - Mahsa Torkamanian-Afshar
- Computer Engineering Department, Architecture and Engineering Faculty, Nisantasi University, Istanbul, Turkey
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran.
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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6
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Yao C, Li Y, Luo L, Xiong Q, Zhong X, Xie F, Feng P. Identification of miRNAs and genes for predicting Barrett's esophagus progressing to esophageal adenocarcinoma using miRNA-mRNA integrated analysis. PLoS One 2021; 16:e0260353. [PMID: 34818353 PMCID: PMC8612537 DOI: 10.1371/journal.pone.0260353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 11/08/2021] [Indexed: 11/29/2022] Open
Abstract
Barrett's esophagus (BE) is defined as any metaplastic columnar epithelium in the distal esophagus, which predisposes to esophageal adenocarcinoma (EAC). Yet, the mechanism through which BE develops to EAC still remain unclear. Moreover, the miRNA-mRNA regulatory network in distinguishing BE from EAC still remains poorly understood. To identify differentially expressed miRNAs (DEMs) and genes (DEGs) between EAC and BE from tissue samples, gene expression microarray datasets GSE13898, GSE26886, GSE1420 and miRNA microarray datasets GSE16456, GSE20099 were downloaded from Gene Expression Omnibus (GEO) database. GEO2R was used to screen the DEMs and DEGs. Pathway and functional enrichment analysis were performed by DAVID database. The protein-protein interaction (PPI) network was constructed by STRING and been visualized by Cytoscape software. Finnal, survival analysis was performed basing TCGA database. A total of 21 DEMs were identified. The enriched functions and pathways analysis inclued Epstein-Barr virus infection, herpesvirus infection and TRP channels. GART, TNFSF11, GTSE1, NEK2, ICAM1, PSMD12, CTNNB1, CDH1, PSEN1, IL1B, CTNND1, JAG1, CDH17, ITCH, CALM1 and ITGA6 were considered as the hub-genes. Hsa-miR-143 and hsa-miR-133b were the highest connectivity target gene. JAG1 was predicted as the largest number of target miRNAs. The expression of hsa-miR-181d, hsa-miR-185, hsa-miR-15b, hsa-miR-214 and hsa-miR-496 was significantly different between normal tissue and EAC. CDH1, GART, GTSE1, NEK2 and hsa-miR-496, hsa-miR-214, hsa-miR-15b were found to be correlated with survival.
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Affiliation(s)
- Chengjiao Yao
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- Department of Geriatrics of the Affiliated Hospital, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Yilin Li
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Lihong Luo
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Qin Xiong
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Xiaowu Zhong
- Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- * E-mail: (PF); (XZ)
| | - Fengjiao Xie
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Peimin Feng
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- * E-mail: (PF); (XZ)
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7
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Zhang QZ, Wen F, Yang HL, Cao YY, Peng RG, Wang YM, Nie L, Qin YK, Wu JJ, Zhao X, Zi D. GADD45α alleviates the CDDP resistance of SK-OV3/cddp cells via redox-mediated DNA damage. Oncol Lett 2021; 22:720. [PMID: 34429760 PMCID: PMC8371983 DOI: 10.3892/ol.2021.12981] [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: 08/26/2020] [Accepted: 03/08/2021] [Indexed: 11/25/2022] Open
Abstract
Epithelial ovarian cancer has the highest mortality rate of all malignant ovarian cancer types. Great progress has been made in the treatment of ovarian cancer in recent years. However, drug resistance has led to a low level of 5-year survival rate of epithelial ovarian cancer, and the molecular mechanism of which remains unknown. The aim of the present study was to identify the role of redox status in the cisplatin (CDDP) resistance of ovarian cancer. CDDP-resistant SK-OV3 (SK-OV3/cddp) cells were prepared and their reactive oxygen species and glutathione levels were investigated. The effects of hydrogen peroxide on the CDDP sensitivity of the SK-OV3/cddp cells and their expression levels of the redox-associated protein growth arrest and DNA damage 45a (GADD45α) were also investigated. In addition, the impact of GADD45α overexpression on cell viability was evaluated in vitro and in vivo, and the levels of Ser-139 phosphorylated H2A histone family member X (γ-H2AX), which is associated with DNA damage, were detected. The results suggested that redox status affected the drug resistance of the ovarian cancer cells by increasing the expression of GADD45α. The overexpression of GADD45α reversed the CDDP resistance of the SK-OV3/cddp cells and increased the level of γ-H2AX. In conclusion, GADD45α alleviated the CDDP resistance of SK-OV3/cddp cells via the induction of redox-mediated DNA damage.
