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Zhou J, Zhang MY, Gao AA, Zhu C, He T, Herman JG, Guo MZ. Epigenetic silencing schlafen-11 sensitizes esophageal cancer to ATM inhibitor. World J Gastrointest Oncol 2024; 16:2060-2073. [DOI: 10.4251/wjgo.v16.i5.2060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/26/2024] [Accepted: 04/01/2024] [Indexed: 05/09/2024] Open
Abstract
BACKGROUND Targeting DNA damage response (DDR) pathway is a cutting-edge strategy. It has been reported that Schlafen-11 (SLFN11) contributes to increase chemosensitivity by participating in DDR. However, the detailed mechanism is unclear.
AIM To investigate the role of SLFN11 in DDR and the application of synthetic lethal in esophageal cancer with SLFN11 defects.
METHODS To reach the purpose, eight esophageal squamous carcinoma cell lines, 142 esophageal dysplasia (ED) and 1007 primary esophageal squamous cell carcinoma (ESCC) samples and various techniques were utilized, including methylation-specific polymerase chain reaction, CRISPR/Cas9 technique, Western blot, colony formation assay, and xenograft mouse model.
RESULTS Methylation of SLFN11 was exhibited in 9.15% of (13/142) ED and 25.62% of primary (258/1007) ESCC cases, and its expression was regulated by promoter region methylation. SLFN11 methylation was significantly associated with tumor differentiation and tumor size (both P < 0.05). However, no significant associations were observed between promoter region methylation and age, gender, smoking, alcohol consumption, TNM stage, or lymph node metastasis. Utilizing DNA damaged model induced by low dose cisplatin, SLFN11 was found to activate non-homologous end-joining and ATR/CHK1 signaling pathways, while inhibiting the ATM/CHK2 signaling pathway. Epigenetic silencing of SLFN11 was found to sensitize the ESCC cells to ATM inhibitor (AZD0156), both in vitro and in vivo.
CONCLUSION SLFN11 is frequently methylated in human ESCC. Methylation of SLFN11 is sensitive marker of ATM inhibitor in ESCC.
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Affiliation(s)
- Jing Zhou
- School of Medicine, NanKai University, Tianjin 300071, China
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Mei-Ying Zhang
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Ai-Ai Gao
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Cheng Zhu
- School of Medicine, NanKai University, Tianjin 300071, China
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Tao He
- Departments of Pathology, Characteristic Medical Center of The Chinese People’s Armed Police Force, Tianjin 300162, China
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, United States
| | - Ming-Zhou Guo
- School of Medicine, NanKai University, Tianjin 300071, China
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
- National Key Laboratory of Kidney Diseases, Chinese PLA General Hospital, Beijing 100853, China
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Zhang M, Li X, Herman JG, Gao A, Wang Q, Yao Y, Shen F, He K, Guo M. Methylation of NRIP3 Is a Synthetic Lethal Marker for Combined PI3K and ATR/ATM Inhibitors in Colorectal Cancer. Clin Transl Gastroenterol 2024; 15:e00682. [PMID: 38235705 PMCID: PMC10962901 DOI: 10.14309/ctg.0000000000000682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/10/2024] [Indexed: 01/19/2024] Open
Abstract
INTRODUCTION The aim of this study was to investigate the epigenetic regulation and underlying mechanism of NRIP3 in colorectal cancer (CRC). METHODS Eight cell lines (SW480, SW620, DKO, LOVO, HT29, HCT116, DLD1, and RKO), 187 resected margin samples from colorectal cancer tissue, 146 cases with colorectal adenomatous polyps, and 308 colorectal cancer samples were used. Methylation-specific PCR, Western blotting, RNA interference assay, and a xenograft mouse model were used. RESULTS NRIP3 exhibited methylation in 2.7% (5/187) of resected margin samples from colorectal cancer tissue, 32.2% (47/146) of colorectal adenomatous polyps, and 50.6% (156/308) of CRC samples, and the expression of NRIP3 was regulated by promoter region methylation. The methylation of NRIP3 was found to be significantly associated with late onset (at age 50 years or older), poor tumor differentiation, lymph node metastasis, and poor 5-year overall survival in CRC (all P < 0.05). In addition, NRIP3 methylation was an independent poor prognostic marker ( P < 0.05). NRIP3 inhibited cell proliferation, colony formation, invasion, and migration, while induced G1/S arrest. NRIP3 suppressed CRC growth by inhibiting PI3K-AKT signaling both in vitro and in vivo . Methylation of NRIP3 sensitized CRC cells to combined PI3K and ATR/ATM inhibitors. DISCUSSION NRIP3 was frequently methylated in both colorectal adenomatous polyps and CRC. The methylation of NRIP3 may potentially serve as an early detection, late-onset, and poor prognostic marker in CRC. NRIP3 is a potential tumor suppressor. NRIP3 methylation is a potential synthetic lethal marker for combined PI3K and ATR/ATM inhibitors.
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Affiliation(s)
- Meiying Zhang
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xiaoyun Li
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
- Department of Gastroenterology, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - James G. Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
| | - Aiai Gao
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Qian Wang
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Yuanxin Yao
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Fangfang Shen
- Department of Gastroenterology, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Kunlun He
- Key Laboratory of Ministry of Industry and Information Technology of Biomedical Engineering and Translational Medicine, Chinese PLA General Hospital, Beijing, China
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
- National Key Laboratory of Kidney Diseases, the First Medical Center, Chinese PLA General Hospital, Beijing, China
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Gao A, Bai P, Zhang M, Yao Y, Herman JG, Guo M. RASSF1A promotes ATM signaling and RASSF1A methylation is a synthetic lethal marker for ATR inhibitors. Epigenomics 2023; 15:1205-1220. [PMID: 38093706 DOI: 10.2217/epi-2023-0306] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023] Open
Abstract
Aim: The mechanism of RASSF1A in DNA damage repair remains to be further clarified for applying to synthetic lethal strategy. Materials & methods: Eight esophageal cancer cell lines, 181 cases of esophageal dysplasia and 1066 cases of primary esophageal squamous cell carcinoma (ESCC) were employed. Methylation-specific PCR, the CRISPR/Cas9 technique, immunoprecipitation assay and a xenograft mouse model were used. Results: RASSF1A was methylated in 2.21% of esophageal dysplasia and 11.73% of ESCC. RASSF1A was also involved in DNA damage repair through activating Hippo signaling. Loss of RASSF1A expression sensitized esophageal cancer cell lines to ataxia telangiectasia mutated and rad3-related (ATR) inhibitor (VE-822) both in vitro and in vivo. Conclusion: RASSF1A methylation is a synthetic lethal marker for ATR inhibitors.
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Affiliation(s)
- Aiai Gao
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Panpan Bai
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
- Henan Advanced Technology Research Institute, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Meiying Zhang
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yuanxin Yao
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
- National Key Laboratory of Kidney Diseases, Beijing, 100853, China
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Marmor HN, Kammer MN, Deppen SA, Shipe M, Welty VF, Patel K, Godfrey C, Billatos E, Herman JG, Wilson DO, Kussrow AK, Bornhop DJ, Maldonado F, Chen H, Grogan EL. Improving lung cancer diagnosis with cancer, fungal, and imaging biomarkers. J Thorac Cardiovasc Surg 2023; 166:669-678.e4. [PMID: 36792410 PMCID: PMC10287834 DOI: 10.1016/j.jtcvs.2022.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Indeterminate pulmonary nodules (IPNs) represent a significant diagnostic burden in health care. We aimed to compare a combination clinical prediction model (Mayo Clinic model), fungal (histoplasmosis serology), imaging (computed tomography [CT] radiomics), and cancer (high-sensitivity cytokeratin fraction 21; hsCYFRA 21-1) biomarker approach to a validated prediction model in diagnosing lung cancer. METHODS A prospective specimen collection, retrospective blinded evaluation study was performed in 3 independent cohorts with 6- to 30-mm IPNs (n = 281). Serum histoplasmosis immunoglobulin G and immunoglobulin M antibodies and hsCYFRA 21-1 levels were measured and a validated CT radiomic score was calculated. Multivariable logistic regression models were estimated with Mayo Clinic model variables, histoplasmosis antibody levels, CT radiomic score, and hsCYFRA 21-1. Diagnostic performance of the combination model was compared with that of the Mayo Clinic model. Bias-corrected clinical net reclassification index (cNRI) was used to estimate the clinical utility of a combination biomarker approach. RESULTS A total of 281 patients were included (111 from a histoplasmosis-endemic region). The combination biomarker model including the Mayo Clinic model score, histoplasmosis antibody levels, radiomics, and hsCYFRA 21-1 level showed improved diagnostic accuracy for IPNs compared with the Mayo Clinic model alone with an area under the receiver operating characteristics curve of 0.80 (95% CI, 0.76-0.84) versus 0.72 (95% CI, 0.66-0.78). Use of this combination model correctly reclassified intermediate risk IPNs into low- or high-risk category (cNRI benign = 0.11 and cNRI malignant = 0.16). CONCLUSIONS The addition of cancer, fungal, and imaging biomarkers improves the diagnostic accuracy for IPNs. Integrating a combination biomarker approach into the diagnostic algorithm of IPNs might decrease unnecessary invasive testing of benign nodules and reduce time to diagnosis for cancer.
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Affiliation(s)
- Hannah N Marmor
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tenn
| | - Michael N Kammer
- Department of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, Tenn
| | - Stephen A Deppen
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tenn; Section of Thoracic Surgery, Tennessee Valley VA Healthcare System, Nashville, Tenn.
| | - Maren Shipe
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tenn
| | - Valerie F Welty
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tenn
| | - Khushbu Patel
- Department of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, Tenn
| | - Caroline Godfrey
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tenn
| | - Ehab Billatos
- Section of Pulmonary and Critical Care Medicine, Boston Medical Center, Boston, Mass
| | - James G Herman
- Division of Hematology/Oncology, University of Pittsburgh Medical Center, Pittsburgh, Pa
| | - David O Wilson
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pa
| | | | | | - Fabien Maldonado
- Department of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, Tenn
| | - Heidi Chen
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tenn
| | - Eric L Grogan
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tenn; Section of Thoracic Surgery, Tennessee Valley VA Healthcare System, Nashville, Tenn
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Zhao Y, O'Keefe CM, Hsieh K, Cope L, Joyce SC, Pisanic TR, Herman JG, Wang TH. Multiplex Digital Methylation-Specific PCR for Noninvasive Screening of Lung Cancer. Adv Sci (Weinh) 2023; 10:e2206518. [PMID: 37039321 DOI: 10.1002/advs.202206518] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/18/2023] [Indexed: 06/04/2023]
Abstract
There remains tremendous interest in developing liquid biopsy assays for detection of cancer-specific alterations, such as mutations and DNA methylation, in cell-free DNA (cfDNA) obtained through noninvasive blood draws. However, liquid biopsy analysis is often challenging due to exceedingly low fractions of circulating tumor DNA (ctDNA), necessitating the use of extended tumor biomarker panels. While multiplexed PCR strategies provide advantages such as higher throughput, their implementation is often hindered by challenges such as primer-dimers and PCR competition. Alternatively, digital PCR (dPCR) approaches generally offer superior performance, but with constrained multiplexing capability. This paper describes development and validation of the first multiplex digital methylation-specific PCR (mdMSP) platform for simultaneous analysis of four methylation biomarkers for liquid-biopsy-based detection of non-small cell lung cancer (NSCLC). mdMSP employs a microfluidic device containing four independent, but identical modules, housing a total of 40 160 nanowells. Analytical validation of the mdMSP platform demonstrates multiplex detection at analytical specificities as low as 0.0005%. The clinical utility of mdMSP is also demonstrated in a cohort of 72 clinical samples of low-volume liquid biopsy specimens from patients with computed tomography (CT)-scan indeterminant pulmonary nodules, exhibiting superior clinical performance when compared to traditional MSP assays for noninvasive detection of early-stage NSCLC.
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Affiliation(s)
- Yang Zhao
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Christine M O'Keefe
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Leslie Cope
- Department of Oncology, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Sonali C Joyce
- The UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
- Division of Hematology and Oncology, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Thomas R Pisanic
- Department of Oncology, Johns Hopkins University, Baltimore, MD, 21287, USA
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - James G Herman
- The UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
- Division of Hematology and Oncology, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21287, USA
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
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Zhao Y, O’Keefe CM, Herman JG, Pisanic TR, Wang TH. Abstract 6510: REM-DREAMing: Low-cost digital microfluidic analysis of DNA methylation heterogeneity for enhanced, liquid biopsy-based detection of early-stage lung cancer. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-6510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
We report the results of a study exploring the ability to exploit molecular heterogeneity in DNA methylation for improving the performance of liquid biopsy-based screening for early-stage (I & II) non-small cell lung cancer (NSCLC). Annual low-dose CT (LDCT) screening is currently recommended for adults aged 50 or older who are at high-risk of developing lung cancer. While this approach has resulted in improvements in survival, the false positive rate of lung nodules detection by LDCT remains over 95%, leading to unnecessary invasive follow-up procedures and further points to the need for new, complementary methods to improve diagnostics performance and reduce patient risk. DNA methylation biomarkers have demonstrated considerable potential as tumor-specific biomarkers for blood-based detection of early-stage NSCLC. Nonetheless, cell-free DNA (cfDNA) assessment techniques, such as methylation-specific PCR (MSP) or bisulfite sequencing, have limited sensitivity to assess epigenetic heterogeneity of rare epiallelic variants in a cost-effective manner. Here we reported a new platform, named REM-DREAMing (Ratiometric-Encoded Multiplex Discrimination of Rare EpiAlleles by Melt), which provides a simple, low-cost solution for multiplexed assessment of loci-specific DNA methylation heterogeneity at single molecule sensitivity. The microfluidic nanoarray contains four independent but identical 10,040 nanowell modules. Methylation biomarkers are differentiated by a ratiometric fluorescence scheme and the assessment of individual epiallele species of each locus are achieved through digitization in the nanoarray and precise high-resolution melt (HRM) analysis. In this study, we explore the potential utility of REM-DREAMing as a complementary assay for improving LDCT screening of NSCLC by testing a cohort of 48 clinical samples (28 cancer and 20 control samples) of low-volume liquid biopsy specimens from patients with CT-scan indeterminant pulmonary nodules. A machine learning algorithm incorporating logistic regression models with leave-one-out cross validation was developed to identify a proper methylation density threshold of each biomarker in the panel. Evaluation of the receiver operation characteristic (ROC) curve yielded an area under the curve (AUC) of 0.97 (95% CI, 0.94-1) with 93% sensitivity at 95% specificity for the REM-DREAMing assay, compared with 93% sensitivity at 62% specificity achieved using a traditional, MSP-based approach. These results suggest that the assessment of intermolecular epigenetic heterogeneity can provide superior clinical performance for cfDNA methylation and noninvasive detection of early-stage NSCLC, in particular. Our results warrant further investigation in a larger sample cohort to validate its utility for improving routine screening of NSCLC in high-risk populations.
Citation Format: Yang Zhao, Christine M. O’Keefe, James G. Herman, Thomas R. Pisanic, Tza-Huei Wang. REM-DREAMing: Low-cost digital microfluidic analysis of DNA methylation heterogeneity for enhanced, liquid biopsy-based detection of early-stage lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6510.
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Affiliation(s)
- Yang Zhao
- 1Johns Hopkins University, Baltimore, MD
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Mascarella MA, Olonisakin TF, Rumde P, Vendra V, Nance MA, Kim S, Kubik MW, Sridharan SS, Ferris RL, Fenton MJ, Clayburgh DR, Ohr JP, Joyce SC, Sen M, Herman JG, Grandis JR, Zandberg DP, Duvvuri U. Response to Neoadjuvant Targeted Therapy in Operable Head and Neck Cancer Confers Survival Benefit. Clin Cancer Res 2023; 29:723-730. [PMID: 36595540 DOI: 10.1158/1078-0432.ccr-22-1768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/01/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023]
Abstract
PURPOSE Neoadjuvant targeted therapy provides a brief, preoperative window of opportunity that can be exploited to individualize cancer care based on treatment response. We investigated whether response to neoadjuvant therapy during the preoperative window confers survival benefit in patients with operable head and neck squamous cell carcinoma (HNSCC). PATIENTS AND METHODS A pooled analysis of treatment-naïve patients with operable HNSCC enrolled in one of three clinical trials from 2009 to 2020 (NCT00779389, NCT01218048, NCT02473731). Neoadjuvant regimens consisted of EGFR inhibitors (n = 83) or anti-ErbB3 antibody therapy (n = 9) within 28 days of surgery. Clinical to pathologic stage migration was compared with disease-free survival (DFS) and overall survival (OS) while adjusting for confounding factors using multivariable Cox regression. Circulating tumor markers validated in other solid tumor models were analyzed. RESULTS 92 of 118 patients were analyzed; all patients underwent surgery following neoadjuvant therapy. Clinical to pathologic downstaging was more frequent in patients undergoing neoadjuvant targeted therapy compared with control cohort (P = 0.048). Patients with pathologic downstage migration had the highest OS [89.5%; 95% confidence interval (CI), 75.7-100] compared with those with no stage change (58%; 95% CI, 46.2-69.8) or upstage (40%; 95% CI, 9.6-70.4; P = 0.003). Downstage migration remained a positive prognostic factor for OS (HR, 0.22; 95% CI, 0.05-0.90) while adjusting for measured confounders. Downstage migration correlated with decreased circulating tumor markers, SOX17 and TAC1 (P = 0.0078). CONCLUSIONS Brief neoadjuvant therapy achieved pathologic downstaging in a subset of patients and was associated with significantly better DFS and OS as well as decreased circulating methylated SOX17 and TAC1.
