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Symonds L, Yu M, Zhang Y, Ou FS, Zemla TJ, Carter K, Bertagnolli M, Innocenti F, Bosch LJW, Meijer GA, Carvalho B, Grady WM, Cohen SA. Evaluation of methylated DCR1 as a biomarker for response to adjuvant irinotecan-based therapy in stage III colon cancer: cancer and leukaemia Group B 89803 (Alliance). Epigenetics 2022; 17:1715-1725. [PMID: 35412430 PMCID: PMC9621073 DOI: 10.1080/15592294.2022.2058225] [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: 07/21/2021] [Revised: 03/01/2022] [Accepted: 03/22/2022] [Indexed: 11/03/2022] Open
Abstract
Aberrantly methylated genes contribute to the landscape of epigenetic alterations in colorectal adenocarcinoma. The global CpG Island methylator phenotype (CIMP) and individually methylated genes are potential prognostic/predictive biomarkers. Research suggests an association between methylated DCR1 (mDCR1) and lack of benefit with irinotecan (IFL) treatment. We assessed the association between DCR1 methylation status and survival in patients receiving adjuvant fluorouracil/ leucovorin (5-FU/LV) or IFL. We analysed data from patients with stage III colon adenocarcinoma randomly assigned to adjuvant 5-FU/LV or IFL in CALGB 89803 (Alliance). The primary endpoint was overall survival (OS), and the secondary endpoint was disease-free survival (DFS). Using tumour sample DNA, we evaluated the association between survival, DCR1 methylation status, and molecular subgroups (BRAF, KRAS, mismatch repair status, CIMP status) using Kaplan-Meier estimator and Cox proportional hazard model. mDCR1 was observed in 221/400 (55%) colon cancers. Histopathologic features were similar between mDCR1 and unmethylated DCR1 (unDCR1) colon cancers. There was no difference in OS (p = 0.83) or DFS (p = 0.85) based on DCR1 methylation status. There was no association between methylation status and response to IFL . In patients with unDCR1 and KRAS-wildtype tumours, those who received IFL had a nearly two-fold worse DFS compared to patients who received 5-FU/LV (HR = 1.85, 95% CI (0.97-3.53, p = 0.06). This relationship was not notable among other subgroups. In stage III colon cancer patients, mDCR1 status did not associate with response to irinotecan. Larger studies may suggest an association between the iridocene response and molecular subgroups.
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Affiliation(s)
- Lynn Symonds
- Division of Oncology, University of Washington, Seattle, WA, USA
| | - Ming Yu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - YuHong Zhang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Guangxi, China
| | - Fang-Shu Ou
- Alliance Statistics and Data Center, Mayo Clinic, Rochester, MN, USA
| | - Tyler J. Zemla
- Alliance Statistics and Data Center, Mayo Clinic, Rochester, MN, USA
| | - Kelly Carter
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Monica Bertagnolli
- Office of the Alliance Group Chair, Boston, MA, USA
- Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Federico Innocenti
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Linda JW Bosch
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Beatriz Carvalho
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - William M. Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Gastroenterology, University of Washington, Seattle, Washington, USA
| | - Stacey A. Cohen
- Division of Oncology, University of Washington, Seattle, WA, USA
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Epigenome-Wide DNA Methylation Profiling in Colorectal Cancer and Normal Adjacent Colon Using Infinium Human Methylation 450K. Diagnostics (Basel) 2022; 12:diagnostics12010198. [PMID: 35054365 PMCID: PMC8775085 DOI: 10.3390/diagnostics12010198] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/31/2021] [Accepted: 01/03/2022] [Indexed: 01/20/2023] Open
Abstract
The aims were to profile the DNA methylation in colorectal cancer (CRC) and to explore cancer-specific methylation biomarkers. Fifty-four pairs of CRCs and the adjacent normal tissues were subjected to Infinium Human Methylation 450K assay and analysed using ChAMP R package. A total of 26,093 differentially methylated probes were identified, which represent 6156 genes; 650 probes were hypermethylated, and 25,443 were hypomethylated. Hypermethylated sites were common in CpG islands, while hypomethylated sites were in open sea. Most of the hypermethylated genes were associated with pathways in cancer, while the hypomethylated genes were involved in the PI3K-AKT signalling pathway. Among the identified differentially methylated probes, we found evidence of four potential probes in CRCs versus adjacent normal; HOXA2 cg06786372, OPLAH cg17301223, cg15638338, and TRIM31 cg02583465 that could serve as a new biomarker in CRC since these probes were aberrantly methylated in CRC as well as involved in the progression of CRC. Furthermore, we revealed the potential of promoter methylation ADHFE1 cg18065361 in differentiating the CRC from normal colonic tissue from the integrated analysis. In conclusion, aberrant DNA methylation is significantly involved in CRC pathogenesis and is associated with gene silencing. This study reports several potential important methylated genes in CRC and, therefore, merit further validation as novel candidate biomarker genes in CRC.