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Affiliation(s)
- Qi-Zhu Zhang
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Fang Wen
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China.,Department of Obstetrics and Gynecology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550004, P.R. China
| | - Han-Lin Yang
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Yan-Yan Cao
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Ren Guo Peng
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Yuan-Mei Wang
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Lei Nie
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Yuan-Kun Qin
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Jin-Jian Wu
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Xing Zhao
- National and Guizhou Joint Engineering Laboratory for Cell Engineering and Biomedicine Technique, Center for Tissue Engineering and Stem Cell Research, Guizhou Province Key Laboratory of Regenerative Medicine, Guiyang, Guizhou 550004, P.R. China
| | - Dan Zi
- Department of Obstetrics and Gynecology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550004, P.R. China.,National and Guizhou Joint Engineering Laboratory for Cell Engineering and Biomedicine Technique, Center for Tissue Engineering and Stem Cell Research, Guizhou Province Key Laboratory of Regenerative Medicine, Guiyang, Guizhou 550004, P.R. China.,Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
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Martinez-Useros J, Martin-Galan M, Florez-Cespedes M, Garcia-Foncillas J. Epigenetics of Most Aggressive Solid Tumors: Pathways, Targets and Treatments. Cancers (Basel) 2021; 13:3209. [PMID: 34198989 PMCID: PMC8267921 DOI: 10.3390/cancers13133209] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 02/06/2023] Open
Abstract
Highly aggressive tumors are characterized by a highly invasive phenotype, and they display chemoresistance. Furthermore, some of the tumors lack expression of biomarkers for target therapies. This is the case of small-cell lung cancer, triple-negative breast cancer, pancreatic ductal adenocarcinoma, glioblastoma, metastatic melanoma, and advanced ovarian cancer. Unfortunately, these patients show a low survival rate and most of the available drugs are ineffective. In this context, epigenetic modifications have emerged to provide the causes and potential treatments for such types of tumors. Methylation and hydroxymethylation of DNA, and histone modifications, are the most common targets of epigenetic therapy, to influence gene expression without altering the DNA sequence. These modifications could impact both oncogenes and tumor suppressor factors, which influence several molecular pathways such as epithelial-to-mesenchymal transition, WNT/β-catenin, PI3K-mTOR, MAPK, or mismatch repair machinery. However, epigenetic changes are inducible and reversible events that could be influenced by some environmental conditions, such as UV exposure, smoking habit, or diet. Changes in DNA methylation status and/or histone modification, such as acetylation, methylation or phosphorylation, among others, are the most important targets for epigenetic cancer therapy. Therefore, the present review aims to compile the basic information of epigenetic modifications, pathways and factors, and provide a rationale for the research and treatment of highly aggressive tumors with epigenetic drugs.
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Affiliation(s)
- Javier Martinez-Useros
- Translational Oncology Division, OncoHealth Institute, Fundacion Jimenez Diaz University Hospital, Avenida Reyes Catolicos 2, 28040 Madrid, Spain;
| | - Mario Martin-Galan
- Translational Oncology Division, OncoHealth Institute, Fundacion Jimenez Diaz University Hospital, Avenida Reyes Catolicos 2, 28040 Madrid, Spain;
| | | | - Jesus Garcia-Foncillas
- Translational Oncology Division, OncoHealth Institute, Fundacion Jimenez Diaz University Hospital, Avenida Reyes Catolicos 2, 28040 Madrid, Spain;
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9
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Song Y, Kamstra JH, Cao Y, Asselman J, Anglès d'Auriac M, Friberg N. High-throughput analyses and Bayesian network modeling highlight novel epigenetic Adverse Outcome Pathway networks of DNA methyltransferase inhibitor mediated transgenerational effects. JOURNAL OF HAZARDOUS MATERIALS 2021; 408:124490. [PMID: 33199140 DOI: 10.1016/j.jhazmat.2020.124490] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/26/2020] [Accepted: 11/03/2020] [Indexed: 06/11/2023]
Abstract
A number of epigenetic modulating chemicals are known to affect multiple generations of a population from a single ancestral exposure, thus posing transgenerational hazards. The present study aimed to establish a high-throughput (HT) analytical workflow for cost-efficient concentration-response analysis of epigenetic and phenotypic effects, and to support the development of novel Adverse Outcome Pathway (AOP) networks for DNA methyltransferase (DNMT) inhibitor-mediated transgenerational effects on aquatic organisms. The model DNMT inhibitor 5-azacytidine (5AC) and the model freshwater crustacean Daphnia magna were used to generate new experimental data and served as prototypes to construct AOPs for aquatic organisms. Targeted HT bioassays (DNMT ELISA, MS-HRM and qPCR) in combination with multigenerational ecotoxicity tests revealed concentration-dependent transgenerational (F0-F3) effects of 5AC on total DNMT activity, DNA promoter methylation, gene body methylation, gene transcription and reproduction. Top sensitive toxicity pathways related to 5AC exposure, such as apoptosis and DNA damage responses were identified in both F0 and F3 using Gaussian Bayesian network modeling. Two novel epigenetic AOP networks on DNMT inhibitor mediated one-generational and transgenerational effects were developed for aquatic organisms and assessed for the weight of evidence. The new HT analytical workflow and AOPs can facilitate future ecological hazard assessment of epigenetic modulating chemicals.