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Affiliation(s)
- Marco A Mascarella
- Division of Head and Neck Surgery, Department of Otolaryngology-Head and Neck Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- Department of Otolaryngology-Head and Neck Surgery, McGill University, Montreal, Quebec, Canada
- Centre for Clinical Epidemiology, Lady Davis Institute of the Jewish General Hospital, Montreal, Quebec, Canada
| | - Tolani F Olonisakin
- Division of Head and Neck Surgery, Department of Otolaryngology-Head and Neck Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Hospital, Baltimore, Maryland
| | - Purva Rumde
- Division of Head and Neck Surgery, Department of Otolaryngology-Head and Neck Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Varun Vendra
- Division of Head and Neck Surgery, Department of Otolaryngology-Head and Neck Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Melonie A Nance
- Division of Head and Neck Surgery, Department of Otolaryngology-Head and Neck Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- VA Pittsburgh Health System, Pittsburgh, Pennsylvania
| | - Seungwon Kim
- Division of Head and Neck Surgery, Department of Otolaryngology-Head and Neck Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- UPMC Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Mark W Kubik
- Division of Head and Neck Surgery, Department of Otolaryngology-Head and Neck Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Shaum S Sridharan
- Division of Head and Neck Surgery, Department of Otolaryngology-Head and Neck Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Robert L Ferris
- Division of Head and Neck Surgery, Department of Otolaryngology-Head and Neck Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- UPMC Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Moon J Fenton
- UPMC Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- Division of Hematology and Oncology, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Daniel R Clayburgh
- Department of Otolaryngology-Head and Neck Surgery, Oregon Health & Science University, Portland, Oregon
| | - James P Ohr
- UPMC Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- Division of Hematology and Oncology, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Sonali C Joyce
- UPMC Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- Division of Hematology and Oncology, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Malabika Sen
- UPMC Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- Division of Hematology and Oncology, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - James G Herman
- UPMC Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- Division of Hematology and Oncology, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Jennifer R Grandis
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, California
| | - Dan P Zandberg
- UPMC Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- Division of Hematology and Oncology, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Umamaheswar Duvvuri
- Division of Head and Neck Surgery, Department of Otolaryngology-Head and Neck Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- UPMC Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
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Yang W, Guo C, Herman JG, Zhu C, Lv H, Su X, Zhang L, Zhang M, Guo M. Epigenetic silencing of JAM3 promotes esophageal cancer development by activating Wnt signaling. Clin Epigenetics 2022; 14:164. [PMID: 36461092 PMCID: PMC9719220 DOI: 10.1186/s13148-022-01388-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 11/27/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The role of JAM3 in different tumors is controversial. The epigenetic regulation and the mechanism of JAM3 remain to be elucidated in human esophageal cancer (EC). METHODS Eleven EC cell lines, 49 cases of esophageal intraepithelial neoplasia (EIN) and 760 cases of primary EC samples were employed. Methylation-specific polymerase chain reaction, immunohistochemistry, MTT, western blot and xenograft mouse models were applied in this study. RESULTS The inverse association between RNA expression and promoter region methylation of JAM3 was found by analyzing 185 cases of EC samples extracted from the TCGA database (p < 0.05). JAM3 was highly expressed in KYSE450, KYSE520, TE1 and YES2 cells, low level expressed in KYSE70 cells and unexpressed in KYSE30, KYSE150, KYSE410, KYSE510, TE13 and BIC1 cells. JAM3 was unmethylated in KYSE450, KYSE520, TE1 and YES2 cells, partial methylated in KYSE70 cells and completely methylated in KYSE30, KYSE150, KYSE410, KYSE510, TE13 and BIC1 cells. The expression of JAM3 is correlated with methylation status. The levels of JAM3 were unchanged in KYSE450, KYSE520, TE1 and YES2 cells, increased in KYSE70 cells and restored expression in KYSE30, KYSE150, KYSE410, KYSE510, TE13 and BIC1 cells after 5-aza-2'-deoxycytidine treatment, suggesting that the expression of JAM3 is regulated by promoter region methylation. JAM3 was methylated in 26.5% (13/49) of EIN and 51.1% (388/760) of primary EC, and methylation of JAM3 was associated significantly with tumor differentiation and family history (all p < 0.05). Methylation of JAM3 is an independent prognostic factor of poor 5-year overall survival (p < 0.05). JAM3 suppresses cell proliferation, colony formation, migration and invasion and induces G1/S arrest and apoptosis in EC. Further study demonstrated that JAM3 suppressed EC cells and xenograft tumor growth by inhibiting Wnt/β-catenin signaling. CONCLUSION JAM3 is frequently methylated in human EC, and the expression of JAM3 is regulated by promoter region methylation. JAM3 methylation is an early detection and prognostic marker of EC. JAM3 suppresses EC growth both in vitro and in vivo by inhibiting Wnt signaling.
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Affiliation(s)
- Weili Yang
- grid.414252.40000 0004 1761 8894Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Chao Guo
- grid.414252.40000 0004 1761 8894Laboratory Animal Center, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - James G. Herman
- grid.478063.e0000 0004 0456 9819The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213 USA
| | - Cheng Zhu
- grid.414252.40000 0004 1761 8894Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China ,grid.216938.70000 0000 9878 7032Medical College of NanKai University, Tianjin, 300071 China
| | - Honghui Lv
- grid.414252.40000 0004 1761 8894Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Xiaomo Su
- grid.414252.40000 0004 1761 8894Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Lirong Zhang
- grid.207374.50000 0001 2189 3846Henan Key Laboratory for Esophageal Cancer Research, Zhengzhou University, 40 Daxue Road, Zhengzhou, 450052 Henan China
| | - Meiying Zhang
- grid.414252.40000 0004 1761 8894Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Mingzhou Guo
- grid.414252.40000 0004 1761 8894Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China ,grid.207374.50000 0001 2189 3846Henan Key Laboratory for Esophageal Cancer Research, Zhengzhou University, 40 Daxue Road, Zhengzhou, 450052 Henan China
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9
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Feng Z, Oberije CJG, van de Wetering AJP, Koch A, Wouters KAD, Vaes N, Masclee AAM, Carvalho B, Meijer GA, Zeegers MP, Herman JG, Melotte V, van Engeland M, Smits KM. Lessons From a Systematic Literature Search on Diagnostic DNA Methylation Biomarkers for Colorectal Cancer: How to Increase Research Value and Decrease Research Waste? Clin Transl Gastroenterol 2022; 13:e00499. [PMID: 35584320 PMCID: PMC9236597 DOI: 10.14309/ctg.0000000000000499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 04/22/2022] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES To improve colorectal cancer (CRC) survival and lower incidence rates, colonoscopy and/or fecal immunochemical test screening are widely implemented. Although candidate DNA methylation biomarkers have been published to improve or complement the fecal immunochemical test, clinical translation is limited. We describe technical and methodological problems encountered after a systematic literature search and provide recommendations to increase (clinical) value and decrease research waste in biomarker research. In addition, we present current evidence for diagnostic CRC DNA methylation biomarkers. METHODS A systematic literature search identified 331 diagnostic DNA methylation marker studies published before November 2020 in PubMed, EMBASE, Cochrane Library, and Google Scholar. For 136 bodily fluid studies, extended data extraction was performed. STARD criteria and level of evidence were registered to assess reporting quality and strength for clinical translation. RESULTS Our systematic literature search revealed multiple issues that hamper the development of DNA methylation biomarkers for CRC diagnosis, including methodological and technical heterogeneity and lack of validation or clinical translation. For example, clinical translation and independent validation were limited, with 100 of 434 markers (23%) studied in bodily fluids, 3 of 434 markers (0.7%) translated into clinical tests, and independent validation for 92 of 411 tissue markers (22%) and 59 of 100 bodily fluids markers (59%). DISCUSSION This systematic literature search revealed that major requirements to develop clinically relevant diagnostic CRC DNA methylation markers are often lacking. To avoid the resulting research waste, clinical needs, intended biomarker use, and independent validation should be better considered before study design. In addition, improved reporting quality would facilitate meta-analysis, thereby increasing the level of evidence and enabling clinical translation.
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Affiliation(s)
- Zheng Feng
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - Cary J. G. Oberije
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
- The D-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, the Netherlands;
| | - Alouisa J. P. van de Wetering
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - Alexander Koch
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - Kim. A. D. Wouters
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - Nathalie Vaes
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - Ad A. M. Masclee
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Maastricht University Medical Center, Maastricht, the Netherlands;
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands;
| | - Beatriz Carvalho
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands;
| | - Gerrit A. Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands;
| | - Maurice P. Zeegers
- Department of Complex Genetics, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, the Netherlands;
- Department of Complex Genetics, CAPHRI – Care and Public Health Research Institute, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - James G. Herman
- Division of Hematology/Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
| | - Veerle Melotte
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
- Department of Clinical Genetics, Erasmus University Medical Center, University of Rotterdam, Rotterdam, the Netherlands;
| | - Manon van Engeland
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - Kim M. Smits
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
- Division of Medical Oncology, Department of Internal Medicine, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands.
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10
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Somasundaram A, Cillo AR, Lampenfeld C, Workman CJ, Kunning S, Oliveri LN, Velez M, Joyce S, Calderon M, Dadey R, Rajasundaram D, Normolle DP, Watkins SC, Herman JG, Kirkwood JM, Lipson EJ, Ferris RL, Bruno TC, Vignali DAA. Systemic immune dysfunction in cancer patients driven by IL6 induction of LAG3 in peripheral CD8+ T cells. Cancer Immunol Res 2022; 10:885-899. [PMID: 35587532 DOI: 10.1158/2326-6066.cir-20-0736] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 06/10/2021] [Accepted: 05/17/2022] [Indexed: 11/16/2022]
Abstract
Many cancer patients do not develop a durable response to the current standard of care immunotherapies, despite substantial advances in targeting immune inhibitory receptors. A potential compounding issue, which may serve as an unappreciated, dominant resistance mechanism, is an inherent systemic immune dysfunction that is often associated with advanced cancer. Minimal response to inhibitory receptor (IR) blockade therapy and increased disease burden have been associated with peripheral CD8+ T-cell dysfunction, characterized by suboptimal T-cell proliferation and chronic expression of IRs (eg. Programmed Death 1 [PD1] and Lymphocyte Activation Gene 3 [LAG3]). Here, we demonstrated that approximately a third of cancer patients analyzed in this study have peripheral CD8+ T cells that expressed robust intracellular LAG3 (LAG3IC), but not surface LAG3 (LAG3SUR) due to A Disintegrin and Metalloproteinase domain-containing protein 10 (ADAM10) cleavage. This associated with poor disease prognosis and decreased CD8+ T-cell function, which could be partially reversed by anti-LAG3. Systemic immune dysfunction was restricted to CD8+ T cells, including, in some cases, a high percentage of peripheral naïve CD8+ T cells, and was driven by the cytokine IL6 via STAT3. These data suggest that additional studies are warrented to determine if the combination of increased LAG3IC in peripheral CD8+ T cells and elevated systemic IL6 can serve as predictive biomarkers and identify which cancer patients may benefit from LAG3 blockade.
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Affiliation(s)
| | | | | | | | | | | | - Maria Velez
- University of Pittsburgh, Pittsburgh, PA, United States
| | - Sonali Joyce
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Michael Calderon
- University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Rebekah Dadey
- University of Pittsburgh, Pittsburgh, PA, United States
| | | | | | | | | | | | - Evan J Lipson
- Johns Hopkins University School of Medicine, BALTIMORE, MD, United States
| | - Robert L Ferris
- University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States
| | - Tullia C Bruno
- University of Colorado Boulder, Pittsburgh, PA, United States
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11
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Massen M, Lommen K, Wouters KAD, Vandersmissen J, van Criekinge W, Herman JG, Melotte V, Schouten LJ, van Engeland M, Smits KM. Technical considerations in PCR-based assay design for diagnostic DNA methylation cancer biomarkers. Clin Epigenetics 2022; 14:56. [PMID: 35477541 PMCID: PMC9047347 DOI: 10.1186/s13148-022-01273-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022] Open
Abstract
Background DNA methylation biomarkers for early detection, risk stratification and treatment response in cancer have been of great interest over the past decades. Nevertheless, clinical implementation of these biomarkers is limited, as only < 1% of the identified biomarkers is translated into a clinical or commercial setting. Technical factors such as a suboptimal genomic location of the assay and inefficient primer or probe design have been emphasized as important pitfalls in biomarker research. Here, we use eleven diagnostic DNA methylation biomarkers for colorectal cancer (ALX4, APC, CDKN2A, MGMT, MLH1, NDRG4, SDC2, SFRP1, SFRP2, TFPI1 and VIM), previously described in a systematic literature search, to evaluate these pitfalls. Results To assess the genomic assay location, the optimal genomic locations according to TCGA data were extracted and compared to the genomic locations used in the published assays for all eleven biomarkers. In addition, all primers and probes were technically evaluated according to several criteria, based on literature and expert opinion. Both assay location and assay design quality varied widely among studies. Conclusions Large variation in both assay location and design hinders the development of future DNA methylation biomarkers as well as inter-study comparability.
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Affiliation(s)
- Maartje Massen
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Kim Lommen
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Kim A D Wouters
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | | | - Wim van Criekinge
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, 9000, Ghent, Belgium
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15232, USA
| | - Veerle Melotte
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Leo J Schouten
- Department of Epidemiology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Kim M Smits
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.
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12
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Kuang C, Park Y, Augustin RC, Lin Y, Hartman DJ, Seigh L, Pai RK, Sun W, Bahary N, Ohr J, Rhee JC, Marks SM, Beasley HS, Shuai Y, Herman JG, Zarour HM, Chu E, Lee JJ, Krishnamurthy A. Pembrolizumab plus azacitidine in patients with chemotherapy refractory metastatic colorectal cancer: a single-arm phase 2 trial and correlative biomarker analysis. Clin Epigenetics 2022; 14:3. [PMID: 34991708 PMCID: PMC8740438 DOI: 10.1186/s13148-021-01226-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/28/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND DNA mismatch repair proficient (pMMR) metastatic colorectal cancer (mCRC) is not responsive to pembrolizumab monotherapy. DNA methyltransferase inhibitors can promote antitumor immune responses. This clinical trial investigated whether concurrent treatment with azacitidine enhances the antitumor activity of pembrolizumab in mCRC. METHODS We conducted a phase 2 single-arm trial evaluating activity and tolerability of pembrolizumab plus azacitidine in patients with chemotherapy-refractory mCRC (NCT02260440). Patients received pembrolizumab 200 mg IV on day 1 and azacitidine 100 mg SQ on days 1-5, every 3 weeks. A low fixed dose of azacitidine was chosen in order to reduce the possibility of a direct cytotoxic effect of the drug, since the main focus of this study was to investigate its potential immunomodulatory effect. The primary endpoint of this study was overall response rate (ORR) using RECIST v1.1., and secondary endpoints were progression-free survival (PFS) and overall survival (OS). Tumor tissue was collected pre- and on-treatment for correlative studies. RESULTS Thirty chemotherapy-refractory patients received a median of three cycles of therapy. One patient achieved partial response (PR), and one patient had stable disease (SD) as best confirmed response. The ORR was 3%, median PFS was 1.9 months, and median OS was 6.3 months. The combination regimen was well-tolerated, and 96% of treatment-related adverse events (TRAEs) were grade 1/2. This trial was terminated prior to the accrual target of 40 patients due to lack of clinical efficacy. DNA methylation on-treatment as compared to pre-treatment decreased genome wide in 10 of 15 patients with paired biopsies and was significantly lower in gene promoter regions after treatment. These promoter demethylated genes represented a higher proportion of upregulated genes, including several immune gene sets, endogenous retroviral elements, and cancer-testis antigens. CD8+ TIL density trended higher on-treatment compared to pre-treatment. Higher CD8+ TIL density at baseline was associated with greater likelihood of benefit from treatment. On-treatment tumor demethylation correlated with the increases in tumor CD8+ TIL density. CONCLUSIONS The combination of pembrolizumab and azacitidine is safe and tolerable with modest clinical activity in the treatment for chemotherapy-refractory mCRC. Correlative studies suggest that tumor DNA demethylation and immunomodulation occurs. An association between tumor DNA demethylation and tumor-immune modulation suggests immune modulation and may result from treatment with azacitidine. Trial registration ClinicalTrials.gov, NCT02260440. Registered 9 October 2014, https://clinicaltrials.gov/ct2/show/NCT02260440 .