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Mahjoubin-Tehran M, Rezaei S, Atkin SL, Montecucco F, Sahebkar A. Decoys as potential therapeutic tools for diabetes. Drug Discov Today 2021; 26:1669-1679. [PMID: 33862194 DOI: 10.1016/j.drudis.2021.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/15/2021] [Accepted: 04/06/2021] [Indexed: 10/21/2022]
Abstract
Current therapeutic approaches for diabetes are focused on improving glycemic control to prevent diabetes-related complications, but such approached are not completely successful. Decoy technologies such as decoy oligodeoxynucleotides (ODNs) and decoy peptides have emerged as therapeutic tools in diabetes. Decoy ODNs carry a DNA recognition motif for the binding of transcription factors in order to trap them and block their effects, whereas decoy peptides mimic the binding structure of the receptor protein, bind to the docking site of the target ligand, and prevent the interaction of the ligand and receptor. This review summarizes the technologies that have been developed to date and the studies that have investigated the therapeutic effects of decoy ODNs and peptides in diabetes.
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Affiliation(s)
- Maryam Mahjoubin-Tehran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Samaneh Rezaei
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Fabrizio Montecucco
- IRCCS Ospedale Policlinico San Martino Genoa - Italian Cardiovascular Network, 10 Largo Benzi, 16132 Genoa, Italy; First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, 9 viale Benedetto XV, 16132 Genoa, Italy
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Polish Mother's Memorial Hospital Research Institute (PMMHRI), Lodz, Poland; School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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Singh D, Tewari M, Singh S, Narayan G. Revisiting the role of TRAIL/TRAIL-R in cancer biology and therapy. Future Oncol 2021; 17:581-596. [PMID: 33401962 DOI: 10.2217/fon-2020-0727] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
TNF-related apoptosis-inducing ligand (TRAIL), a member of the TNF superfamily, can induce apoptosis in cancer cells, sparing normal cells when bound to its associated death receptors (DR4/DR5). This unique mechanism makes TRAIL a potential anticancer therapeutic agent. However, clinical trials of recombinant TRAIL protein and TRAIL receptor agonist monoclonal antibodies have shown disappointing results due to its short half-life, poor pharmacokinetics and the resistance of the cancer cells. This review summarizes TRAIL-induced apoptotic and survival pathways as well as mechanisms leading to apoptotic resistance. Recent development of methods to overcome cancer cell resistance to TRAIL-induced apoptosis, such as protein modification, combination therapy and TRAIL-based gene therapy, appear promising. We also discuss the challenges and opportunities in the development of TRAIL-based therapies for the treatment of human cancers.