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Affiliation(s)
- You Song
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349 Oslo, Norway.
| | - Jorke H Kamstra
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, PO Box 80177, NL-3508 TD Utrecht, The Netherlands
| | - Yang Cao
- Clinical Epidemiology and Biostatistics, School of Medical Sciences, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
| | - Jana Asselman
- Blue Growth Research Lab, Ghent University, Bluebridge building, Ostend Science Park 1, 8400 Ostend, Belgium
| | - Marc Anglès d'Auriac
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349 Oslo, Norway
| | - Nikolai Friberg
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349 Oslo, Norway; University of Copenhagen, Freshwater Biological Section, Universitetsparken 4, 3rd floor, 2100 Copenhagen, Denmark; University of Leeds, water@leeds, School of Geography, Leeds LS2 9JT UK
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10
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Faria GM, Soares IDP, D'Alincourt Salazar M, Amorim MR, Pessoa BL, da Fonseca CO, Quirico-Santos T. Intranasal perillyl alcohol therapy improves survival of patients with recurrent glioblastoma harboring mutant variant for MTHFR rs1801133 polymorphism. BMC Cancer 2020; 20:294. [PMID: 32264844 PMCID: PMC7137265 DOI: 10.1186/s12885-020-06802-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/29/2020] [Indexed: 12/19/2022] Open
Abstract
Background Polymorphisms in MTHFR gene influence risk and overall survival of patients with brain tumor. Global genomic DNA (gDNA) methylation profile from tumor tissues is replicated in peripheral leukocytes. This study aimed to draw a correlation between rs1801133 MTHFR variants, gDNA methylation and overall survival of patients with recurrent glioblastoma (rGBM) under perillyl alcohol (POH) treatment. Methods gDNA from whole blood was extracted using a commercially available kit (Axygen) and quantified by spectrophotometry. Global gDNA methylation was determined by ELISA and rs1801133 polymorphism by PCR-RFLP. Statistical analysis of gDNA methylation profile and rs1801133 variants included Mann-Whitney, Kruskal-Wallis, Spearman point-biserial correlation tests (SPSS and Graphpad Prism packages; significant results for effect size higher than 0.4). Prognostic value of gDNA methylation and rs1801133 variants considered survival profiles at 25 weeks of POH treatment, having the date of protocol adhesion as starting count and death as the final event. Results Most rGBM patients showed global gDNA hypomethylation (median = 31.7%) and a significant, moderate and negative correlation between TT genotype and gDNA hypomethylation (median = 13.35%; rho = − 0.520; p = 0.003) compared to CC variant (median = 32.10%), which was not observed for CT variant (median = 33.34%; rho = − 0.289; p = 0.06). gDNA hypermethylated phenotype (median = 131.90%) exhibited significant, moderate and negative correlations between TT genotype (median = 112.02%) and gDNA hypermethylation levels when compared to CC (median = 132.45%; rho = − 0,450; p = 0.04) or CT (median = 137.80%; rho = − 0.518; p = 0.023) variants. TT variant of rs1801133 significantly decreased gDNA methylation levels for both patient groups, when compared to CC (d values: hypomethylated = 1.189; hypermethylated = 0.979) or CT (d values: hypomethylated = 0.597; hypermethylated = 1.167) variants. Positive prognostic for rGBM patients may be assigned to gDNA hypermethylation for survivors above 25 weeks of treatment (median = 88 weeks); and TT variant of rs1801133 regardless POH treatment length. Conclusion rGBM patients under POH-based therapy harboring hypermethylated phenotype and TT variant for rs1801133 had longer survival. Intranasal POH therapy mitigates detrimental effects of gDNA hypomethylation and improved survival of patients with rGBM harboring TT mutant variant for MTHFR rs1801133 polymorphism. Trial registration CONEP -9681- 25,000.009267 / 2004. Registered 12th July, 2004.