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Affiliation(s)
- Chaoyuan Kuang
- UPMC Hillman Cancer Center, Pittsburgh, USA.
- Division of Hematology-Oncology, Department of Medicine, School of Medicine, University of Pittsburgh, UPMC Cancer Pavilion, 5150 Centre Avenue, Room 463, Pittsburgh, PA, 15232, USA.
- Hillman Cancer Center Cancer Therapeutics Program, Pittsburgh, USA.
- Albert Einstein Cancer Center, Montefiore Einstein Cancer Center, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Chanin 628, Bronx, NY, 10461, USA.
| | - Yongseok Park
- Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA
| | - Ryan C Augustin
- Division of General Internal Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Yan Lin
- UPMC Hillman Cancer Center, Pittsburgh, USA
- Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA
| | - Douglas J Hartman
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Lindsey Seigh
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Reetesh K Pai
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Weijing Sun
- UPMC Hillman Cancer Center, Pittsburgh, USA
- Division of Hematology-Oncology, Department of Medicine, School of Medicine, University of Pittsburgh, UPMC Cancer Pavilion, 5150 Centre Avenue, Room 463, Pittsburgh, PA, 15232, USA
- Hillman Cancer Center Cancer Therapeutics Program, Pittsburgh, USA
- University of Kansas Cancer Center, Westwood, USA
| | - Nathan Bahary
- UPMC Hillman Cancer Center, Pittsburgh, USA
- Division of Hematology-Oncology, Department of Medicine, School of Medicine, University of Pittsburgh, UPMC Cancer Pavilion, 5150 Centre Avenue, Room 463, Pittsburgh, PA, 15232, USA
- Hillman Cancer Center Cancer Therapeutics Program, Pittsburgh, USA
- AHN Cancer Institute, Pittsburgh, USA
| | - James Ohr
- UPMC Hillman Cancer Center, Pittsburgh, USA
| | | | | | | | | | - James G Herman
- UPMC Hillman Cancer Center, Pittsburgh, USA
- Division of Hematology-Oncology, Department of Medicine, School of Medicine, University of Pittsburgh, UPMC Cancer Pavilion, 5150 Centre Avenue, Room 463, Pittsburgh, PA, 15232, USA
- Hillman Cancer Center Cancer Epidemiology and Prevention Program, Pittsburgh, USA
| | - Hassane M Zarour
- UPMC Hillman Cancer Center, Pittsburgh, USA
- Division of Hematology-Oncology, Department of Medicine, School of Medicine, University of Pittsburgh, UPMC Cancer Pavilion, 5150 Centre Avenue, Room 463, Pittsburgh, PA, 15232, USA
- Hillman Cancer Center Cancer Immunology and Immunotherapy Program, Pittsburgh, USA
| | - Edward Chu
- UPMC Hillman Cancer Center, Pittsburgh, USA
- Division of Hematology-Oncology, Department of Medicine, School of Medicine, University of Pittsburgh, UPMC Cancer Pavilion, 5150 Centre Avenue, Room 463, Pittsburgh, PA, 15232, USA
- Hillman Cancer Center Cancer Therapeutics Program, Pittsburgh, USA
- Albert Einstein Cancer Center, Montefiore Einstein Cancer Center, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Chanin 628, Bronx, NY, 10461, USA
| | - James J Lee
- UPMC Hillman Cancer Center, Pittsburgh, USA
- Division of Hematology-Oncology, Department of Medicine, School of Medicine, University of Pittsburgh, UPMC Cancer Pavilion, 5150 Centre Avenue, Room 463, Pittsburgh, PA, 15232, USA
- Hillman Cancer Center Cancer Therapeutics Program, Pittsburgh, USA
| | - Anuradha Krishnamurthy
- UPMC Hillman Cancer Center, Pittsburgh, USA
- Division of Hematology-Oncology, Department of Medicine, School of Medicine, University of Pittsburgh, UPMC Cancer Pavilion, 5150 Centre Avenue, Room 463, Pittsburgh, PA, 15232, USA
- Hillman Cancer Center Cancer Therapeutics Program, Pittsburgh, USA
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13
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Li H, Yang W, Zhang M, He T, Zhou F, G Herman J, Hu L, Guo M. Methylation of TMEM176A, a key ERK signaling regulator, is a novel synthetic lethality marker of ATM inhibitors in human lung cancer. Epigenomics 2021; 13:1403-1419. [PMID: 34558311 DOI: 10.2217/epi-2021-0217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aim: The role of TMEM176A methylation in lung cancer and its therapeutic application remains unclear. Materials and methods: Nine lung cancer cell lines and 123 cases of cancer tissue samples were employed. Results: TMEM176A was methylated in 53.66% of primary lung cancer. Restoration of TMEM176A expression induced cell apoptosis and G2/M phase arrest, and inhibited colony formation, cell proliferation, migration and invasion. TMEM176A suppressed H1299 cell xenograft growth in mice. Methylation of TMEM176A activated ERK signaling and sensitized H1299 and H23 cells to AZD0156, an ATM inhibitor. Conclusion: The expression of TMEM176A is regulated by promoter region methylation. Methylation of TMEM176A is a potential lung cancer diagnostic marker and a novel synthetic lethal therapeutic marker for AZD0156.
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Affiliation(s)
- Hongxia Li
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.,Faculty of Environmental & Life Science, Beijing Key Laboratory of Environmental & Oncology, Beijing University of Technology, Beijing, 100124, China
| | - Weili Yang
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Meiying Zhang
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Tao He
- Department of Pathology, Characteristic Medical Center of The Chinese People's Armed Police Force, Tianjin, 300162, China
| | - Fuyou Zhou
- Department of Thoracic Surgery, Anyang Tumor Hospital, Anyang, 455000, Henan, China
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Suite 2.18/Research, Pittsburgh, PA 15213, USA
| | - Liming Hu
- Faculty of Environmental & Life Science, Beijing Key Laboratory of Environmental & Oncology, Beijing University of Technology, Beijing, 100124, China
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.,Henan Key Laboratory for Esophageal Cancer Research, Zhengzhou University, 40 Daxue Road, Zhengzhou, Henan, 450052, China.,State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853, China
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14
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Du W, Gao A, Herman JG, Wang L, Zhang L, Jiao S, Guo M. Methylation of NRN1 is a novel synthetic lethal marker of PI3K-Akt-mTOR and ATR inhibitors in esophageal cancer. Cancer Sci 2021; 112:2870-2883. [PMID: 33931924 PMCID: PMC8253287 DOI: 10.1111/cas.14917] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/03/2021] [Accepted: 04/13/2021] [Indexed: 12/17/2022] Open
Abstract
Wnt, PI3K-Akt-mTOR, and NF-κB pathways were reported to be involved in DNA damage repair (DDR). DDR-deficient cancers become critically dependent on backup DNA repair pathways. Neuritin 1 (NRN1) is reported to be involved in PI3K-Akt-mTOR, and its role in DDR remains unclear. Methylation-specific PCR, siRNA, flow cytometry, esophageal cancer cell lines, and xenograft mouse models were used to examine the role of NRN1 in esophageal cancer. The expression of NRN1 is frequently repressed by promoter region methylation in human esophageal cancer cells. NRN1 was methylated in 50.4% (510/1012) of primary esophageal cancer samples. NRN1 methylation is associated significantly with age (P < .001), tumor size (P < .01), TNM stage (P < .001), differentiation (P < .001) and alcohol consumption (P < .05). We found that NRN1 methylation is an independent prognostic factor for poor 5-y overall survival (P < .001). NRN1 inhibits colony formation, cell proliferation, migration, and invasion, and induces apoptosis and G1/S arrest in esophageal cancer cells. NRN1 suppresses KYSE150 and KYSE30 cells xenografts growth in nude mice. PI3K signaling is reported to activate ATR signaling by targeting CHK1, the downstream component of ATR. By analyzing the synthetic efficiency of NVP-BEZ235 (PI3K inhibitor) and VE-822 (an ATR inhibitor), we found that the combination of NVP-BEZ235 and VE-822 increased cytotoxicity in NRN1 methylated esophageal cancer cells, as well as KYSE150 cell xenografts. In conclusion, NRN1 suppresses esophageal cancer growth both in vitro and in vivo by inhibiting PI3K-Akt-mTOR signaling. Methylation of NRN1 is a novel synthetic lethal marker for PI3K-Akt-mTOR and ATR inhibitors in human esophageal cancer.
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Affiliation(s)
- Wushuang Du
- Department of OncologyChinese PLA General HospitalBeijingChina
- Department of Gastroenterology & HepatologyChinese PLA General HospitalBeijingChina
| | - Aiai Gao
- Department of Gastroenterology & HepatologyChinese PLA General HospitalBeijingChina
| | - James G. Herman
- UPMC Hillman Cancer CenterUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Lidong Wang
- Henan Key Laboratory for Esophageal Cancer ResearchZhengzhou UniversityZhengzhouChina
| | - Lirong Zhang
- Henan Key Laboratory for Esophageal Cancer ResearchZhengzhou UniversityZhengzhouChina
| | - Shunchang Jiao
- Department of OncologyChinese PLA General HospitalBeijingChina
- Beijing Key Laboratory of Cell Engineering & AntibodyBeijingChina
| | - Mingzhou Guo
- Department of Gastroenterology & HepatologyChinese PLA General HospitalBeijingChina
- Henan Key Laboratory for Esophageal Cancer ResearchZhengzhou UniversityZhengzhouChina
- State Key Laboratory of Kidney DiseasesChinese PLA General HospitalBeijingChina
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15
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Rademakers G, Massen M, Koch A, Draht MX, Buekers N, Wouters KAD, Vaes N, De Meyer T, Carvalho B, Meijer GA, Herman JG, Smits KM, van Engeland M, Melotte V. Identification of DNA methylation markers for early detection of CRC indicates a role for nervous system-related genes in CRC. Clin Epigenetics 2021; 13:80. [PMID: 33858496 PMCID: PMC8048074 DOI: 10.1186/s13148-021-01067-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/04/2021] [Indexed: 12/17/2022] Open
Abstract
Purpose Colonoscopy and the fecal immunochemical test (FIT) are currently the most widely used screening modalities for colorectal cancer (CRC), however, both with their own limitations. Here we aim to identify and validate stool-based DNA methylation markers for the early detection of CRC and investigate the biological pathways prone to DNA methylation. Methods DNA methylation marker discovery was performed using The Cancer Genome Atlas (TCGA) colon adenocarcinoma data set consisting of normal and primary colon adenocarcinoma tissue. The performance of the five best candidate markers and a previously identified marker, NDRG4, was evaluated on tissues and whole stool samples of healthy subjects and CRC patients using quantitative MSP assays. The results were compared and combined with FIT data. Finally, pathway and gene ontology enrichment analyses were performed using ToppFun, GOrilla and clusterProfiler. Results GDNF, HAND2, SLC35F3, SNAP91 and SORCS1 were ranked as the best performing markers. Gene combinations of all five markers, NDRG4 and FIT were evaluated to establish the biomarker panel with the highest diagnostic potential, resulting in the identification of GDNF/SNAP91/NDRG4/FIT as the best performing marker panel. Pathway and gene ontology enrichment analyses revealed that genes associated with the nervous system were enriched in the set of best performing CRC-specific biomarkers. Conclusion In silico discovery analysis using TCGA-derived data yielded a novel DNA-methylation-based assay for the early detection of CRC, potentially improving current screening modalities. Additionally, nervous system-related pathways were enriched in the identified genes, indicating an epigenetic regulation of neuronal genes in CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01067-9.
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Affiliation(s)
- Glenn Rademakers
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Maartje Massen
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Alexander Koch
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Muriel X Draht
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Nikkie Buekers
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Kim A D Wouters
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Nathalie Vaes
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Beatriz Carvalho
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Kim M Smits
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Veerle Melotte
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands. .,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.
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16
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Baretti M, Karunasena E, Zahurak M, Walker R, Zhao Y, Pisanic TR, Wang TH, Greten TF, Duffy AG, Gootjes E, Meijer G, Verheul HMW, Ahuja N, Herman JG, Azad NS. A phase 2 trial of gemcitabine and docetaxel in patients with metastatic colorectal adenocarcinoma with methylated checkpoint with forkhead and ring finger domain promoter and/or microsatellite instability phenotype. Clin Transl Sci 2021; 14:954-963. [PMID: 33811727 PMCID: PMC8212722 DOI: 10.1111/cts.12960] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/17/2020] [Accepted: 11/22/2020] [Indexed: 12/13/2022] Open
Abstract
Abstract We previously reported CHFR methylation in a subset of colorectal cancer (CRC; ∼30%) with high concordance with microsatellite instability (MSI). We also showed that CHFR methylation predicted for sensitivity to docetaxel, whereas the MSI‐high phenotypes were sensitive to gemcitabine. We hypothesized that this subset of patients with CRC would be selectively sensitive to gemcitabine and docetaxel. We enrolled a Phase 2 trial of gemcitabine and docetaxel in patients with MSI‐high and/or CHFR methylated CRC. The primary objective was Response Evaluation Criteria in Solid Tumors (RECIST) 1.1 response rate. Enrolled patients were treated with gemcitabine 800 mg/m2 on days 1 and 8 and docetaxel 70 mg/m2 on day 8 of each 21‐day cycle. A total of 6 patients with CHFR‐methylated, MSI‐high CRC were enrolled from September 2012 to August 2016. The study was closed in September of 2017 due to poor accrual prior to reaching the first interim assessment of response rate, which would have occurred at 10 patients. No RECIST criteria tumor responses were observed, with 3 patients (50%) having stable disease as best response, 1 lasting more than 9 months. Median progression‐free survival (PFS) was 1.79 months (95% confidence interval [CI] = 1.28, not available [NA]) and median overall survival (OS) was 15.67 months (95% CI = 4.24, NA). Common grade 3 toxicities were lymphopenia (67%), leukopenia (33%), and anemia (33%). Although negative, this study establishes a proof‐of‐concept for the implementation of epigenetic biomarkers (CHFR methylation/MSI) as inclusion criteria in a prospective clinical trial to optimize combinatorial strategies in the era of personalized medicine. Study Highlights WHAT IS THE CURRENT KNOWLEDGE ON THE TOPIC?
CHFR silencing via DNA methylation has been suggested to be predictive of taxane sensitivity in diverse tumors. The frequent association of CHFR methylation with microsatellite instability (MSI) suggested a possible combination therapy with gemcitabine, because the MSI phenotype may result in sensitivity to nucleoside analogues.
WHAT QUESTION DID THIS STUDY ADDRESS?
We hypothesized that metastatic colorectal cancer (mCRC), which have CHFR methylation and MSI phenotype were sensitive to gemcitabine and docetaxel, and have designed this Phase 2 trial in biomarker‐selected mCRC to test this prediction.
WHAT DOES THIS STUDY ADD TO OUR KNOWLEDGE?
The study enrolled a molecularly defined subgroup of patients with colorectal cancer (CRC) and showed that the combination is safe in this population. Nevertheless, due to poor enrollment and early termination, no conclusions on the primary and secondary end points could be made.
HOW MIGHT THIS CHANGE CLINICAL PHARMACOLOGY OR TRANSLATIONAL SCIENCE?
This study supports the feasibility of implementing DNA methylation markers in a prospective clinical trial and further efforts toward their application as predictive biomarkers for therapeutic agents in defined subsets of patients are warranted.