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Affiliation(s)
- Deepika Singh
- Department of Molecular & Human Genetics, Cancer Genetics Laboratory, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Mallika Tewari
- Department of Surgical Oncology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Sunita Singh
- Department of Zoology, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi, 221005, India
| | - Gopeshwar Narayan
- Department of Molecular & Human Genetics, Cancer Genetics Laboratory, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
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Irvine AF, Waise S, Green EW, Stuart B. A non-linear optimisation method to extract summary statistics from Kaplan-Meier survival plots using the published P value. BMC Med Res Methodol 2020; 20:269. [PMID: 33126853 PMCID: PMC7596943 DOI: 10.1186/s12874-020-01092-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 07/30/2020] [Indexed: 12/14/2022] Open
Abstract
Background Meta-analyses of studies evaluating survival (time-to-event) outcomes are a powerful technique to assess the strength of evidence for a given disease or treatment. However, these studies rely on the adequate reporting of summary statistics in the source articles to facilitate further analysis. Unfortunately, many studies, especially within the field of prognostic research do not report such statistics, making secondary analyses challenging. Consequently, methods have been developed to infer missing statistics from the commonly published Kaplan-Meier (KM) plots but are liable to error especially when the published number at risk is not included. Methods We therefore developed a method using non-linear optimisation (nlopt) that only requires the KM plot and the commonly published P value to better estimate the underlying censoring pattern. We use this information to then calculate the natural logarithm of the hazard ratio (ln (HR)) and its variance (var) ln (HR), statistics important for meta-analyses. Results We compared this method to the Parmar method which also does not require the number at risk to be published. In a validation set consisting of 13 KM studies, a statistically significant improvement in calculating ln (HR) when using an exact P value was obtained (mean absolute error 0.014 vs 0.077, P = 0.003). Thus, when the true HR has a value of 1.5, inference of the HR using the proposed method would set limits between 1.49/1.52, an improvement of the 1.39/1.62 limits obtained using the Parmar method. We also used Monte Carlo simulations to establish recommendations for the number and positioning of points required for the method. Conclusion The proposed non-linear optimisation method is an improvement on the existing method when only a KM plot and P value are included and as such will enhance the accuracy of meta-analyses performed for studies analysing time-to-event outcomes. The nlopt source code is available, as is a simple-to-use web implementation of the method.
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Affiliation(s)
- Andrew F Irvine
- Faculty of Medicine, University of Southampton, Southampton, UK. .,Present Address: Department of Pathology and Data Analytics, University of Leeds, Leeds, UK.
| | - Sara Waise
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Edward W Green
- The German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Beth Stuart
- Faculty of Medicine, University of Southampton, Southampton, UK
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Romero-Garcia S, Prado-Garcia H, Carlos-Reyes A. Role of DNA Methylation in the Resistance to Therapy in Solid Tumors. Front Oncol 2020; 10:1152. [PMID: 32850327 PMCID: PMC7426728 DOI: 10.3389/fonc.2020.01152] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022] Open
Abstract
Despite the recent advances in chemotherapeutic treatments against cancer, some types of highly aggressive and invasive cancer develop drug resistance against conventional therapies, which continues to be a major problem in the fight against cancer. In recent years, studies of alterations of DNA methylome have given us a better understanding of the role of DNA methylation in the development of tumors. DNA methylation (DNAm) is an epigenetic change that promotes the covalent transfer of methyl groups to DNA. This process suppresses gene expression through the modulation of the transcription machinery access to the chromatin or through the recruitment of methyl binding proteins. DNAm is regulated mainly by DNA methyltransferases. Aberrant DNAm contributes to tumor progression, metastasis, and resistance to current anti-tumoral therapies. Aberrant DNAm may occur through hypermethylation in the promoter regions of tumor suppressor genes, which leads to their silencing, while hypomethylation in the promoter regions of oncogenes can activate them. In this review, we discuss the impact of dysregulated methylation in certain genes, which impact signaling pathways associated with apoptosis avoidance, metastasis, and resistance to therapy. The analysis of methylome has revealed patterns of global methylation, which regulate important signaling pathways involved in therapy resistance in different cancer types, such as breast, colon, and lung cancer, among other solid tumors. This analysis has provided gene-expression signatures of methylated region-specific DNA that can be used to predict the treatment outcome in response to anti-cancer therapy. Additionally, changes in cancer methylome have been associated with the acquisition of drug resistance. We also review treatments with demethylating agents that, in combination with standard therapies, seem to be encouraging, as tumors that are in early stages can be successfully treated. On the other hand, tumors that are in advanced stages can be treated with these combination schemes, which could sensitize tumor cells that are resistant to the therapy. We propose that rational strategies, which combine specific demethylating agents with conventional treatment, may improve overall survival in cancer patients.