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Affiliation(s)
- Giselle M Faria
- Instituto de Biologia, Universidade Federal Fluminense, Niteroi, Rio de Janeiro, ZC, 24020-141, Brazil.,Programa de Pós-graduação em Neurologia, Faculdade de Medicina, Universidade Federal Fluminense, Niteroi, Rio de Janeiro, 24020-141, Brazil
| | - Igor D P Soares
- Instituto de Biologia, Universidade Federal Fluminense, Niteroi, Rio de Janeiro, ZC, 24020-141, Brazil
| | | | - Marcia R Amorim
- Instituto de Biologia, Universidade Federal Fluminense, Niteroi, Rio de Janeiro, ZC, 24020-141, Brazil
| | - Bruno L Pessoa
- Programa de Pós-graduação em Neurologia, Faculdade de Medicina, Universidade Federal Fluminense, Niteroi, Rio de Janeiro, 24020-141, Brazil.,Departamento de Medicina Especializada, Unidade de Pesquisa Clínica (UPC-HUAP), Universidade Federal Fluminense, Niteroi, RJ, Brazil
| | - Clovis O da Fonseca
- Departamento de Medicina Especializada, Unidade de Pesquisa Clínica (UPC-HUAP), Universidade Federal Fluminense, Niteroi, RJ, Brazil
| | - Thereza Quirico-Santos
- Instituto de Biologia, Universidade Federal Fluminense, Niteroi, Rio de Janeiro, ZC, 24020-141, Brazil. .,Programa de Pós-graduação em Neurologia, Faculdade de Medicina, Universidade Federal Fluminense, Niteroi, Rio de Janeiro, 24020-141, Brazil. .,Programa de Pós-graduação em Ciencia e Biotecnologia, Universidade Federal Fluminense, Niteroi, Rio de Janeiro, 24020-141, Brazil.
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11
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Fila M, Chojnacki C, Chojnacki J, Blasiak J. Is an "Epigenetic Diet" for Migraines Justified? The Case of Folate and DNA Methylation. Nutrients 2019; 11:E2763. [PMID: 31739474 PMCID: PMC6893742 DOI: 10.3390/nu11112763] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/05/2019] [Accepted: 11/12/2019] [Indexed: 12/15/2022] Open
Abstract
Migraines are a common disease with limited treatment options and some dietary factors are recognized to trigger headaches. Although migraine pathogenesis is not completely known, aberrant DNA methylation has been reported to be associated with its occurrence. Folate, an essential micronutrient involved in one-carbon metabolism and DNA methylation, was shown to have beneficial effects on migraines. Moreover, the variability of the methylenetetrahydrofolate reductase gene, important in both folate metabolism and migraine pathogenesis, modulates the beneficial effects of folate for migraines. Therefore, migraine could be targeted by a folate-rich, DNA methylation-directed diet, but there are no data showing that beneficial effects of folate consumption result from its epigenetic action. Furthermore, contrary to epigenetic drugs, epigenetic diets contain many compounds, some yet unidentified, with poorly known or completely unknown potential to interfere with the epigenetic action of the main dietary components. The application of epigenetic diets for migraines and other diseases requires its personalization to the epigenetic profile of a patient, which is largely unknown. Results obtained so far do not warrant the recommendation of any epigenetic diet as effective in migraine prevention and therapy. Further studies including a folate-rich diet fortified with valproic acid, another modifier of epigenetic profile effective in migraine prophylaxis, may help to clarify this issue.
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Affiliation(s)
- Michal Fila
- Department of Neurology, Polish Mother Memorial Hospital, Research Institute, 93-338 Lodz, Poland;
| | - Cezary Chojnacki
- Department of Clinical Nutrition and Gastroenterological Diagnostics, Medical University of Lodz, 90-647 Lodz, Poland; (C.C.); (J.C.)
| | - Jan Chojnacki
- Department of Clinical Nutrition and Gastroenterological Diagnostics, Medical University of Lodz, 90-647 Lodz, Poland; (C.C.); (J.C.)