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Affiliation(s)
- Marina Baretti
- Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Enusha Karunasena
- Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Marianna Zahurak
- Department of Oncology, Biostatistics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rosalind Walker
- Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Yang Zhao
- Johns Hopkins Institute for NanoBioTechnology, Baltimore, Maryland, USA
| | - Thomas R Pisanic
- Johns Hopkins Institute for NanoBioTechnology, Baltimore, Maryland, USA
| | - Tza-Huei Wang
- Johns Hopkins Institute for NanoBioTechnology, Baltimore, Maryland, USA
| | - Tim F Greten
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Austin G Duffy
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Elske Gootjes
- Amsterdam University Medical Center, location VUMC, Amsterdam and Radboud UMC, Nijmegen, The Netherlands
| | - Gerrit Meijer
- Amsterdam University Medical Center, location VUMC, Amsterdam and Radboud UMC, Nijmegen, The Netherlands
| | - Henk M W Verheul
- Amsterdam University Medical Center, location VUMC, Amsterdam and Radboud UMC, Nijmegen, The Netherlands
| | - Nita Ahuja
- Oncology and Pathology, Smilow Cancer Hospital, Yale University School of Medicine, New Haven, Connecticut, USA
| | - James G Herman
- Department of Medicine, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Nilofer S Azad
- Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
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17
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Abstract
The contribution of DNA-methylation based gene silencing to carcinogenesis is well established. Increasingly, DNA-methylation is examined using genome-wide techniques, with recent public efforts yielding immense data sets of diverse malignancies representing the vast majority of human cancer related disease burden. Whereas mutation events may group preferentially or in high frequency with a given histology, mutations are poor classifiers of tumour type. Here we examine the hypothesis that cancer-specific DNA-methylation reflects the tissue of origin or carcinogenic risk factor, and these methylation abnormalities may be used to faithfully classify tumours according to histology. We present an analysis of 7427 tumours representing 19 human malignancies and 708 normal samples demonstrating that specific tumour changes in methylation can correctly determine site of origin and tumour histology with 86% overall accuracy. Examination of misclassified tumours reveals underlying shared biology as the source of misclassifications, including common cell of origin or risk factors.
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Affiliation(s)
- Ludmila Danilova
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Laboratory of System Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - John Wrangle
- Hollings Cancer Center, Department of Medicine, The Medical University of South Carolina, Charleston, SC, USA
| | - James G Herman
- UPMC Hillman Cancer Center, Department of Medicine, The University of Pittsburgh, Pittsburgh, PA, USA
| | - Leslie Cope
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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18
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Farooq M, Herman JG. Noninvasive Diagnostics for Early Detection of Lung Cancer: Challenges and Potential with a Focus on Changes in DNA Methylation. Cancer Epidemiol Biomarkers Prev 2020; 29:2416-2422. [PMID: 33148791 DOI: 10.1158/1055-9965.epi-20-0704] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/20/2020] [Accepted: 10/13/2020] [Indexed: 11/16/2022] Open
Abstract
Lung cancer remains the leading cause of cancer deaths in the United States and the world. Early detection of this disease can reduce mortality, as demonstrated for low-dose computed tomography (LDCT) screening. However, there remains a need for improvements in lung cancer detection to complement LDCT screening and to increase adoption of screening. Molecular changes in the tumor, and the patient's response to the presence of the tumor, have been examined as potential biomarkers for diagnosing lung cancer. There are significant challenges to developing an effective biomarker with sufficient sensitivity and specificity for the early detection of lung cancer, particularly the detection of circulating tumor DNA, which is present in very small quantities. We will review approaches to develop biomarkers for the early detection of lung cancer, with special consideration to detection of rare tumor events, focus on the use of DNA methylation-based detection in plasma and sputum, and discuss the promise and challenges of lung cancer early detection. Plasma-based detection of lung cancer DNA methylation may provide a simple cost-effective method for the early detection of lung cancer.See all articles in this CEBP Focus section, "NCI Early Detection Research Network: Making Cancer Detection Possible."
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Affiliation(s)
- Maria Farooq
- Department of Medicine, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - James G Herman
- Department of Medicine, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania. .,UPMC Hillman Comprehensive Cancer Center, Pittsburgh, Pennsylvania
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19
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Liu B, Ricarte Filho J, Mallisetty A, Villani C, Kottorou A, Rodgers K, Chen C, Ito T, Holmes K, Gastala N, Valyi-Nagy K, David O, Gaba RC, Ascoli C, Pasquinelli M, Feldman LE, Massad MG, Wang TH, Jusue-Torres I, Benedetti E, Winn RA, Brock MV, Herman JG, Hulbert A. Detection of Promoter DNA Methylation in Urine and Plasma Aids the Detection of Non-Small Cell Lung Cancer. Clin Cancer Res 2020; 26:4339-4348. [PMID: 32430478 PMCID: PMC7442601 DOI: 10.1158/1078-0432.ccr-19-2896] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/16/2020] [Accepted: 05/14/2020] [Indexed: 12/15/2022]
Abstract
PURPOSE Low-dose CT screening can reduce lung cancer-related mortality. However, CT screening has an FDR of nearly 96%. We sought to assess whether urine samples can be a source for DNA methylation-based detection of non-small cell lung cancer (NSCLC). EXPERIMENTAL DESIGN This nested case-control study of subjects with suspicious nodules on CT imaging obtained plasma and urine samples preoperatively. Cases (n = 74) had pathologic confirmation of NSCLC. Controls (n = 27) had a noncancer diagnosis. We detected promoter methylation in plasma and urine samples using methylation on beads and quantitative methylation-specific real-time PCR for cancer-specific genes (CDO1, TAC1, HOXA7, HOXA9, SOX17, and ZFP42). RESULTS DNA methylation at cancer-specific loci was detected in both plasma and urine, and was more frequent in patients with cancer compared with controls for all six genes in plasma and in CDO1, TAC1, HOXA9, and SOX17 in urine. Univariate and multivariate logistic regression analysis showed that methylation detection in each one of six genes in plasma and CDO1, TAC1, HOXA9, and SOX17 in urine were significantly associated with the diagnosis of NSCLC, independent of age, race, and smoking pack-years. When methylation was detected for three or more genes in both plasma and urine, the sensitivity and specificity for lung cancer diagnosis were 73% and 92%, respectively. CONCLUSIONS DNA methylation-based biomarkers in plasma and urine could be useful as an adjunct to CT screening to guide decision-making regarding further invasive procedures in patients with pulmonary nodules.
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Affiliation(s)
- Bin Liu
- Cancer Center, University of Illinois at Chicago, Chicago, Illinois
| | | | - Apurva Mallisetty
- Department of Surgery, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Cassandra Villani
- Department of Surgery, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Anastasia Kottorou
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Clinical and Molecular Oncology Laboratory, Medical School, University of Patras, Patras, Greece
| | - Kristen Rodgers
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Chen Chen
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - Tomoaki Ito
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Surgery, Juntendo University Shizuoka Hospital, Juntendo University School of Medicine, Shizuoka, Japan
| | - Kyla Holmes
- Cancer Center, University of Illinois at Chicago, Chicago, Illinois
| | - Nicole Gastala
- Department of Family Medicine, Mile Square Health Center, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Klara Valyi-Nagy
- Department of Pathology, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Odile David
- Department of Pathology, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Ron C Gaba
- Department of Radiology, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Christian Ascoli
- Department of Pulmonary, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Mary Pasquinelli
- Department of Pulmonary, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Lawrence E Feldman
- Department of Hematology and Oncology, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Malek G Massad
- Department of Surgery, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Tza-Huei Wang
- Department of Biomedical Engineering and Institute for Nano Biotechnology, The Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Ignacio Jusue-Torres
- Department of Neurological Surgery, Loyola University Stritch School of Medicine, Maywood, Illinois
| | - Enrico Benedetti
- Department of Surgery, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Robert A Winn
- Cancer Center, University of Illinois at Chicago, Chicago, Illinois
- Department of Pulmonary, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Malcolm V Brock
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Cancer Center, Department of Oncology, The Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - James G Herman
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.
| | - Alicia Hulbert
- Cancer Center, University of Illinois at Chicago, Chicago, Illinois.
- Department of Surgery, University of Illinois at Chicago College of Medicine, Chicago, Illinois
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20
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Lommen K, Feng Z, Oberije CJ, van de Wetering AJP, Odeh S, Koch A, Aarts MJB, van Roermund JG, Schouten LJ, Oosterwijk E, Vaes N, Masclee AAM, Carvalho B, Meijer GA, Zeegers MP, Herman JG, Tjan-Heijnen VC, Melotte V, van Engeland M, Smits K. Abstract A62: Clinical translation of liquid biopsy DNA methylation biomarkers: Lessons from two systematic reviews. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.liqbiop20-a62] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Very few (<0.1%) of DNA methylation biomarkers are eventually translated into clinical practice, even though over 5,000 have been published over the last decades. In an attempt to create an overview of the current evidence on these markers, we performed two systematic reviews on diagnostic DNA methylation biomarkers in liquid biopsies, for colorectal cancer (CRC) and renal cell carcinoma (RCC) (1). Here, we present the evidence of these systematic reviews and provide novel recommendations to improve the current clinical translation of DNA methylation biomarkers.
Methods: For CRC, we identified 109 bodily fluid biomarker studies published before January 2019 in PubMed, Embase, Cochrane Library, or Google Scholar. For RCC, we identified 6 liquid biopsy studies up to January 2019 in these databases. Data extraction (study design, patient characteristics, disease stage, tumor location, technical assays, diagnostic measures) was performed on published reports. STARD criteria and Level of Evidence (LoE) were registered to assess reporting quality and strength for clinical translation, and forest plots were generated to summarize diagnostic performance of the biomarkers.
Findings: Our systematic literature search revealed multiple issues that hamper the development of DNA methylation biomarkers for RCC and CRC diagnosis, including methodologic and technical heterogeneity and lack of validation or clinical translation. Among the most important issues were a lack of translation from tissue into liquid biopsy; for CRC 88/389 (23%) CRC markers were studied in liquid biopsies, and for RCC these numbers were 15/44 (34%). In addition, results showed a lack of independent validation, with 37/88 (42%) CRC markers and 9/15 (60%) RCC markers in liquid biopsies studied in more than one study or study population. Also, inappropriate marker identification and primer design, lack of true clinical need definition, and low reporting quality were issues that were recognized in our systematic literature searches. These issues all hamper the development of the field, keep the LoE low, and hinder the translation of DNA methylation biomarkers into clinical tests.
Interpretation: Our systematic literature searches revealed that major requirements to develop clinically relevant diagnostic DNA methylation markers are often lacking. To avoid the resulting research waste, clinical needs, intended biomarker use, and independent validation should be better considered prior to study design. In addition, improved reporting quality would facilitate meta-analysis, thereby increasing LoE and enabling clinical translation.
Reference: 1. Lommen et al. Eur Urol Oncol 2019; https://doi.org/10.1016/j.euo.2019.07.011.
Citation Format: Kim Lommen, Zheng Feng, Cary J.G. Oberije, Alouisa J. P. van de Wetering, Selena Odeh, Alexander Koch, Maureen J. B. Aarts, Joep G. van Roermund, Leo J. Schouten, Egbert Oosterwijk, Nathalie Vaes, Ad A. M. Masclee, Beatriz Carvalho, Gerrit A. Meijer, Maurice P. Zeegers, James G. Herman, Vivianne C. Tjan-Heijnen, Veerle Melotte, Manon van Engeland, Kim Smits. Clinical translation of liquid biopsy DNA methylation biomarkers: Lessons from two systematic reviews [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A62.
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Affiliation(s)
- Kim Lommen
- 1Department of Pathology, GROW—School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands,
| | - Zheng Feng
- 1Department of Pathology, GROW—School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands,
| | - Cary J.G. Oberije
- 2Department of Pathology & Department of Precision Medicine, GROW—School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands,
| | - Alouisa J. P. van de Wetering
- 3Division of Gastroenterology and Hepatology, Department of Internal Medicine, GROW—School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands,
| | - Selena Odeh
- 1Department of Pathology, GROW—School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands,
| | - Alexander Koch
- 1Department of Pathology, GROW—School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands,
| | - Maureen J. B. Aarts
- 4Department of Medical Oncology, GROW—School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands,
| | - Joep G. van Roermund
- 5Department of Urology, GROW—School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands,
| | - Leo J. Schouten
- 6Department of Epidemiology, GROW—School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands,
| | - Egbert Oosterwijk
- 7Department of Urology, Radboud University Medical Center, Nijmegen, the Netherlands,
| | - Nathalie Vaes
- 1Department of Pathology, GROW—School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands,
| | - Ad A. M. Masclee
- 8Division of Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, the Netherlands,
| | - Beatriz Carvalho
- 9Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands,
| | - Gerrit A. Meijer
- 9Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands,
| | - Maurice P. Zeegers
- 10Department of Complex Genetics, NUTRIM School of Nutrition and Translational Research in Metabolism & CAPHRI – Care and Public Health Research Institute, Maastricht University Medical Center, Maastricht, the Netherlands,
| | - James G. Herman
- 11Division of Hematology/Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, PA
| | - Vivianne C. Tjan-Heijnen
- 4Department of Medical Oncology, GROW—School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands,
| | - Veerle Melotte
- 1Department of Pathology, GROW—School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands,
| | - Manon van Engeland
- 1Department of Pathology, GROW—School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands,
| | - Kim Smits
- 1Department of Pathology, GROW—School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands,
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Hu L, Zhou F, Li H, Herman JG, Hu L, Guo M, He T. Epigenetic Silencing of TMEM176A Activates ERK Signaling in Human Lung Cancer. J Surg Oncol 2020. [DOI: 10.31487/j.jso.2020.02.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Background: The function of TMEM176A in human lung cancer remains to be elucidated.
Materials & Methods: Nine cell lines and 123 cases of lung cancers were employed.
Results: TMEM176A was highly expressed in H727 cells, reduced expression was observed in A549, H446
and H460 cells, loss of expression was found in H157, H1563, H358, H1299 and H23 cells. TMEM176A
was unmethylated in H727 cells, partially methylated in A549, H446 and H460 cells, and fully methylated
in H157, H1563, H358, H1299 and H23 cells. Loss of/reduced expression of TMEM176A is correlated to
promoter region methylation. Restoration of TMEM176A expression was induced by 5-AZA-2-
deoxycytidine in complete methylated cells, increased expression of TMEM176A was observed in partially
methylated cells. These results suggest that TMEM176A is regulated by promoter region methylation in
lung cancer cells. TMEM176A was methylated in 53.66% (66/123) of non-small cell lung cancers
(NSCLCs) samples. Reduced expression of TMEM176A was associated with promoter region methylation
in 40 cases of matched primary NSCLCs and adjacent tissue samples (P<0.05). TMEM176A expression
induced cell apoptosis, inhibited colony formation, cell proliferation, migration and invasion.
Conclusion: Methylation of TMEM176A activated ERK signaling in lung cancer cells. TMEM176A
suppressed human lung cancer cell xenograft growth in mice.
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22
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Chen C, Huang X, Yin W, Peng M, Wu F, Wu X, Tang J, Chen M, Wang X, Hulbert A, Brock MV, Liu W, Herman JG, Yu F. Ultrasensitive DNA hypermethylation detection using plasma for early detection of NSCLC: a study in Chinese patients with very small nodules. Clin Epigenetics 2020; 12:39. [PMID: 32138766 PMCID: PMC7057485 DOI: 10.1186/s13148-020-00828-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/11/2020] [Indexed: 12/18/2022] Open
Abstract
PURPOSE We had previously developed highly sensitive DNA methylation detection to diagnose lung cancer in patients with pulmonary nodules. To validate this approach and determine clinical utility in Chinese patients with indeterminate pulmonary nodules, we assessed the diagnostic accuracy for early stage lung cancer in plasma samples. EXPERIMENTAL DESIGN Patients with CT-detected small lung nodules (diameter ≤ 3.0 cm) were included. Cases (n = 163) had staged IA or IB non-small cell lung cancer (NSCLC), while controls (n = 83) had non-cancerous lesions. Promoter methylation of eight lung cancer-specific genes (CDO1, TAC1, SOX17, HOXA7, HOXA9, GATA4, GATA5, and PAX5) was detected using nanoparticle-based DNA extraction (MOB) followed by qMSP. RESULTS Methylation detection for CDO1, TAC1, SOX17, and HOXA7 in plasma was significantly higher in cases compared with the benign group (p < 0.001). The sensitivity and specificity for lung cancer diagnosis using individual gene was 41-69% and 49-82%. A three-gene combination of the best individual genes has sensitivity and specificity of 90% and 71%, with area under the receiver operating curve (AUC) of 0.88, (95% CI 0.84-0.93). Furthermore, three-gene combinations detected even the smallest lung nodules, with the combination of CDO1, SOX17, and HOXA7 having the overall best performance, while the combination of CDO1, TAC1, and SOX17 was best in tumor sizes less than 1.0 cm. CONCLUSIONS Using modified MOB-qMSP, high sensitivity and specificity, for the detection of circulating tumor DNA was obtained for early stage NSCLC. This strategy has great potential to identify patients at high risk and improve the diagnosis of lung cancer at an earlier stage.