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Affiliation(s)
- Susana Romero-Garcia
- Department of Chronic-Degenerative Diseases, National Institute of Respiratory Diseases "Ismael Cosío Villegas", Mexico City, Mexico
| | - Heriberto Prado-Garcia
- Department of Chronic-Degenerative Diseases, National Institute of Respiratory Diseases "Ismael Cosío Villegas", Mexico City, Mexico
| | - Angeles Carlos-Reyes
- Department of Chronic-Degenerative Diseases, National Institute of Respiratory Diseases "Ismael Cosío Villegas", Mexico City, Mexico
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Liu L, Shao Z, Lv J, Xu F, Ren S, Jin Q, Yang J, Ma W, Xie H, Zhang D, Chen X. Identification of Early Warning Signals at the Critical Transition Point of Colorectal Cancer Based on Dynamic Network Analysis. Front Bioeng Biotechnol 2020; 8:530. [PMID: 32548109 PMCID: PMC7272579 DOI: 10.3389/fbioe.2020.00530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 05/04/2020] [Indexed: 12/22/2022] Open
Abstract
Colorectal cancer (CRC) is one of the leading causes of cancer-related death worldwide. Due to the lack of early diagnosis methods and warning signals of CRC and its strong heterogeneity, the determination of accurate treatments for CRC and the identification of specific early warning signals are still urgent problems for researchers. In this study, the expression profiles of cancer tissues and the expression profiles of tumor-adjacent tissues in 28 CRC patients were combined into a human protein–protein interaction (PPI) network to construct a specific network for each patient. A network propagation method was used to obtain a mutant giant cluster (GC) containing more than 90% of the mutation information of one patient. Next, mutation selection rules were applied to the GC to mine the mutation sequence of driver genes in each CRC patient. The mutation sequences from patients with the same type CRC were integrated to obtain the mutation sequences of driver genes of different types of CRC, which provide a reference for the diagnosis of clinical CRC disease progression. Finally, dynamic network analysis was used to mine dynamic network biomarkers (DNBs) in CRC patients. These DNBs were verified by clinical staging data to identify the critical transition point between the pre-disease state and the disease state in tumor progression. Twelve known drug targets were found in the DNBs, and 6 of them have been used as targets for anticancer drugs for clinical treatment. This study provides important information for the prognosis, diagnosis and treatment of CRC, especially for pre-emptive treatments. It is of great significance for reducing the incidence and mortality of CRC.
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Affiliation(s)
- Lei Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhuo Shao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jiaxuan Lv
- School of Stomatology, Harbin Medical University, Harbin, China
| | - Fei Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Sibo Ren
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Qing Jin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jingbo Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Weifang Ma
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hongbo Xie
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Denan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiujie Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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Abstract
Twenty-five years ago, the cytotoxic drug irinotecan (IRT) was first approved in Japan for the treatment of cancer. For more than two decades, the IRT prodrug has largely contributed to the treatment of solid tumors worldwide. Nowadays, this camptothecin derivative targeting topoisomerase 1 remains largely used in combination regimen, like FOLFIRI and FOLFIRINOX, to treat metastatic or advanced solid tumors, such as colon, gastric and pancreatic cancers and others. This review highlights recent discoveries in the field of IRT and its derivatives, including analogues of the active metabolite SN38 (such as FL118), the recently approved liposomal form Nal-IRI and SN38-based immuno-conjugates currently in development (such as sacituzumab govitecan). New information about the IRT mechanism of action are presented, including the discovery of a new protein target, the single-stranded DNA-binding protein FUBP1. Significant progress has been made also to better understand and manage the main limiting toxicities of IRT, chiefly neutropenia and diarrhea. The role of drug-induced inflammation and dysbiosis is underlined and strategies to limit the intestinal toxicity of IRT are discussed (use of β-glucuronidase inhibitors, plant extracts, probiotics). The detailed knowledge of the metabolism of IRT has enabled the identification of potential biomarkers to guide patient selection and to limit drug-induced toxicities, but no robust IRT-specific therapeutic biomarker has been approved yet. IRT is a versatile chemotherapeutic agent which combines well with a variety of anticancer drugs. It offers a large range of drug combinations with cytotoxic agents, targeted products and immuno-active biotherapeutics, to treat a variety of advanced solid carcinoma, sarcoma and cancers with progressive central nervous system diseases. A quarter of century after its first launch, IRT remains an essential anticancer drug, largely prescribed, useful to many patients and scientifically inspiring.