| | - Janusz Blasiak
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland
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12
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Min DJ, Vural S, Krushkal J. Association of transcriptional levels of folate-mediated one-carbon metabolism-related genes in cancer cell lines with drug treatment response. Cancer Genet 2019; 237:19-38. [DOI: 10.1016/j.cancergen.2019.05.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 05/09/2019] [Accepted: 05/29/2019] [Indexed: 02/08/2023]
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13
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Phillips L, Gill AJ, Baxter RC. Novel Prognostic Markers in Triple-Negative Breast Cancer Discovered by MALDI-Mass Spectrometry Imaging. Front Oncol 2019; 9:379. [PMID: 31139569 PMCID: PMC6527753 DOI: 10.3389/fonc.2019.00379] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 04/23/2019] [Indexed: 11/29/2022] Open
Abstract
There are no widely-accepted prognostic markers currently available to predict outcomes in patients with triple-negative breast cancer (TNBC), and no targeted therapies with confirmed benefit. We have used MALDI mass spectrometry imaging (MSI) of tryptic peptides to compare regions of cancer and benign tissue in 10 formalin-fixed, paraffin-embedded sections of TNBC tumors. Proteins were identified by reference to a peptide library constructed by LC-MALDI-MS/MS analyses of the same tissues. The prognostic significance of proteins that distinguished between cancer and benign regions was estimated by Kaplan-Meier analysis of their gene expression from public databases. Among peptides that distinguished between cancer and benign tissue in at least 3 tissues with a ROC area under the curve >0.7, 14 represented proteins identified from the reference library, including proteins not previously associated with breast cancer. Initial network analysis using the STRING database showed no obvious functional relationships except among collagen subunits COL1A1, COL1A2, and COL63A, but manual curation, including the addition of EGFR to the analysis, revealed a unique network connecting 10 of the 14 proteins. Kaplan-Meier survival analysis to examine the relationship between tumor expression of genes encoding the 14 proteins, and recurrence-free survival (RFS) in patients with basal-like TNBC showed that, compared to low expression, high expression of nine of the genes was associated with significantly worse RFS, most with hazard ratios >2. In contrast, in estrogen receptor-positive tumors, high expression of these genes showed only low, or no, association with worse RFS. These proteins are proposed as putative markers of RFS in TNBC, and some may also be considered as possible targets for future therapies.
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Affiliation(s)
- Leo Phillips
- Hormones and Cancer Group, University of Sydney, Kolling Institute, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Anthony J Gill
- Cancer Diagnosis and Pathology Group, University of Sydney, Kolling Institute, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Robert C Baxter
- Hormones and Cancer Group, University of Sydney, Kolling Institute, Royal North Shore Hospital, St Leonards, NSW, Australia
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14
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Hall PE, Lewis R, Syed N, Shaffer R, Evanson J, Ellis S, Williams M, Feng X, Johnston A, Thomson JA, Harris FP, Jena R, Matys T, Jefferies S, Smith K, Wu BW, Bomalaski JS, Crook T, O'Neill K, Paraskevopoulos D, Khadeir RS, Sheaff M, Pacey S, Plowman PN, Szlosarek PW. A Phase I Study of Pegylated Arginine Deiminase (Pegargiminase), Cisplatin, and Pemetrexed in Argininosuccinate Synthetase 1-Deficient Recurrent High-grade Glioma. Clin Cancer Res 2019; 25:2708-2716. [PMID: 30796035 DOI: 10.1158/1078-0432.ccr-18-3729] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/30/2018] [Accepted: 02/12/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Patients with recurrent high-grade gliomas (HGG) are usually managed with alkylating chemotherapy ± bevacizumab. However, prognosis remains very poor. Preclinically, we showed that HGGs are a target for arginine depletion with pegargiminase (ADI-PEG20) due to epimutations of argininosuccinate synthetase (ASS1) and/or argininosuccinate lyase (ASL). Moreover, ADI-PEG20 disrupts pyrimidine pools in ASS1-deficient HGGs, thereby impacting sensitivity to the antifolate, pemetrexed. PATIENTS AND METHODS We expanded a phase I trial of ADI-PEG20 with pemetrexed and cisplatin (ADIPEMCIS) to patients with ASS1-deficient recurrent HGGs (NCT02029690). Patients were enrolled (01/16-06/17) to receive weekly ADI-PEG20 36 mg/m2 intramuscularly plus pemetrexed 500 mg/m2 and cisplatin 75 mg/m2 intravenously once every 3 weeks for up to 6 cycles. Patients with disease control were allowed ADI-PEG20 maintenance. The primary endpoints were safety, tolerability, and preliminary estimates of efficacy. RESULTS Ten ASS1-deficient heavily pretreated patients were treated with ADIPEMCIS therapy. Treatment was well tolerated with the majority of adverse events being Common Terminology Criteria for Adverse Events v4.03 grade 1-2. The best overall response was stable disease in 8 patients (80%). Plasma arginine was suppressed significantly below baseline with a reciprocal increase in citrulline during the sampling period. The anti-ADI-PEG20 antibody titer rose during the first 4 weeks of treatment before reaching a plateau. Median progression-free survival (PFS) was 5.2 months (95% confidence interval (CI), 2.5-20.8) and overall survival was 6.3 months (95% CI, 1.8-9.7). CONCLUSIONS In this recurrent HGG study, ADIPEMCIS was well tolerated and compares favorably to historical controls. Additional trials of ADI-PEG20 in HGG are planned.