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Affiliation(s)
- Chen Chen
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Xiaojie Huang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Wei Yin
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Muyun Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Fang Wu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Xia Wu
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Jingqun Tang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Mingjiu Chen
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Xiang Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Alicia Hulbert
- Department of Surgery, University of Illinois at Chicago School of Medicine, Chicago, IL, USA
| | - Malcolm V Brock
- Department of Surgery, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Wenliang Liu
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China.
| | - James G Herman
- UPMC Hillman Cancer Center, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Fenglei Yu
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China.
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23
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Abstract
Phenotypic and functional heterogeneity is one of the hallmarks of human cancers. Tumor genotype variations among tumors within different patients are known as interpatient heterogeneity, and variability among multiple tumors of the same type arising in the same patient is referred to as intra-patient heterogeneity. Subpopulations of cancer cells with distinct phenotypic and molecular features within a tumor are called intratumor heterogeneity (ITH). Since Nowell proposed the clonal evolution of tumor cell populations in 1976, tumor heterogeneity, especially ITH, was actively studied. Research has focused on the genetic basis of cancer, particularly mutational activation of oncogenes or inactivation of tumor-suppressor genes (TSGs). The phenomenon of ITH is commonly explained by Darwinian-like clonal evolution of a single tumor. Despite the monoclonal origin of most cancers, new clones arise during tumor progression due to the continuous acquisition of mutations. It is clear that disruption of the "epigenetic machinery" plays an important role in cancer development. Aberrant epigenetic changes occur more frequently than gene mutations in human cancers. The epigenome is at the intersection of the environment and genome. Epigenetic dysregulation occurs in the earliest stage of cancer. The current trend of epigenetic therapy is to use epigenetic drugs to reverse and/or delay future resistance to cancer therapies. A majority of cancer therapies fail to achieve durable responses, which is often attributed to ITH. Epigenetic therapy may reverse drug resistance in heterogeneous cancer. Complete understanding of genetic and epigenetic heterogeneity may assist in designing combinations of targeted therapies based on molecular information extracted from individual tumors.
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Affiliation(s)
- Mingzhou Guo
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, 40 Daxue Road, Zhengzhou, Henan 450052 China
| | - Yaojun Peng
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Aiai Gao
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Chen Du
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - James G Herman
- 3The Hillman Cancer Center, University of Pittsburgh Cancer Institute, 5117 Centre Ave., Pittsburgh, PA 15213 USA
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24
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Sen M, Kindsfather A, Danilova L, Zhang F, Colombo R, LaPorte MG, Kurland BF, Huryn DM, Wipf P, Herman JG. PTPRT epigenetic silencing defines lung cancer with STAT3 activation and can direct STAT3 targeted therapies. Epigenetics 2019; 15:604-617. [PMID: 31595832 DOI: 10.1080/15592294.2019.1676597] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Signal Transducers and Activators of Transcription-3 (STAT3), a potent oncogenic transcription factor, is constitutively activated in lung cancer, but mutations in pathway genes are infrequent. Protein Tyrosine Phosphatase Receptor-T (PTPRT) is an endogenous inhibitor of STAT3 and PTPRT loss-of-function represents one potential mechanism of STAT3 hyperactivation as observed in other malignancies. We determined the role of PTPRT promoter methylation and sensitivity to STAT3 pathway inhibitors in non-small cell lung cancer (NSCLC). TCGA and Pittsburgh lung cancer cohort methylation data revealed hypermethylation of PTPRT associated with diminished mRNA expression in a subset of NSCLC patients. We report frequent hypermethylation of the PTPRT promoter which correlates with transcriptional silencing of PTPRT and increased STAT3 phosphorylation (Y705) as determined by methylation-specific PCR (MSP) and real time quantitative reverse transcription (RT)-PCR in NSCLC cell lines. Silencing of PTPRT using siRNA in H520 lung cancer cell line resulted in increased pSTAT3Tyr705 and upregulation of STAT3 target genes such as Cyclin D1 and Bcl-XL expression. We show this association of PRPRT methylation with upregulation of the STAT3 target genes Cyclin D1 and Bcl-XL in patient derived lung tumour samples. We further demonstrate that PTPRT promoter methylation associated with different levels of pSTAT3Ty705 in lung cancer cell lines had selective sensitivity to STAT3 pathway small molecule inhibitors (SID 864,669 and SID 4,248,543). Our data strongly suggest that silencing of PTPRT by promoter hypermethylation is an important mechanism of STAT3 hyperactivation and targeting STAT3 may be an effective approach for the development of new lung cancer therapeutics.
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Affiliation(s)
- Malabika Sen
- Department of Hematology/Oncology, UPMC Hillman Cancer Center , Pittsburgh, PA, USA
| | - Audrey Kindsfather
- Department of Hematology/Oncology, UPMC Hillman Cancer Center , Pittsburgh, PA, USA
| | - Ludmila Danilova
- Department of Oncology, Laboratory of Systems Biology and Computational Genetics, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, MD, USA.,Vavilov Institute of General Genetics, Russian Academy of Sciences , Moscow, Russia
| | - Feng Zhang
- Chemical Diversity Center, University of Pittsburgh , Pittsburgh, PA, USA
| | - Raffaele Colombo
- Chemical Diversity Center, University of Pittsburgh , Pittsburgh, PA, USA
| | - Matthew G LaPorte
- Chemical Diversity Center, University of Pittsburgh , Pittsburgh, PA, USA
| | - Brenda F Kurland
- Department of Biostatistics, University of Pittsburgh , Pittsburgh, PA, USA
| | - Donna M Huryn
- Chemical Diversity Center, University of Pittsburgh , Pittsburgh, PA, USA
| | - Peter Wipf
- Chemical Diversity Center, University of Pittsburgh , Pittsburgh, PA, USA
| | - James G Herman
- Department of Hematology/Oncology, UPMC Hillman Cancer Center , Pittsburgh, PA, USA
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25
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Robins HI, Eickhoff J, Gilbert MR, Armstrong TS, Shi W, De Groot JF, Schultz CJ, Hunter GK, Valeinis E, Roach M, Youssef EF, Souhami L, Howard SP, Lieberman FS, Herman JG, Zhang P, Mehta MP. The association between BMI and BSA-temozolomide-induced myelosuppression toxicities: a correlative analysis of NRG oncology RTOG 0525. Neurooncol Pract 2019; 6:473-478. [PMID: 31832217 DOI: 10.1093/nop/npz006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Fearing increased myelotoxicity, many practitioners adjust the body surface area (BSA)-calculated doses in obese patients. Regarding temozolomide (TMZ), a prior study suggested men with a BSA >2 m2 may experience increased toxicity; however, surprisingly, the inverse observation was noted in women, ie, BSA <2 m2 was associated with higher toxicity. To further clarify this issue, data derived from a large clinical trial were analyzed. Methods The incidence of grade 3 and 4 myelotoxicity in a newly diagnosed glioblastoma phase 3 trial (RTOG 0525) was statistically correlated with BMI and separately with BSA. All patients received radiation and TMZ followed by adjuvant standard dose TMZ vs dose-dense TMZ; dosing regimen-associated myelotoxicity and BMI/BSA were analyzed separately. Obesity was defined as a BMI ≥30. Results There was no statistically significant correlation between gender and BSA and the occurrence of myotoxicities. For the standard arm, surprisingly the incidence of grade 3/4 myotoxicities in patients with a BMI <30 was significantly higher than in patients with a BMI ≥30 (12% vs 1%, odds ratio [OR] 12.5, P < .001). There was no significant difference between obese and nonobese patients (BMI "cut-point" of 30) in the dose-dense arm (OR = 0.9, 95% confidence interval: 0.4-1.6). The grade hematological 3/4 toxicity rate was significantly higher in women vs men (14% vs 8%) P = .009 in spite of the lack of association between gender and BSA or BMI. Conclusion TMZ dosing based on actual BSA is recommended with the caveat that woman are likely at higher toxicity risk.
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Affiliation(s)
- H Ian Robins
- University of Wisconsin Hospital and Clinics, Madison
| | - Jens Eickhoff
- University of Wisconsin Hospital and Clinics, Madison
| | - Mark R Gilbert
- National Institutes of Health Clinical Center Neuro-Oncology Branch, Bethesda, MD
| | | | - Wenyin Shi
- Thomas Jefferson University Hospital, Philadelphia, PA
| | | | | | | | - Egils Valeinis
- Pauls Stradiņš Clinical University Hospital, Riga, Latvia
| | - Mack Roach
- University of California San Francisco Medical Center-Mount Zion
| | | | - Luis Souhami
- McGill University Health Centre, Montreal, Québec, Canada
| | | | | | | | - Peixin Zhang
- NRG Oncology Statistics and Data Management Center, Philadelphia, PA
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26
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Poh W, Dilley RL, Moliterno AR, Maciejewski JP, Pratz KW, McDevitt MA, Herman JG. BRCA1 Promoter Methylation Is Linked to Defective Homologous Recombination Repair and Elevated miR-155 to Disrupt Myeloid Differentiation in Myeloid Malignancies. Clin Cancer Res 2019; 25:2513-2522. [PMID: 30692098 DOI: 10.1158/1078-0432.ccr-18-0179] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 10/04/2018] [Accepted: 01/16/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Defective homologous recombination (HR) has been reported in multiple myeloid disorders, suggesting a shared dysregulated pathway in these diverse malignancies. Because targeting HR-defective cancers with PARP inhibition (PARPi) has yielded clinical benefit, improved understanding of HR defects is needed to implement this treatment modality. EXPERIMENTAL DESIGN We used an ex vivo irradiation-based assay to evaluate HR repair, HR gene promoter methylation, and mRNA expression in primary myeloid neoplastic cells. In vitro BRCA1 gene silencing was achieved to determine the consequences on HR repair, sensitivity to PARPi, and expression of miR-155, an oncogenic miRNA. RESULTS Impaired HR repair was frequently detected in myeloid neoplasm samples (9/21, 43%) and was linked to promoter methylation-mediated transcriptional repression of BRCA1, which was not observed for other members of the HR pathway (BRCA2, ATM, ATR, FANC-A). In vitro BRCA1 knockdown increased sensitivity to PARP inhibition, and BRCA1 expression is inversely correlated with miR-155 expression, a finding reproduced in vitro with BRCA1 knockdown. Increased miR-155 was associated with PU.1 and SHIP1 repression, known myeloid differentiation factors that are frequently downregulated during leukemic transformation. CONCLUSIONS This study demonstrates frequent defective HR, associated with BRCA1 epigenetic silencing, in a broad range of myeloid neoplasms. The increased prevalence of BRCA1 promoter methylation, resulting in repressed BRCA1, may have an additional role in leukemogenesis by increasing miR-155 expression, which then inhibits transcription factors associated with normal myeloid differentiation. Further study of HR defects may facilitate the identification of HR-defective myeloid neoplasms sensitive to PARPi.
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Affiliation(s)
- Weijie Poh
- Graduate Program in Pathobiology, Johns Hopkins School of Medicine, Baltimore, Maryland.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Robert L Dilley
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alison R Moliterno
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jaroslaw P Maciejewski
- Translational Hematology and Oncology Research, Cleveland Clinic/Taussig Cancer Institute, Cleveland, Ohio
| | - Keith W Pratz
- Division of Hematological Malignancy, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Michael A McDevitt
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Division of Hematological Malignancy, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - James G Herman
- Graduate Program in Pathobiology, Johns Hopkins School of Medicine, Baltimore, Maryland. .,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland.,Division of Hematology/Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
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27
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O’Keefe CM, Pisanic TR, Zec H, Overman MJ, Herman JG, Wang TH. Facile profiling of molecular heterogeneity by microfluidic digital melt. Sci Adv 2018; 4:eaat6459. [PMID: 30263958 PMCID: PMC6157960 DOI: 10.1126/sciadv.aat6459] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/14/2018] [Indexed: 05/05/2023]
Abstract
This work presents a digital microfluidic platform called HYPER-Melt (high-density profiling and enumeration by melt) for highly parallelized copy-by-copy DNA molecular profiling. HYPER-Melt provides a facile means of detecting and assessing sequence variations of thousands of individual DNA molecules through digitization in a nanowell microchip array, allowing amplification and interrogation of individual template molecules by detecting HRM fluorescence changes due to sequence-dependent denaturation. As a model application, HYPER-Melt is used here for the detection and assessment of intermolecular heterogeneity of DNA methylation within the promoters of classical tumor suppressor genes. The capabilities of this platform are validated through serial dilutions of mixed epialleles, with demonstrated detection limits as low as 1 methylated variant in 2 million unmethylated templates (0.00005%) of a classic tumor suppressor gene, CDKN2A (p14ARF). The clinical potential of the platform is demonstrated using a digital assay for NDRG4, a tumor suppressor gene that is commonly methylated in colorectal cancer, in liquid biopsies of healthy and colorectal cancer patients. Overall, the platform provides the depth of information, simplicity of use, and single-molecule sensitivity necessary for rapid assessment of intermolecular variation contributing to genetic and epigenetic heterogeneity for challenging applications in embryogenesis, carcinogenesis, and rare biomarker detection.
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Affiliation(s)
- Christine M. O’Keefe
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
| | - Thomas R. Pisanic
- Johns Hopkins Institute for NanoBioTechnology, Baltimore, MD 21218, USA
| | - Helena Zec
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
| | - Michael J. Overman
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - James G. Herman
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15232, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
- Johns Hopkins Institute for NanoBioTechnology, Baltimore, MD 21218, USA
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Corresponding author.
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28
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Lerner L, Zheng L, Kottorou A, Chen C, Ito T, Rodgers K, Lee B, Winn R, Benedetti E, Wang TH, Brock MV, Herman JG, Hulbert A. Abstract 3308: Urine epigenetic biomarkers for NSCLC diagnosis. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Purpose:
The National Lung Cancer Screening Trial showed mortality reduction on patients with NSCLC by the use of Low-dose CT screening. The study exhibits an unreasonably high false positive rate of 96.6%, which can to lead to significant morbidity and mortality from unnecessary tests. This study aim to determine if methylated promoter regions of a panel of genes that are correlated with Non-Small Cell Lung Cancer can be detected in urine from patients with lung cancer versus those without.
Materials and Methods:
We conducted a prospective case-control study recruiting subjects from the Lung Cancer Spore Trial. Urine and pre-operative CT scans were obtained from all patients. We processed the urine using the Methylation on Beads assay to isolate and bisulfite treat circulating DNA and then employed Quantitative Methylation Specific Real-Time PCR to detect promoter methylation status of the genes: CDO1, TAC1, HOXA7, HOXA9, SOX17 and ZFP42. Sensitivity, specificity, PPV and NPV values were calculated for each gene methylation status.
Results:
34 patients were studied, including 23 patients with NSCLC and 11 patients with benign non-cancerous lesions. The sensitivity, specificity, PPV and NPV values for lung cancer detection in urine are shown in Table 1. Sensitivities ranged 43-96%, Specificities 64-91%, PPV 71-100% and NPV 40-67%. Promoter methylation of the gene panel CDO1, TAC1, HOXA7, HOXA9, SOX17 and ZPF42 has a 78% sensitivity, 91% specificity, 95% PPV and 67% NPV for lung cancer detection.
Conclusion:
Our study suggests that urine can provide a highly sensitive and specific non-invasive route for lung cancer detection. These results are very promising and could potentially reduce unnecessary morbidity and mortality in people undergoing screening for NSCLC by use of a non-invasive method that could be more accessible on primary care centers. However, further studies and validation with larger sample sizes and different populations are necessary before its application to clinical practice.
Patients with positive gene methylation from urine samples and its accuracy for NSCLC detection.Cancer (n=23)Cancer (n=23)Control (n=11)Control (n=11)nSensitivitynSpecificityPPVNPVCDO114611919353TAC11565010010058SOX1716704648050HOXA711483737940HOXA910431919143ZPF4222969187167Panel of genes18781919567
Citation Format: Lane Lerner, Lily Zheng, Anastasia Kottorou, Chen Chen, Tomoaki Ito, Kristen Rodgers, Beverly Lee, Robert Winn, Enrico Benedetti, Tza- Huei Wang, Malcolm V. Brock, James G. Herman, Alicia Hulbert. Urine epigenetic biomarkers for NSCLC diagnosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3308.