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Lee V, Wang J, Zahurak M, Gootjes E, Verheul HM, Parkinson R, Kerner Z, Sharma A, Rosner G, De Jesus-Acosta A, Laheru D, Le DT, Oganesian A, Lilly E, Brown T, Jones P, Baylin S, Ahuja N, Azad N. A Phase I Trial of a Guadecitabine (SGI-110) and Irinotecan in Metastatic Colorectal Cancer Patients Previously Exposed to Irinotecan. Clin Cancer Res 2018; 24:6160-6167. [PMID: 30097434 DOI: 10.1158/1078-0432.ccr-18-0421] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/29/2018] [Accepted: 08/07/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE Chemotherapeutic resistance eventually develops in all patients with metastatic colorectal cancer (mCRC). Gene silencing through promoter demethylation is one potential reversible mechanism of resistance with administration of hypomethylating agents. We evaluated the safety and tolerability of guadecitabine and irinotecan in patients with mCRC previously treated with irinotecan. PATIENTS AND METHODS In this 3+3 dose-escalation study, patients with mCRC previously exposed to irinotecan received guadecitabine days 1 to 5 of a 28-day cycle and irinotecan 125 mg/m2 days 8 and 15 [dose level (DL) 1, guadecitabine 45 mg/m2; DL -1: guadecitabine 30 mg/m2; DL -1G: guadecitabine 30 mg/m2 with growth factor support (GFS); DL 1G: guadecitabine 45 mg/m2 with GFS]. RESULTS Twenty-two patients were treated across four DLs. Dose-limiting toxicities were neutropenic fever (DL 1 and -1G), biliary drain infection (DL -1), colonic obstruction (DL -1), and severe dehydration (DL 1G). Most common toxicities were neutropenia (82% any grade, 77% Grade 3/4), neutropenic fever (23%), leukopenia (73% any grade, 50% Grade 3/4), and injection site reactions (64% total, 0% Grade 3/4). Patients received a median of 4.5 cycles of treatment; 12/17 evaluable patients had stable disease as best response, with one having initial disease progression but subsequently durable partial response. Circulating tumor DNA showed decrease in global demethylation by LINE-1 after treatment. CONCLUSIONS We report the first study of chemo-priming with epigenetic therapy in gastrointestinal cancers. Guadecitabine 45 mg/m2 and irinotecan 125 mg/m2 with GFS was safe and tolerable in patients with mCRC, with early indication of benefit. These data have provided the basis for an ongoing phase II randomized, multicenter trial.
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Affiliation(s)
- Valerie Lee
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Judy Wang
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marianna Zahurak
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Elske Gootjes
- Cancer Center Amsterdam, VU University Medical Center, Amsterdam, the Netherlands
| | - Henk M Verheul
- Cancer Center Amsterdam, VU University Medical Center, Amsterdam, the Netherlands
| | - Rose Parkinson
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Zachary Kerner
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Anup Sharma
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Gary Rosner
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Daniel Laheru
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Dung T Le
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Ellen Lilly
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Thomas Brown
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Stephen Baylin
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nita Ahuja
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nilofer Azad
- Johns Hopkins University School of Medicine, Baltimore, Maryland.
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Cha Y, Kim SY, Yeo HY, Baek JY, Choi MK, Jung KH, Dong SM, Chang HJ. Association of CHFR Promoter Methylation with Treatment Outcomes of Irinotecan-Based Chemotherapy in Metastatic Colorectal Cancer. Neoplasia 2018; 21:146-155. [PMID: 30562637 PMCID: PMC6297269 DOI: 10.1016/j.neo.2018.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 11/27/2018] [Indexed: 02/08/2023] Open
Abstract
Aberrant promoter methylation plays a vital role in colorectal carcinogenesis. However, its role in treatment responses is unclear, especially for metastatic disease. Here, we investigated the association between promoter methylation and treatment outcomes of irinotecan-based chemotherapy in 102 patients with metastatic colorectal cancer. Promoter methylation was examined by methylation-specific polymerase chain reaction for three loci (CHFR, WRN, and SULF2) associated with chemotherapy response and five CpG island methylator phenotype (CIMP)–specific markers (CACNA1G, IGF2, NEUROG1, RUNX3, and SOCS1). Association between CHFR methylation and in vitro sensitivity to irinotecan was also evaluated. Promoter methylation of CHFR, WRN, and SULF2 was identified in 16 (15.7%), 24 (23.5%), and 33 (32.4%) patients, respectively. CIMP status was positive in 22 (21.6%) patients. CHFR methylation was associated with a significantly longer time to progression (TTP) (median: 8.77 vs. 4.43 months, P = .019), with trends favoring higher overall survival (OS) (median: 22.83 vs. 20.17 months, P = .300) and response rates (31.3% vs. 17.4%, P = .300). For patients with unmethylated CHFR, TTP (median: 5.60 vs. 3.53, P = .020) and OS (median: 20.57 vs. 9.23, P = .006) were significantly different according to CIMP status. Colorectal cancer cell lines with CHFR methylation demonstrated increased sensitivity to irinotecan. Both CHFR overexpression and combination with 5-aza-2′-deoxycytidine reversed irinotecan sensitivity in CHFR-methylated cell lines, whereas CHFR knockdown in unmethylated cells restored sensitivity to irinotecan. These data suggest that CHFR methylation may be associated with favorable treatment outcomes of irinotecan-based chemotherapy in patients with metastatic colorectal cancer.