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Affiliation(s)
- Peter E Hall
- Department of Oncology, Barts Health NHS Trust, London, United Kingdom
| | - Rachel Lewis
- Department of Oncology, Barts Health NHS Trust, London, United Kingdom
| | - Nelofer Syed
- Department of Medicine, Imperial College, London, United Kingdom
| | - Richard Shaffer
- St. Luke's Cancer Centre, Royal Surrey County Hospital, Guildford, United Kingdom
| | - Jane Evanson
- Department of Radiology, Barts Health NHS Trust, London, United Kingdom
| | - Stephen Ellis
- Department of Radiology, Barts Health NHS Trust, London, United Kingdom
| | - Matthew Williams
- Department of Oncology, Imperial College Healthcare NHS Trust, London, United Kingdom
| | | | | | | | - Fiona P Harris
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Raj Jena
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Tomasz Matys
- Department of Radiology, University of Cambridge, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Sarah Jefferies
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Kate Smith
- Department of Oncology, Barts Health NHS Trust, London, United Kingdom
| | - Bor-Wen Wu
- Polaris Pharmaceuticals Inc., San Diego, California
| | | | - Timothy Crook
- St. Luke's Cancer Centre, Royal Surrey County Hospital, Guildford, United Kingdom
| | - Kevin O'Neill
- Department of Neurosurgery, Imperial College Healthcare NHS Trust, London, United Kingdom
| | | | - Ramsay S Khadeir
- Centre for Molecular Oncology, Queen Mary University of London, London, United Kingdom
| | - Michael Sheaff
- Department of Pathology, Barts Health NHS Trust, London, United Kingdom
| | - Simon Pacey
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Piers N Plowman
- Department of Oncology, Barts Health NHS Trust, London, United Kingdom
| | - Peter W Szlosarek
- Department of Oncology, Barts Health NHS Trust, London, United Kingdom.
- Centre for Molecular Oncology, Queen Mary University of London, London, United Kingdom
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15
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Monks A, Zhao Y, Hose C, Hamed H, Krushkal J, Fang J, Sonkin D, Palmisano A, Polley EC, Fogli LK, Konaté MM, Miller SB, Simpson MA, Voth AR, Li MC, Harris E, Wu X, Connelly JW, Rapisarda A, Teicher BA, Simon R, Doroshow JH. The NCI Transcriptional Pharmacodynamics Workbench: A Tool to Examine Dynamic Expression Profiling of Therapeutic Response in the NCI-60 Cell Line Panel. Cancer Res 2018; 78:6807-6817. [PMID: 30355619 PMCID: PMC6295263 DOI: 10.1158/0008-5472.can-18-0989] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/24/2018] [Accepted: 10/16/2018] [Indexed: 12/31/2022]
Abstract
: The intracellular effects and overall efficacies of anticancer therapies can vary significantly by tumor type. To identify patterns of drug-induced gene modulation that occur in different cancer cell types, we measured gene-expression changes across the NCI-60 cell line panel after exposure to 15 anticancer agents. The results were integrated into a combined database and set of interactive analysis tools, designated the NCI Transcriptional Pharmacodynamics Workbench (NCI TPW), that allows exploration of gene-expression modulation by molecular pathway, drug target, and association with drug sensitivity. We identified common transcriptional responses across agents and cell types and uncovered gene-expression changes associated with drug sensitivity. We also demonstrated the value of this tool for investigating clinically relevant molecular hypotheses and identifying candidate biomarkers of drug activity. The NCI TPW, publicly available at https://tpwb.nci.nih.gov, provides a comprehensive resource to facilitate understanding of tumor cell characteristics that define sensitivity to commonly used anticancer drugs. SIGNIFICANCE: The NCI Transcriptional Pharmacodynamics Workbench represents the most extensive compilation to date of directly measured longitudinal transcriptional responses to anticancer agents across a thoroughly characterized ensemble of cancer cell lines.