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Affiliation(s)
- Lane Lerner
- 1University of Illinois at Chicago, Chicago, IL
| | - Lily Zheng
- 1University of Illinois at Chicago, Chicago, IL
| | | | - Chen Chen
- 3The Second Xiangya Hospital CSU, Xiangya, China
| | - Tomoaki Ito
- 4Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Beverly Lee
- 4Johns Hopkins University School of Medicine, Baltimore, MD
| | - Robert Winn
- 1University of Illinois at Chicago, Chicago, IL
| | | | - Tza- Huei Wang
- 5Johns Hopkins Whiting School of Engineering, Baltimore, MD
| | | | - James G. Herman
- 6University of Pittsburgh School of Medicine, Pittsburgh, PA
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Koch A, Meijer GA, Herman JG, Criekinge WV, Engeland MV. Abstract 3291: The human cancer DNA methylation marker atlas. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
For decades, scientists have been searching for cancer biomarkers to improve the diagnosis and treatment of cancer. This resource-intensive and time-consuming endeavor has resulted in thousands of biomarker publications, but translation of these markers into clinical practice hardly takes place. Estimations by Poste (2011) and Kern (2012) put the number of published markers that are used in the clinic below one percent. This failure to translate biomedical findings into clinical applications has been termed the translational research valley of death (Butler, 2008).
If we are to cross this biomedical valley of death for DNA methylation markers, we have to increase the scientific quality and reproducibility of biomarker research, reduce the number of markers lost in translation, and accelerate the development of clinically useful markers. This will require a large-scale, coordinated effort from all stakeholders: scientists, funding organizations, scientific journals, private partners, and patients.
We have devised a strategy to tackle these issues and improve the reliability, efficiency and translation of cancer DNA methylation markers, while at the same time promoting data sharing. At the heart of this strategy is the construction of a database of all published markers. This marker atlas would provide researchers with a valuable resource where they can find and evaluate existing markers or, in collaboration with private partners, have a marker experimentally validated. Using the collected data, we also plan to develop a reporting standard for DNA methylation markers. The ultimate goal of our efforts is to offer cancer patients more and better biomarkers. We have summarized our approach in an article submitted to Nature Reviews Clinical Oncology for review.
While our submitted article announces our intent to create the marker atlas, we would like to present the first version of the database to the research community at AACR, together with the insights we will have gained by then and an update on our progress with the reporting standard. In our initial analyses for example, we counted over 14,000 publications describing an estimated 2,422 cancer DNA methylation markers (compared to fourteen commercially available markers (0.6%), a clinical translation rate in line with the numbers published by Poste and Kern). Based on the data collected between the submission of this abstract and the AACR conference, we will be able to improve this estimate, giving us a more accurate view of the current status of the cancer DNA methylation biomarker field.
The AACR conference would be the perfect platform to introduce the marker atlas to the wider cancer research community and to grow community support. Not only would it provide us with expert feedback and increase the number of collaborators, community-wide support will be indispensable for the longevity of what we believe to be a valuable resource. More information on the atlas can be found online at cancermatlas.com.
Citation Format: Alexander Koch, Gerrit A. Meijer, James G. Herman, Wim Van Criekinge, Manon van Engeland. The human cancer DNA methylation marker atlas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3291.
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30
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Yan W, Wu K, Herman JG, Xu X, Yang Y, Dai G, Guo M. Retinoic acid-induced 2 (RAI2) is a novel tumor suppressor, and promoter region methylation of RAI2 is a poor prognostic marker in colorectal cancer. Clin Epigenetics 2018; 10:69. [PMID: 29796120 PMCID: PMC5966878 DOI: 10.1186/s13148-018-0501-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 05/11/2018] [Indexed: 11/25/2022] Open
Abstract
Background Reduced expression of retinoic acid-induced 2 (RAI2) was found in breast cancer. The regulation and function of RAI2 in human colorectal cancer (CRC) remain unclear. Methods Eight CRC cell lines and 237 cases of primary CRC were analyzed. Methylation-specific PCR (MSP), flow cytometry, xenograft mouse model, and shRNA technique were employed. Results RAI2 was completely methylated in RKO, LOVO, and HCT116 cells; partially methylated in HT29 cells; and unmethylated in SW480, SW620, DLD1, and DKO cells. RAI2 was methylated in 53.6% (127/237) of primary colorectal cancer. Methylation of RAI2 was significantly associated with gender (P < 0.001), TNM stage (P < 0.001), and lymph node metastasis (P < 0.001). Analyzing by the Kaplan-Meier method, methylation of RAI2 was significantly associated with poor 5-year overall survival (OS) (P = 0.0035) and 5-year relapse-free survival (RFS) (P = 0.0062). According to Cox proportional hazards model analysis, RAI2 methylation was an independent poor prognostic marker for 5-year OS (P = 0.002) and poor 5-year RFS (P = 0.022). RAI2 suppressed cell proliferation, migration, and invasion and induced cell apoptosis in CRC. In addition, RAI2 inhibited AKT signaling in CRC cells and suppressed human CRC cell xenograft growth in mice. Conclusion RAI2 is frequently methylated in human CRC, and the expression of RAI2 is regulated by promoter region methylation. Methylation of RAI2 is an independent poor prognostic marker of CRC. RAI2 suppresses CRC cell growth both in vitro and in vivo. RAI2 suppresses CRC by inhibiting AKT signaling.
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Affiliation(s)
- Wenji Yan
- 1Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China.,2Department of Oncology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Kongming Wu
- 3Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - James G Herman
- 4The Hillman Cancer Center, University of Pittsburgh Cancer Institute, 5117 Centre Ave, Pittsburgh, Pennsylvania 15213 USA
| | - Xiuduan Xu
- 1Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Yunsheng Yang
- 1Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Guanghai Dai
- 2Department of Oncology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Mingzhou Guo
- 1Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
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31
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Wang Y, He T, Herman JG, Linghu E, Yang Y, Fuks F, Zhou F, Song L, Guo M. Correction to: Methylation of ZNF331 is an independent prognostic marker of colorectal cancer and promotes colorectal cancer growth. Clin Epigenetics 2018; 10:36. [PMID: 29569636 PMCID: PMC5851308 DOI: 10.1186/s13148-018-0467-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Yuzhu Wang
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 China.,2Department of Geriatric Digestive System, Chinese PLA Navy General Hospital, 6 Fucheng Road, Beijing, 100048 China
| | - Tao He
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 China
| | - James G Herman
- 3The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213 USA
| | - Enqiang Linghu
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 China
| | - Yunsheng Yang
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 China
| | - François Fuks
- 4Laboratory of Cancer Epigenetics, Free University of Brussels (U.L.B.), 1070 Brussels, Belgium
| | - Fuyou Zhou
- 5Department of Thoracic Surgery, Anyang Tumor Hospital, Anyang, 455000 China
| | - Linjie Song
- 6Department of General Surgery, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 China.,7Medical College of NanKai University, Tianjin, 300071 China
| | - Mingzhou Guo
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 China
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32
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Viúdez A, Carvalho FLF, Maleki Z, Zahurak M, Laheru D, Stark A, Azad NS, Wolfgang CL, Baylin S, Herman JG, De Jesus-Acosta A. A new immunohistochemistry prognostic score (IPS) for recurrence and survival in resected pancreatic neuroendocrine tumors (PanNET). Oncotarget 2018; 7:24950-61. [PMID: 26894863 PMCID: PMC5041882 DOI: 10.18632/oncotarget.7436] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/23/2016] [Indexed: 01/04/2023] Open
Abstract
Pancreatic neuroendocrine tumor (PanNET) is a neoplastic entity in which few prognostic factors are well-known. Here, we aimed to evaluate the prognostic significance of N-myc downstream-regulated gen-1 (NDRG-1), O6-methylguanine DNA methyltransferase (MGMT) and Pleckstrin homology-like domain family A member 3 (PHLDA-3) by immunohistochemistry (IHC) and methylation analysis in 92 patients with resected PanNET and follow-up longer than 24 months. In multivariate analyses, ki-67 and our immunohistochemistry prognostic score (IPS-based on MGMT, NDRG-1 and PHLDA-3 IHC expression) were independent prognostic factors for disease-free-survival (DFS), while age and IPS were independent prognostic factors for overall survival (OS). Our IPS could be a useful prognostic biomarker for recurrence and survival in patients following resection for PanNET.
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Affiliation(s)
- Antonio Viúdez
- Department of Medical Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Medical Institutions, Baltimore, Maryland, USA.,Department of Medical Oncology, Complejo Hospitalario de Navarra-Instituto de Investigaciones Sanitarias de Navarra-IDISNA, Pamplona, Navarra, Spain
| | - Filipe L F Carvalho
- Department of Medical Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Zahra Maleki
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Marianna Zahurak
- The Division of Biostatistics and Bioinformatics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Daniel Laheru
- Department of Medical Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Alejandro Stark
- Department of Medical Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Nilofer S Azad
- Department of Medical Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Christopher L Wolfgang
- Department of Medical Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Stephen Baylin
- Department of Medical Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - James G Herman
- Department of Medical Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Ana De Jesus-Acosta
- Department of Medical Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
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33
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Gao D, Herman JG, Guo M. The clinical value of aberrant epigenetic changes of DNA damage repair genes in human cancer. Oncotarget 2018; 7:37331-37346. [PMID: 26967246 PMCID: PMC5095080 DOI: 10.18632/oncotarget.7949] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/20/2016] [Indexed: 12/22/2022] Open
Abstract
The stability and integrity of the human genome are maintained by the DNA damage repair (DDR) system. Unrepaired DNA damage is a major source of potentially mutagenic lesions that drive carcinogenesis. In addition to gene mutation, DNA methylation occurs more frequently in DDR genes in human cancer. Thus, DNA methylation may play more important roles in DNA damage repair genes to drive carcinogenesis. Aberrant methylation patterns in DNA damage repair genes may serve as predictive, diagnostic, prognostic and chemosensitive markers of human cancer. MGMT methylation is a marker for poor prognosis in human glioma, while, MGMT methylation is a sensitive marker of glioma cells to alkylating agents. Aberrant epigenetic changes in DNA damage repair genes may serve as therapeutic targets. Treatment of MLH1-methylated colon cancer cell lines with the demethylating agent 5′-aza-2′-deoxycytidine induces the expression of MLH1 and sensitizes cancer cells to 5-fluorouracil. Synthetic lethality is a more exciting approach in patients with DDR defects. PARP inhibitors are the most effective anticancer reagents in BRCA-deficient cancer cells.
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Affiliation(s)
- Dan Gao
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing, China.,Medical College of NanKai University, Tianjin, China
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Mingzhou Guo
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing, China
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Volonte D, Vyas AR, Chen C, Dacic S, Stabile LP, Kurland BF, Abberbock SR, Burns TF, Herman JG, Di YP, Galbiati F. Caveolin-1 promotes the tumor suppressor properties of oncogene-induced cellular senescence. J Biol Chem 2017; 293:1794-1809. [PMID: 29247004 DOI: 10.1074/jbc.m117.815902] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 12/04/2017] [Indexed: 11/06/2022] Open
Abstract
Oncogene-induced senescence (OIS) is considered a powerful tumor suppressor mechanism. Caveolin-1 acts as a scaffolding protein to functionally regulate signaling molecules. We demonstrate that a lack of caveolin-1 expression inhibits oncogenic K-Ras (K-RasG12V)-induced premature senescence in mouse embryonic fibroblasts and normal human bronchial epithelial cells. Oncogenic K-Ras induces senescence by limiting the detoxification function of MTH1. We found that K-RasG12V promotes the interaction of caveolin-1 with MTH1, which results in inhibition of MTH1 activity. Lung cancer cells expressing oncogenic K-Ras have bypassed the senescence barrier. Interestingly, overexpression of caveolin-1 restores cellular senescence in both A549 and H460 lung cancer cells and inhibits their transformed phenotype. In support of these findings, our in vivo data demonstrate that overexpression of oncogenic K-Ras (K-RasG12D) induces cellular senescence in the lung of wildtype but not caveolin-1-null mice. A lack of K-RasG12D-induced premature senescence in caveolin-1-null mice results in the formation of more abundant lung tumors. Consistent with these data, caveolin-1-null mice overexpressing K-RasG12D display accelerated mortality. Finally, our animal data were supported by human sample analysis in which we show that caveolin-1 expression is dramatically down-regulated in lung adenocarcinomas from lung cancer patients, both at the mRNA and protein levels, and that low caveolin-1 expression is associated with poor survival. Together, our data suggest that lung cancer cells escape oncogene-induced premature senescence through down-regulation of caveolin-1 expression to progress from premalignant lesions to cancer.
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Affiliation(s)
| | - Avani R Vyas
- From the Department of Pharmacology and Chemical Biology
| | - Chen Chen
- the Department of Environmental and Occupational Health, and
| | - Sanja Dacic
- the Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Laura P Stabile
- From the Department of Pharmacology and Chemical Biology.,the Lung Cancer Program, University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania 15232
| | - Brenda F Kurland
- the Lung Cancer Program, University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania 15232.,the Department of Biostatistics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania 15261, and
| | - Shira R Abberbock
- the Lung Cancer Program, University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania 15232
| | - Timothy F Burns
- the Lung Cancer Program, University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania 15232
| | - James G Herman
- the Lung Cancer Program, University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania 15232
| | - Yuanpu Peter Di
- the Department of Environmental and Occupational Health, and
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Guo Y, Peng Y, Gao D, Zhang M, Yang W, Linghu E, Herman JG, Fuks F, Dong G, Guo M. Silencing HOXD10 by promoter region hypermethylation activates ERK signaling in hepatocellular carcinoma. Clin Epigenetics 2017; 9:116. [PMID: 29075359 PMCID: PMC5654145 DOI: 10.1186/s13148-017-0412-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 09/27/2017] [Indexed: 12/12/2022] Open
Abstract
Background Hepatocellular carcinoma is the fifth most common malignancy and the third leading cause of cancer-related death worldwide. Dysregulation of HomeoboxD10 (HOXD10) was found to suppress or promote cancer progression in different cancer types. The function and regulation of HOXD10 remain unclear in human hepatocellular carcinoma (HCC). Methods Primary HCC samples (117), normal liver tissue samples (15), and 13 HCC cell lines (SNU182, SNU449, HBXF344, SMMC7721, Huh7, HepG2, LM3, PLC/PRF/5, BEL7402, SNU387, SNU475, QGY7703, and Huh1) were included in this study. Methylation-specific PCR, flow cytometry, western blot, transwell, siRNA, and chromatin immunoprecipitation assays were employed. Results HOXD10 was methylated in 76.9% (90/117) of human primary HCC samples. HOXD10 methylation was significantly associated with vessel cancerous embolus, tumor cell differentiation, and the 3-year overall survival rate (all P < 0.05). The expression of HOXD10 was regulated by promoter region methylation. HOXD10 suppressed colony formation, cell proliferation, cell invasion and migration, and induced G2/M phase arrest and apoptosis in HCC cells. HOXD10 suppressed HCC cell xenograft growth in mice. HOXD10 suppresses HCC growth by inhibiting ERK signaling. Conclusion HOXD10 is frequently methylated in human HCC, and the expression of HOXD10 is regulated by promoter region methylation. HOXD10 suppresses HCC cell growth both in vitro and in vivo. HOXD10 suppresses human HCC by inhibiting ERK signaling. Electronic supplementary material The online version of this article (10.1186/s13148-017-0412-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yulin Guo
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China.,Department of General Surgery, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Yaojun Peng
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Dan Gao
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China.,Medical College of NanKai University, #94 Weijin Road, Tianjin, 300071 China
| | - Meiying Zhang
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China.,Medical College of NanKai University, #94 Weijin Road, Tianjin, 300071 China
| | - Weili Yang
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China.,Medical College of NanKai University, #94 Weijin Road, Tianjin, 300071 China
| | - Enqiang Linghu
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Suite 2.18/Research, Pittsburgh, PA 15213 USA
| | - François Fuks
- Laboratory of Cancer Epigenetics, Free University of Brussels (U.L.B.), 808 Route de Lennik, 1070 Brussels, Belgium
| | - Guanglong Dong
- Department of General Surgery, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Mingzhou Guo
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
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Yoneyama T, Gorry M, Miller MA, Gaither-Davis A, Lin Y, Moss ML, Griffith LG, Lauffenburger DA, Stabile LP, Herman JG, Vujanovic NL. Modification of proteolytic activity matrix analysis (PrAMA) to measure ADAM10 and ADAM17 sheddase activities in cell and tissue lysates. J Cancer 2017; 8:3916-3932. [PMID: 29187866 PMCID: PMC5705993 DOI: 10.7150/jca.20779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/06/2017] [Indexed: 01/29/2023] Open
Abstract
Increases in expression of ADAM10 and ADAM17 genes and proteins have been evaluated, but not validated as cancer biomarkers. Specific enzyme activities better reflect enzyme cellular functions, and might be better biomarkers than enzyme genes or proteins. However, no high throughput assay is available to test this possibility. Recent studies have developed the high throughput real-time proteolytic activity matrix analysis (PrAMA) that integrates the enzymatic processing of multiple enzyme substrates with mathematical-modeling computation. The original PrAMA measures with significant accuracy the activities of individual metalloproteinases expressed on live cells. To make the biomarker assay usable in clinical practice, we modified PrAMA by testing enzymatic activities in cell and tissue lysates supplemented with broad-spectrum non-MP enzyme inhibitors, and by maximizing the assay specificity using systematic mathematical-modeling analyses. The modified PrAMA accurately measured the absence and decreases of ADAM10 sheddase activity (ADAM10sa) and ADAM17sa in ADAM10-/- and ADAM17-/- mouse embryonic fibroblasts (MEFs), and ADAM10- and ADAM17-siRNA transfected human cancer cells, respectively. It also measured the restoration and inhibition of ADAM10sa in ADAM10-cDNA-transfected ADAM10-/- MEFs and GI254023X-treated human cancer cell and tissue lysates, respectively. Additionally, the modified PrAMA simultaneously quantified with significant accuracy ADAM10sa and ADAM17sa in multiple human tumor specimens, and showed the essential characteristics of a robust high throughput multiplex assay that could be broadly used in biomarker studies. Selectively measuring specific enzyme activities, this new clinically applicable assay is potentially superior to the standard protein- and gene-expression assays that do not distinguish active and inactive enzyme forms.