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Affiliation(s)
- Yongjun Cha
- Center for Colorectal Cancer, National Cancer Center, Goyang, Korea; Precision Medicine Branch, Division of Precision Medicine, Research Institute of National Cancer Center, Goyang, Korea
| | - Sun Young Kim
- Center for Colorectal Cancer, National Cancer Center, Goyang, Korea
| | - Hyun Yang Yeo
- Precision Medicine Branch, Division of Precision Medicine, Research Institute of National Cancer Center, Goyang, Korea
| | - Ji Yeon Baek
- Center for Colorectal Cancer, National Cancer Center, Goyang, Korea; Translational Research Branch, Division of Translational Science, Research Institute of National Cancer Center, Goyang, Korea
| | - Moon Ki Choi
- Center for Colorectal Cancer, National Cancer Center, Goyang, Korea
| | - Kyung Hae Jung
- Center for Colorectal Cancer, National Cancer Center, Goyang, Korea
| | - Seung Myung Dong
- Molecular Epidemiology Branch, Division of Cancer Epidemiology and Prevention, Research Institute of National Cancer Center, Goyang, Korea.
| | - Hee Jin Chang
- Center for Colorectal Cancer, National Cancer Center, Goyang, Korea; Precision Medicine Branch, Division of Precision Medicine, Research Institute of National Cancer Center, Goyang, Korea.
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de Vroome SW, Holst S, Girondo MR, van der Burgt YEM, Mesker WE, Tollenaar RAEM, Wuhrer M. Serum N-glycome alterations in colorectal cancer associate with survival. Oncotarget 2018; 9:30610-30623. [PMID: 30093973 PMCID: PMC6078140 DOI: 10.18632/oncotarget.25753] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 06/25/2018] [Indexed: 12/15/2022] Open
Abstract
Proteins are routinely measured in clinical laboratories for diagnosis, prognosis and therapy monitoring. Nevertheless, both test improvements (performance) and innovations (biomarkers) are needed, and protein N-glycosylation offers a rich source of potential markers. Here, we have analyzed the total serum N-glycome in a matched case-control study (124 cases versus 124 controls) of colorectal cancer patients. The results were validated in an independent sample cohort (both 61 cases versus 61 controls) and further tested in post-operative samples of cured patients. Our results revealed significant differences between patients and controls, with increased size (antennae) and sialylation of the N-glycans in the colorectal cancer patient sera as compared to mainly di-antennary N-glycans in sera from controls. Furthermore, glycan alterations showed strong associations with cancer stage and survival: The five-year survival rate largely varied between patients with an altered serum N-glycome (46%) and an N-glycome similar to controls (87%). Importantly, the total serum N-glycome showed prognostic value beyond age and stage. This clinical glycomics study provides novel serum biomarker candidates and shows the potential of total serum N-glycans as a prognostic panel. Moreover, serum N-glycome changes reverted to a control-like profile after successful treatment as was demonstrated from pre- and post-operative samples.
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Affiliation(s)
- Stefan W de Vroome
- Department of Surgery, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Stephanie Holst
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Mar Rodriguez Girondo
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Yuri E M van der Burgt
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Wilma E Mesker
- Department of Surgery, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Rob A E M Tollenaar
- Department of Surgery, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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Comprehensive expression analysis of TNF-related apoptosis-inducing ligand and its receptors in colorectal cancer: Correlation with MAPK alterations and clinicopathological associations. Pathol Res Pract 2018; 214:826-834. [DOI: 10.1016/j.prp.2018.04.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/25/2018] [Accepted: 04/27/2018] [Indexed: 12/17/2022]
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