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Affiliation(s)
- Anne Monks
- Molecular Pharmacology Group, Frederick National Laboratory for Cancer Research sponsored by the NCI, Frederick, Maryland
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, Maryland
| | - Curtis Hose
- Molecular Pharmacology Group, Frederick National Laboratory for Cancer Research sponsored by the NCI, Frederick, Maryland
| | - Hossein Hamed
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, Maryland
| | - Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, Maryland
| | - Jianwen Fang
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, Maryland
| | - Dmitriy Sonkin
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, Maryland
| | - Alida Palmisano
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, Maryland
| | - Eric C Polley
- Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, Maryland
| | - Laura K Fogli
- Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, Maryland
| | - Mariam M Konaté
- Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, Maryland
| | - Sarah B Miller
- Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, Maryland
| | - Melanie A Simpson
- Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research sponsored by the NCI, Frederick, Maryland
| | - Andrea Regier Voth
- Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research sponsored by the NCI, Frederick, Maryland
| | - Ming-Chung Li
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, Maryland
| | - Erik Harris
- Molecular Pharmacology Group, Frederick National Laboratory for Cancer Research sponsored by the NCI, Frederick, Maryland
| | - Xiaolin Wu
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the NCI, Frederick, Maryland
| | - John W Connelly
- Molecular Pharmacology Group, Frederick National Laboratory for Cancer Research sponsored by the NCI, Frederick, Maryland
| | - Annamaria Rapisarda
- Molecular Pharmacology Group, Frederick National Laboratory for Cancer Research sponsored by the NCI, Frederick, Maryland
| | - Beverly A Teicher
- Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, Maryland
| | - Richard Simon
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, Maryland
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, Maryland.
- Center for Cancer Research, NCI, NIH, Bethesda, Maryland
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16
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Ferreira LL, Cunha-Oliveira T, Veloso CD, Costa CF, Wallace KB, Oliveira PJ. Single nanomolar doxorubicin exposure triggers compensatory mitochondrial responses in H9c2 cardiomyoblasts. Food Chem Toxicol 2018; 124:450-461. [PMID: 30557669 DOI: 10.1016/j.fct.2018.12.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 12/08/2018] [Accepted: 12/13/2018] [Indexed: 12/31/2022]
Abstract
Dose-dependent and cumulative cardiotoxicity associated with doxorubicin (DOX) is the main limitation of anticancer therapy. Pediatric cancer survivors are particularly vulnerable, and no effective prevention measures are available. The aim of the present study was to investigate the persistent effects of nanomolar DOX concentrations and determine whether a pretreatment would induce mitochondrial adaptations in H9c2 cardiomyoblasts. H9c2 cells were incubated with DOX (10 and 25 nM) for 24 h, followed by 9 days of recovery in drug-free medium. We found that the sub-therapeutic DOX treatment induced persistent hypertrophy and dose-dependent cell cycle arrest in G2/M. Glycolytic activity, indirectly based on extracellular acidification rate, and basal respiration were significantly decreased in DOX-treated cells compared to controls, although both groups showed similar maximal respiration. Additionally, nanomolar DOX pretreatment resulted in upregulation of mitochondrial DNA transcripts accompanied by a decrease in DNA methyltransferase 1 (DNMT1) and global methylation levels. Finally, the pretreatment with DOX ameliorated H9c2 cells resistance against a subsequent exposure to DOX. These results suggest that nanomolar DOX pretreatment induced a beneficial and possibly epigenetic-based mitochondrial adaptation, raising the possibility that an early sub-therapeutic DOX treatment can be used as a preconditioning and protective approach during anticancer therapies.
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Affiliation(s)
- Luciana L Ferreira
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech Building, Biocant Park, 3060-197, Cantanhede, Portugal.
| | - Teresa Cunha-Oliveira
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech Building, Biocant Park, 3060-197, Cantanhede, Portugal.
| | - Caroline D Veloso
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech Building, Biocant Park, 3060-197, Cantanhede, Portugal.
| | - Cláudio F Costa
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech Building, Biocant Park, 3060-197, Cantanhede, Portugal.
| | - Kendall B Wallace
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, 55812, USA.
| | - Paulo J Oliveira
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech Building, Biocant Park, 3060-197, Cantanhede, Portugal.
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17
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MacGregor TP, Carter R, Gillies RS, Findlay JM, Kartsonaki C, Castro-Giner F, Sahgal N, Wang LM, Chetty R, Maynard ND, Cazier JB, Buffa F, McHugh PJ, Tomlinson I, Middleton MR, Sharma RA. Translational study identifies XPF and MUS81 as predictive biomarkers for oxaliplatin-based peri-operative chemotherapy in patients with esophageal adenocarcinoma. Sci Rep 2018; 8:7265. [PMID: 29739952 PMCID: PMC5940885 DOI: 10.1038/s41598-018-24232-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 02/09/2018] [Indexed: 02/06/2023] Open
Abstract
Oxaliplatin-based chemotherapy is used to treat patients with esophageal adenocarcinoma (EAC), but no biomarkers are currently available for patient selection. We performed a prospective, clinical trial to identify potential biomarkers associated with clinical outcomes. Tumor tissue was obtained from 38 patients with resectable EAC before and after 2 cycles of oxaliplatin-fluorouracil chemotherapy. Pre-treatment mRNA expression of 280 DNA repair (DNAR) genes was tested for association with histopathological regression at surgery, disease-free survival (DFS) and overall survival (OS). High expression of 13 DNA damage repair genes was associated with DFS less than one year (P < 0.05); expression of 11 DNAR genes were associated with worse OS (P < 0.05). From clinical associations with outcomes, two genes, ERCC1 and EME1, were identified as candidate biomarkers. In cell lines in vitro, we showed the mechanism of action related to repair of oxaliplatin-induced DNA damage by depletion and knockout of protein binding partners of the candidate biomarkers, XPF and MUS81 respectively. In clinical samples from the clinical trial, pre-treatment XPF protein levels were associated with pathological response, and MUS81 protein was associated with 1-year DFS. XPF and MUS81 merit further validation in prospective clinical trials as biomarkers that may predict clinical response of EAC to oxaliplatin-based chemotherapy.