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Affiliation(s)
- Toshie Yoneyama
- Department of Pathology, University of Pittsburgh Cancer Institute, Pittsburgh, PA.,VAPHS, Pittsburgh, PA
| | - Michael Gorry
- Department of Pathology, University of Pittsburgh Cancer Institute, Pittsburgh, PA.,VAPHS, Pittsburgh, PA
| | - Miles A Miller
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Autumn Gaither-Davis
- Department of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, PA
| | - Yan Lin
- Department of Biostatistics, University of Pittsburgh Cancer Institute, Pittsburgh, PA
| | | | - Linda G Griffith
- Department of Biologic Engineering, Massachusetts Institute of Technology
| | | | - Laura P Stabile
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, Pittsburgh, PA
| | - James G Herman
- Department of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, PA
| | - Nikola L Vujanovic
- Department of Pathology, University of Pittsburgh Cancer Institute, Pittsburgh, PA.,Department of Immunology, University of Pittsburgh Cancer Institute, Pittsburgh, PA.,VAPHS, Pittsburgh, PA
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Wang Y, He T, Herman JG, Linghu E, Yang Y, Fuks F, Zhou F, Song L, Guo M. Methylation of ZNF331 is an independent prognostic marker of colorectal cancer and promotes colorectal cancer growth. Clin Epigenetics 2017; 9:115. [PMID: 29075358 PMCID: PMC5648453 DOI: 10.1186/s13148-017-0417-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/05/2017] [Indexed: 12/22/2022] Open
Abstract
Background ZNF331 was reported to be a transcriptional repressor. Methylation of the promoter region of ZNF331 has been found frequently in human esophageal and gastric cancers. The function and methylation status of ZNF331 remain to be elucidated in human colorectal cancer (CRC). Methods Six colorectal cancer cell lines, 146 cases of primary colorectal cancer samples, and 10 cases of noncancerous colorectal mucosa were analyzed in this study using the following techniques: methylation specific PCR (MSP), qRT-PCR, siRNA, flow cytometry, xenograft mice, MTT, colony formation, and transfection assays. Results Loss of ZNF331 expression was found in DLD1 and SW48 cells, reduced expression was found in SW480, SW620, and HCT116 cells, and high level expression was detected in DKO cells. Complete methylation of the ZNF331 in the promoter region was found in DLD1 and SW48 cells, partial methylation was found in SW480, SW620, and HCT116 cells, and unmethylation was detected in DKO cells. Loss of/reduced expression of ZNF331 is correlated with promoter region methylation. Restoration of ZNF331 expression was induced by 5-aza-2′-deoxycytidine (DAC) in DLD1 and SW48 cells. These results suggest that ZNF331 expression is regulated by promoter region methylation in CRC cells. ZNF331 was methylated in 67.1% (98/146) of human primary colorectal cancer samples. Methylation of ZNF331 was significantly associated with tumor size, overall survival (OS), and disease-free survival (DFS) (p < 0.01, p < 0.01, p < 0.05). Methylation of ZNF331 was an independent poor prognostic marker for 5-year OS and 5-year DFS (both p < 0.05). ZNF331 suppressed cell proliferation and colony formation in CRC cells and suppressed human CRC cell xenograft growth in mice. Conclusions ZNF331 is frequently methylated in human colorectal cancer, and the expression of ZNF331 is regulated by promoter region methylation. Methylation of ZNF331 is a poor prognostic marker of CRC.
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Affiliation(s)
- Yuzhu Wang
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 China.,Department of Geriatric Digestive System, Chinese PLA Navy General Hospital, 6 Fucheng Road, Beijing, 100048 China
| | - Tao He
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 China
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213 USA
| | - Enqiang Linghu
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 China
| | - Yunsheng Yang
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 China
| | - François Fuks
- Laboratory of Cancer Epigenetics, Free University of Brussels (U.L.B.), 1070 Brussels, Belgium
| | - Fuyou Zhou
- Department of Thoracic Surgery, Anyang Tumor Hospital, Anyang, 455000 China
| | - Linjie Song
- Department of General Surgery, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 China.,Medical College of NanKai University, Tianjin, 300071 China
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 China
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Wang Y, Zhang Y, Herman JG, Linghu E, Guo M. Epigenetic silencing of TMEM176A promotes esophageal squamous cell cancer development. Oncotarget 2017; 8:70035-70048. [PMID: 29050260 PMCID: PMC5642535 DOI: 10.18632/oncotarget.19550] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 06/27/2017] [Indexed: 12/30/2022] Open
Abstract
The function of human transmembrane protein 176A (TMEM176A) in cancer remains unclear. To understand the function and mechanism of TMEM176A in human esophageal cancer development, 13 esophageal cancer cell lines and 267 cases of primary esophageal squamous cell cancer (ESCC) samples were analyzed by methylation specific PCR (MSP), flow cytometry, immunohistochemistry and transfection assays. TMEM176A was highly expressed in BIC1 cells and loss of TMEM176A expression was found in TE1, TE3, TE13, KYSE140, KYSE180, KYSE410, KYSE450, KYSE520, Segl, KYSE150, YES2 and COLO680N cells. Complete methylation was detected in TE1, TE3, TE13, KYSE140, KYSE180, KYSE410, KYSE450, KYSE520, Segl, KYSE150, YES2 and COLO680N cells, while unmethylation was detected in BIC1 cells. Restoration of TMEM176A expression was induced by 5-aza-2’-deoxycytidine treatment in methylated cell lines. TMEM176A was methylated in 66.7% (178/267) of primary esophageal cancer samples, and promoter region methylation was significantly associated with tumor differentiation (p<0.001) and loss off/reduced expression of TMEM176A (p<0.05). Methylation of TMEM176A was significantly associated with poor 5-year overall survival (p < 0.05). Cox proportional hazards model analysis suggest that TMEM176A methylation is an independent prognostic factor for poor 5-years OS. TMEM176A inhibited cell invasion and migration, and induced apoptosis in esophageal cancer cells. TMEM176A suppressed esophageal cancer cell growth both in vitro and in vivo. In conclusion, TMEM176A is frequently methylated in human ESCC and the expression of TMEM176A is regulated by promoter region methylation. TMEM176A methylation may serve as a diagnostic and prognostic marker in ESCC. TMEM176A is a potential tumor suppressor in human ESCC.
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Affiliation(s)
- Ying Wang
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing 100853, China.,Department of Gastroenterology, The Affiliated Fu Xing Hospital of Capital Medical University, Beijing 100038, China
| | - You Zhang
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing 100853, China
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Enqiang Linghu
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing 100853, China
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing 100853, China
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Gao D, Han Y, Yang Y, Herman JG, Linghu E, Zhan Q, Fuks F, Lu ZJ, Guo M. Methylation of TMEM176A is an independent prognostic marker and is involved in human colorectal cancer development. Epigenetics 2017; 12:575-583. [PMID: 28678648 DOI: 10.1080/15592294.2017.1341027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common malignancy and the fourth most common cause of cancer related death worldwide. This study was designed to find tumor suppressors involved in CRC development by performing RNA-seq. Eight CRC cell lines and 130 cases of primary CRC samples were used. RNA-seq, methylation-specific PCR (MSP), flow cytometry, transwell assays, and a xenograft mouse model were used. Reduction of TMEM176A expression was confirmed in human CRC cells by RNA-seq. TMEM176A was expressed in LS180 and SW620 cells, loss of TMEM176A expression was observed in LOVO, HCT116, RKO, and DLD1 cells, and reduced TMEM176A expression was found in HT29 and SW480 cells. Unmethylation of the TMEM176A promoter was found in LS180 and SW620 cells, whereas complete methylation was found in LOVO, HCT116, RKO, and DLD1 cells, and partial methylation was found in HT29 and SW480 cells. Promoter region methylation correlated with loss of/reduced expression of TMEM176A. Re-expression of TMEM176A was induced by 5-aza-2'-deoxycytidine. TMEM176A was methylated in 50.77% of primary colorectal cancers. Methylation of TMEM176A was associated with tumor metastasis (P<0.05) and was an independent prognostic factor for 5-year overall survival (OS) according to Cox proportional hazards model analysis (P<0.05). TMEM176A induced apoptosis and inhibited cell migration and invasion in CRC cells. TMEM176A suppressed CRC cell growth both in vitro and in vivo. Our results suggest that expression of TMEM176A is regulated by promoter region methylation. TMEM176A methylation is an independent prognostic marker for 5-year OS in CRC, and may act as a tumor suppressor in CRC.
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Affiliation(s)
- Dan Gao
- a Department of Gastroenterology & Hepatology , Chinese PLA General Hospital , Beijing , China.,b School of Medicine, Nankai University , Tianjin , China
| | - Yingjie Han
- a Department of Gastroenterology & Hepatology , Chinese PLA General Hospital , Beijing , China.,b School of Medicine, Nankai University , Tianjin , China
| | - Yang Yang
- c MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing , China
| | - James G Herman
- d The Hillman Cancer Center, University of Pittsburgh Cancer Institute , Pittsburgh , PA , USA
| | - Enqiang Linghu
- a Department of Gastroenterology & Hepatology , Chinese PLA General Hospital , Beijing , China
| | - Qimin Zhan
- e Laboratory of Molecular Oncology , Peking University Cancer Hospital & Institute , Beijing , China
| | - François Fuks
- f Laboratory of Cancer Epigenetics , Free University of Brussels (U.L.B.) , Brussels , Belgium
| | - Zhi John Lu
- c MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing , China
| | - Mingzhou Guo
- a Department of Gastroenterology & Hepatology , Chinese PLA General Hospital , Beijing , China
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Pelosof L, Yerram S, Armstrong T, Chu N, Danilova L, Yanagisawa B, Hidalgo M, Azad N, Herman JG. GPX3 promoter methylation predicts platinum sensitivity in colorectal cancer. Epigenetics 2017; 12:540-550. [PMID: 27918237 PMCID: PMC5687334 DOI: 10.1080/15592294.2016.1265711] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/05/2016] [Accepted: 11/21/2016] [Indexed: 12/27/2022] Open
Abstract
Epigenetic control of gene expression is a major determinant of tumor phenotype and has been found to influence sensitivity to individual chemotherapeutic agents. Glutathione peroxidase 3 (GPX3, plasma glutathione peroxidase) is a key component of cellular antioxidant regulation and its gene has been reported to be methylated in specific tumor types. GPX3 role in oxidative damage has been associated with sensitivity to platinums in other tumors but its importance in colorectal cancer (CRC) has not been determined. We examined the role of GPX3 methylation in colorectal carcinoma in determining sensitivity to platinum drugs using primary tumor specimens, cell lines, knockdown cell lines, and tumor cell line xenografts. We find GPX3 promoter region methylation in approximately one third of CRC samples and GPX3 methylation leads to reduced GPX3 expression and increased oxaliplatin and cisplatin sensitivity. In contrast, in cell lines with high baseline levels of GPX3 expression or with the ability to increase GPX3 expression, platinum resistance is increased. The cisplatin IC50 in GPX3-methylated cell lines is approximately 6-fold lower than that in GPX3-unmethylated lines. Additionally, knockdown cell lines with essentially no GPX3 expression require N-acetylcysteine to survive in culture underscoring the importance of GPX3 in redox biology. In vivo, GPX3 methylation predicts tumor xenograft sensitivity to platinum with regression of GPX3 knockdown xenografts with platinum treatment but continued growth of GPX3 wild type xenografts in the presence of platinum. These studies demonstrate the importance of GPX3 for CRC cells resistance to platinums and the potential utility of GPX3 methylation status as a predictive biomarker for platinum sensitivity in CRC.
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Affiliation(s)
- Lorraine Pelosof
- Cancer Biology Program, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sashidhar Yerram
- Gastrointestinal Cancer Program, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Todd Armstrong
- Gastrointestinal Cancer Program, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nina Chu
- Gastrointestinal Cancer Program, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ludmila Danilova
- Bioinformatics, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia
| | - Breann Yanagisawa
- Cancer Biology Program, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Manuel Hidalgo
- Division of Hematology-Oncology, Beth Israel Deaconess Medical Center, Boston, MD, USA
| | - Nilofer Azad
- Gastrointestinal Cancer Program, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Chemical Therapeutics Program, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James G. Herman
- Cancer Biology Program, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lung Cancer Program, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
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Sen M, Kindsfather A, Herman JG. Abstract 3365: Epigenetic inactivation of PTPRT and sensitivity to STAT3 inhibition in lung cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Signal Transducers and Activators of Transcription-3 (STAT3), a potent oncogenic transcription factor is persistently activated in several malignancies including lung cancer. Protein Tyrosine Phosphatase Receptor-T (PTPRT) is an endogenous inhibitor of STAT3 transcriptional activity, and is methylated in many types of human cancer. Loss-of-function of PTPRT by promoter methylation contributes to STAT3 mediated growth and survival and represent one of the plausible mechanism of STAT3 hyperactivation. We report identification of hypermethylation in CpG islands of the PTPRT promoter which correlates with its transcriptional silencing as well as expression of pSTAT3 protein and STAT3 target genes in both lung cancer cell lines and primary human tumors. Analyses of the TCGA (The Cancer Genome Atlas) data revealed that PTPRT promoter is frequently hypermethylated in a subset of lung squamous cell carcinoma and approximately 25% of adenocarcinoma tumors in association with downregulation of PTPRT mRNA expression. This observation was verified in vitro using lung cancer cell lines. Out of the 7 lung cancer cell lines examined, one lung cancer cell line showed lack of methylation (only unmethylated sequences) of the PTPRT promoter region and revealed mRNA expression (H520). All 6 cell lines which showed PTPRT promoter methylation had nearly absent PTPRT mRNA and had high levels of pSTAT3Tyr705, while H520 had little or no pSTAT3Tyr705 protein expression. Silencing of PTPRT using siRNA in H520, where PTPRT was not endogenously silenced by promoter hypermethylation, resulted in the upregulation of the STAT3 target genes such as cyclin D1 and Bcl-XL mRNA and protein expression as well as increased pSTAT3Tyr705 level. Analyses of the methylation status in the PTPRT promoter region in primary lung tumor samples revealed methylation in one of the 3 tumor samples. This correlated with increased STAT3 target genes (cyclin D1 and Bcl-XL) mRNA expression. In lung cancer cell lines, PTPRT promoter methylation is associated with sensitivity to STAT3 inhibition. Our data suggests that silencing of PTPRT by promoter hypermethylation is a frequent mechanism of STAT3 hyperactivation, and targeting STAT3 may be an effective molecular targeted approach in the treatment of this subset of lung cancer.