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Affiliation(s)
- T P MacGregor
- NIHR Oxford Biomedical Research Centre, Department of Oncology, University of Oxford, Oxford, UK
| | - R Carter
- NIHR Oxford Biomedical Research Centre, Department of Oncology, University of Oxford, Oxford, UK
| | - R S Gillies
- NIHR Oxford Biomedical Research Centre, Department of Oncology, University of Oxford, Oxford, UK
- Department of Upper GI Surgery, Churchill Hospital, Oxford, UK
| | - J M Findlay
- Department of Upper GI Surgery, Churchill Hospital, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - C Kartsonaki
- NIHR Oxford Biomedical Research Centre, Department of Oncology, University of Oxford, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit (MRC PHRU) at the University of Oxford, Oxford, UK
| | - F Castro-Giner
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - N Sahgal
- Ludwig Institute for Cancer Research, University of Oxford, Nuffield Department of Medicine, Oxford, UK
| | - L M Wang
- NIHR Oxford Biomedical Research Centre/Department of Cellular Pathology/Radcliffe Department of Medicine, Oxford University Hospitals and University of Oxford, Oxford, UK
- Department of Laboratory Medicine, Changi General Hospital, Singapore, Singapore
| | - R Chetty
- Laboratory Medicine Programme, University Health Network, Toronto, Canada
| | - N D Maynard
- Department of Upper GI Surgery, Churchill Hospital, Oxford, UK
| | - J B Cazier
- NIHR Oxford Biomedical Research Centre, Department of Oncology, University of Oxford, Oxford, UK
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - F Buffa
- NIHR Oxford Biomedical Research Centre, Department of Oncology, University of Oxford, Oxford, UK
| | - P J McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - I Tomlinson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M R Middleton
- NIHR Oxford Biomedical Research Centre, Department of Oncology, University of Oxford, Oxford, UK
| | - R A Sharma
- NIHR Oxford Biomedical Research Centre, Department of Oncology, University of Oxford, Oxford, UK.
- NIHR University College London Hospitals Biomedical Research Centre, UCL Cancer Institute, University College London, London, UK.
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18
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Krushkal J, Zhao Y, Hose C, Monks A, Doroshow JH, Simon R. Longitudinal Transcriptional Response of Glycosylation-Related Genes, Regulators, and Targets in Cancer Cell Lines Treated With 11 Antitumor Agents. Cancer Inform 2017; 16:1176935117747259. [PMID: 29276373 PMCID: PMC5734428 DOI: 10.1177/1176935117747259] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/18/2017] [Indexed: 01/25/2023] Open
Abstract
Cellular glycosylation processes are vital to cell functioning. In malignant cells, they are profoundly altered. We used time-course gene expression data from the NCI-60 cancer cell lines treated with 11 antitumor agents to analyze expression changes of genes involved in glycosylation pathways, genes encoding glycosylation targets or regulators, and members of cancer pathways affected by glycosylation. We also identified glycosylation genes for which pretreatment expression levels or changes after treatment were correlated with drug sensitivity. Their products are involved in N-glycosylation and O-glycosylation, fucosylation, biosynthesis of poly-N-acetyllactosamine, removal of misfolded proteins, binding to hyaluronic acid and other glycans, and cell adhesion. Tumor cell sensitivity to multiple agents was correlated with transcriptional response of C1GALT1C1, FUCA1, SDC1, MUC1; members of the MGAT, GALNT, B4GALT, B3GNT, MAN, and EDEM families; and other genes. These genes may be considered as potential candidates for drug targeting in combination therapy to enhance treatment response.
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Affiliation(s)
- Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Curtis Hose
- Molecular Pharmacology Group, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Anne Monks
- Molecular Pharmacology Group, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis and Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Richard Simon
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
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