Citation Format: Malabika Sen, Audrey Kindsfather, James G. Herman. Epigenetic inactivation of PTPRT and sensitivity to STAT3 inhibition in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3365. doi:10.1158/1538-7445.AM2017-3365
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Affiliation(s)
- Malabika Sen
- University of Pittsburgh Cancer Institute, Pittsburgh, PA
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Bosch LJW, Trooskens G, Snaebjornsson P, Coupé VMH, Mongera S, Haan JC, Richman SD, Koopman M, Tol J, de Meyer T, Louwagie J, Dehaspe L, van Grieken NCT, Ylstra B, Verheul HMW, van Engeland M, Nagtegaal ID, Herman JG, Quirke P, Seymour MT, Punt CJA, van Criekinge W, Carvalho B, Meijer GA. Decoy receptor 1 ( DCR1) promoter hypermethylation and response to irinotecan in metastatic colorectal cancer. Oncotarget 2017; 8:63140-63154. [PMID: 28968978 PMCID: PMC5609910 DOI: 10.18632/oncotarget.18702] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 05/23/2017] [Indexed: 12/11/2022] Open
Abstract
Diversity in colorectal cancer biology is associated with variable responses to standard chemotherapy. We aimed to identify and validate DNA hypermethylated genes as predictive biomarkers for irinotecan treatment of metastatic CRC patients. Candidate genes were selected from 389 genes involved in DNA Damage Repair by correlation analyses between gene methylation status and drug response in 32 cell lines. A large series of samples (n=818) from two phase III clinical trials was used to evaluate these candidate genes by correlating methylation status to progression-free survival after treatment with first-line single-agent fluorouracil (Capecitabine or 5-fluorouracil) or combination chemotherapy (Capecitabine or 5-fluorouracil plus irinotecan (CAPIRI/FOLFIRI)). In the discovery (n=185) and initial validation set (n=166), patients with methylated Decoy Receptor 1 (DCR1) did not benefit from CAPIRI over Capecitabine treatment (discovery set: HR=1.2 (95%CI 0.7-1.9, p=0.6), validation set: HR=0.9 (95%CI 0.6-1.4, p=0.5)), whereas patients with unmethylated DCR1 did (discovery set: HR=0.4 (95%CI 0.3-0.6, p=0.00001), validation set: HR=0.5 (95%CI 0.3-0.7, p=0.0008)). These results could not be replicated in the external data set (n=467), where a similar effect size was found in patients with methylated and unmethylated DCR1 for FOLFIRI over 5FU treatment (methylated DCR1: HR=0.7 (95%CI 0.5-0.9, p=0.01), unmethylated DCR1: HR=0.8 (95%CI 0.6-1.2, p=0.4)). In conclusion, DCR1 promoter hypermethylation status is a potential predictive biomarker for response to treatment with irinotecan, when combined with capecitabine. This finding could not be replicated in an external validation set, in which irinotecan was combined with 5FU. These results underline the challenge and importance of extensive clinical evaluation of candidate biomarkers in multiple trials.
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Affiliation(s)
- Linda J W Bosch
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.,Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Geert Trooskens
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Petur Snaebjornsson
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.,Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Veerle M H Coupé
- Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
| | - Sandra Mongera
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Josien C Haan
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Susan D Richman
- Pathology and Tumour Biology, University of Leeds, Leeds, UK
| | - Miriam Koopman
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jolien Tol
- Department of Internal Medicine, Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands
| | - Tim de Meyer
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | | | - Luc Dehaspe
- MDxHealth, SA, Liège, Belgium.,Genomics Core Facility, UZ Leuven, Leuven, Belgium
| | | | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk M W Verheul
- Department of Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology and Developmental Biology and Maastricht University Medical Center, Maastricht, The Netherlands
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - James G Herman
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Philip Quirke
- Pathology and Tumour Biology, University of Leeds, Leeds, UK
| | - Matthew T Seymour
- St James's Institute of Oncology, St James's University Hospital, Leeds, UK
| | - Cornelis J A Punt
- Department of Medical Oncology, Academic Medical Center, Amsterdam, The Netherlands
| | - Wim van Criekinge
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.,Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium.,MDxHealth, SA, Liège, Belgium
| | - Beatriz Carvalho
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.,Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.,Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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He T, Zhang M, Zheng R, Zheng S, Linghu E, Herman JG, Guo M. Methylation of SLFN11 is a marker of poor prognosis and cisplatin resistance in colorectal cancer. Epigenomics 2017; 9:849-862. [PMID: 28403629 DOI: 10.2217/epi-2017-0019] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: The expression of human SLFN11 was reported to sensitize cancer cells to DNA damaging agents. This study is to explore the epigenetic change and the function of SLFN11 in human colorectal cancer (CRC). Materials & methods: Six CRC cell lines and 128 primary CRC samples were used. Results: SLFN11 was methylated in 55.47% (71/128) of primary CRC. The expression of SLFN11 was regulated by promoter region methylation. Methylation of SLFN11 was significantly associated with age, poor 5-year overall survival and 5-year relapse-free survival (all p < 0.05). SLFN11 suppressed CRC cell growth both in vitro and in vivo and sensitized CRC cells to cisplatin. Conclusion: SLFN11 is frequently methylated in human CRC, and the expression of SLFN11 is regulated by promoter region methylation. Methylation of SLFN11 reduced the sensitivity of CRC cells to cisplatin.
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Affiliation(s)
- Tao He
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing 100853, China
- Department of Pathology, The Affiliated Hospital of Logistics University of Chinese People's Armed Police Force, Tianjin 300162, China
| | - Meiying Zhang
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing 100853, China
- Medical College, NanKai University, Tianjin 300071, China
| | - Ruipan Zheng
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing 100853, China
- Medical College, NanKai University, Tianjin 300071, China
| | - Shufang Zheng
- Department of Pathology, The Affiliated Hospital of Logistics University of Chinese People's Armed Police Force, Tianjin 300162, China
| | - Enqiang Linghu
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing 100853, China
| | - James G Herman
- Medical College, NanKai University, Tianjin 300071, China
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing 100853, China
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Gao D, Herman JG, Cui H, Jen J, Fuks F, Brock MV, Ushijima T, Croce C, Akiyama Y, Guo M. Meeting Report of the Fifth International Cancer Epigenetics Conference in Beijing, China, October 2016. Epigenomics 2017; 9:937-941. [PMID: 28530839 DOI: 10.2217/epi-2017-0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Fifth International Cancer Epigenetics Conference, Beijing, China, 21-23 October 2016 This meeting reported many new findings in the field of cancer epigenetics, including basic science, translational and clinical studies. In this report, we summarize some of the main advancements and prospects in cancer epigenetics presented at this meeting.
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Affiliation(s)
- Dan Gao
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing 100853, China.,School of Medicine, Nankai University, Tianjin 300071, China
| | - James G Herman
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburg, PA 15232, USA
| | - Hengmi Cui
- Institute of Epigenetics & Epigenomics, Yangzhou University, Yangzhou 225000, China
| | - Jin Jen
- Department of Laboratory of Medicine & Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Francois Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels 1070, Belgium
| | - Malcolm V Brock
- Oncology Center, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Carlo Croce
- Department of Cancer Biology & Genetics, College of Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Yoshimitsu Akiyama
- Department of Molecular Oncology, Graduate School of Medical & Dental Sciences, Tokyo Medical & Dental University, Tokyo 113-8519, Japan
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing 100853, China
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45
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Hulbert A, Jusue-Torres I, Stark A, Chen C, Rodgers K, Lee B, Griffin C, Yang A, Huang P, Wrangle J, Belinsky SA, Wang TH, Yang SC, Baylin SB, Brock MV, Herman JG. Early Detection of Lung Cancer Using DNA Promoter Hypermethylation in Plasma and Sputum. Clin Cancer Res 2017; 23:1998-2005. [PMID: 27729459 PMCID: PMC6366618 DOI: 10.1158/1078-0432.ccr-16-1371] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/17/2016] [Accepted: 09/20/2016] [Indexed: 12/12/2022]
Abstract
Purpose: CT screening can reduce death from lung cancer. We sought to improve the diagnostic accuracy of lung cancer screening using ultrasensitive methods and a lung cancer-specific gene panel to detect DNA methylation in sputum and plasma.Experimental Design: This is a case-control study of subjects with suspicious nodules on CT imaging. Plasma and sputum were obtained preoperatively. Cases (n = 150) had pathologic confirmation of node-negative (stages I and IIA) non-small cell lung cancer. Controls (n = 60) had non-cancer diagnoses. We detected promoter methylation using quantitative methylation-specific real-time PCR and methylation-on-beads for cancer-specific genes (SOX17, TAC1, HOXA7, CDO1, HOXA9, and ZFP42).Results: DNA methylation was detected in plasma and sputum more frequently in people with cancer compared with controls (P < 0.001) for five of six genes. The sensitivity and specificity for lung cancer diagnosis using the best individual genes was 63% to 86% and 75% to 92% in sputum, respectively, and 65% to 76% and 74% to 84% in plasma, respectively. A three-gene combination of the best individual genes has sensitivity and specificity of 98% and 71% using sputum and 93% and 62% using plasma. Area under the receiver operating curve for this panel was 0.89 [95% confidence interval (CI), 0.80-0.98] in sputum and 0.77 (95% CI, 0.68-0.86) in plasma. Independent blinded random forest prediction models combining gene methylation with clinical information correctly predicted lung cancer in 91% of subjects using sputum detection and 85% of subjects using plasma detection.Conclusions: High diagnostic accuracy for early-stage lung cancer can be obtained using methylated promoter detection in sputum or plasma. Clin Cancer Res; 23(8); 1998-2005. ©2016 AACR.
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Affiliation(s)
- Alicia Hulbert
- Sidney Kimmel Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ignacio Jusue-Torres
- Department of Neurosurgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alejandro Stark
- Department of Mechanical Engineering, The Johns Hopkins University, Baltimore, Maryland
| | - Chen Chen
- Sidney Kimmel Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Thoracic Surgery, Second Xiangya Hospital of Central South University, Changsha, Hunan, PR China
| | - Kristen Rodgers
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Beverly Lee
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Candace Griffin
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Andrew Yang
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Peng Huang
- Sidney Kimmel Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - John Wrangle
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Steven A Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Tza-Huei Wang
- Sidney Kimmel Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Mechanical Engineering, The Johns Hopkins University, Baltimore, Maryland
- Department of Biomedical Engineering and Institute for NanoBioTechnology, The Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Stephen C Yang
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stephen B Baylin
- Sidney Kimmel Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Malcolm V Brock
- Sidney Kimmel Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - James G Herman
- Sidney Kimmel Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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van Vlodrop IJH, Joosten SC, De Meyer T, Smits KM, Van Neste L, Melotte V, Baldewijns MMLL, Schouten LJ, van den Brandt PA, Jeschke J, Yi JM, Schuebel KE, Ahuja N, Herman JG, Aarts MJ, Bosman FT, Van Criekinge W, van Engeland M. A Four-Gene Promoter Methylation Marker Panel Consisting of GREM1, NEURL, LAD1, and NEFH Predicts Survival of Clear Cell Renal Cell Cancer Patients. Clin Cancer Res 2017; 23:2006-2018. [PMID: 27756787 DOI: 10.1158/1078-0432.ccr-16-1236] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/02/2016] [Accepted: 09/24/2016] [Indexed: 11/16/2022]
Abstract
Purpose: The currently used prognostic models for patients with nonmetastatic clear cell renal cell carcinoma (ccRCC) are based on clinicopathologic features and might be improved by adding molecular markers. Epigenetic alterations occur frequently in ccRCC and are promising biomarkers. The aim of this study is to identify prognostic promoter methylation markers for ccRCC.Experimental Design: We integrated data generated by massive parallel sequencing of methyl-binding domain enriched DNA and microarray-based RNA expression profiling of 5-aza-2'-deoxycytidine-treated ccRCC cell lines to comprehensively characterize the ccRCC methylome. A selection of the identified methylation markers was evaluated in two independent series of primary ccRCC (n = 150 and n = 185) by methylation-specific PCR. Kaplan-Meier curves and log-rank tests were used to estimate cause-specific survival. HRs and corresponding 95% confidence intervals (CI) were assessed using Cox proportional hazard models. To assess the predictive capacity and fit of models combining several methylation markers, HarrellC statistic and the Akaike Information Criterion were used.Results: We identified four methylation markers, that is, GREM1, NEURL, LAD1, and NEFH, that individually predicted prognosis of patients with ccRCC. The four markers combined were associated with poorer survival in two independent patient series (HR, 3.64; 95% CI, 1.02-13.00 and HR, 7.54; 95% CI, 2.68-21.19). These findings were confirmed in a third series of ccRCC cases from The Cancer Genome Atlas (HR, 3.60; 95% CI, 2.02-6.40).Conclusions: A four-gene promoter methylation marker panel consisting of GREM1, NEURL, LAD1, and NEFH predicts outcome of patients with ccRCC and might be used to improve current prognostic models. Clin Cancer Res; 23(8); 2006-18. ©2016 AACR.
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Affiliation(s)
- Iris J H van Vlodrop
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Sophie C Joosten
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Tim De Meyer
- BioBix: Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Kim M Smits
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
- Department of Radiation Oncology (MAASTRO), GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Leander Van Neste
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Veerle Melotte
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Marcella M L L Baldewijns
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Leo J Schouten
- Department of Epidemiology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Piet A van den Brandt
- Department of Epidemiology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Jana Jeschke
- The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
| | - Joo Mi Yi
- Research Institute, Dongnam Institute of Radiological and Medical Sciences (DIRAMS), Jangan-eup, Gijang-gun, Busan, Korea
| | - Kornel E Schuebel
- The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nita Ahuja
- The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Maureen J Aarts
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Fred T Bosman
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Wim Van Criekinge
- BioBix: Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands.
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Viúdez A, Carvalho FL, Maleki Z, Zahurak M, Laheru D, Stark A, Azad NS, Wolfgang CL, Baylin S, Herman JG, De Jesus-Acosta A. Correction: A new immunohistochemistry prognostic score (IPS) for recurrence and survival in resected pancreatic neuroendocrine tumors (PanNET). Oncotarget 2017; 8:18617. [PMID: 28407701 PMCID: PMC5392354 DOI: 10.18632/oncotarget.16155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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48
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Zhang M, Linghu E, Zhan Q, He T, Cao B, Brock MV, Herman JG, Xiang R, Guo M. Methylation of DACT2 accelerates esophageal cancer development by activating Wnt signaling. Oncotarget 2017; 7:17957-69. [PMID: 26919254 PMCID: PMC4951263 DOI: 10.18632/oncotarget.7647] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 02/06/2016] [Indexed: 01/11/2023] Open
Abstract
Esophageal cancer is one of the most common malignancies worldwide. DACT2 is frequently methylated in human lung, hepatic, gastric and thyroid cancers. The methylation status and function of DACT2 remain to be elucidated in human esophageal cancer. Ten esophageal cancer cell lines, 42 cases of dysplasia and 126 cases of primary esophageal cancer samples were analyzed in this study. The expression of DACT2 was detected in YES2 cells, while reduced DACT2 expression levels were found in TE8 and KYSE70 cells, and complete loss of DACT2 expression was found in KYSE30, KYSE140, KYSE150, KYSE410, KYSE450, TE3 and TE7 cells. Loss of expression or reduced expression of DACT2 correlated with promoter region hypermethylation in esophageal cancer cells. Restoration of DACT2 expression was induced by 5-aza-2′-deoxycytidine. In human primary esophageal squamous carcinoma, 69% (87/126) of samples were methylated. Methylation of DACT2 was significantly associated with tumor stage and metastasis (P < 0.01, P < 0.05). DACT2 suppressed colony formation, cell migration and invasion in esophageal cancer cells, and it also suppressed esophageal cancer cell xenograft growth. DACT2 inhibited Wnt signaling in human esophageal cancer cells. In conclusion, DACT2 is frequently methylated in human esophageal cancer and its expression is regulated by promoter region methylation. DACT2 suppresses esophageal cancer growth by inhibiting Wnt signaling.
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Affiliation(s)
- Meiying Zhang
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing 100853, China.,Medical College of NanKai University, Tianjin 300071, China
| | - Enqiang Linghu
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing 100853, China
| | - Qimin Zhan
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, P.R.China
| | - Tao He
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing 100853, China
| | - Baoping Cao
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing 100853, China
| | - Malcolm V Brock
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21231, USA
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Rong Xiang
- Medical College of NanKai University, Tianjin 300071, China
| | - Mingzhou Guo
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing 100853, China
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49
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Gojo I, Beumer JH, Pratz KW, McDevitt MA, Baer MR, Blackford AL, Smith BD, Gore SD, Carraway HE, Showel MM, Levis MJ, Dezern AE, Gladstone DE, Ji JJ, Wang L, Kinders RJ, Pouquet M, Ali-Walbi I, Rudek MA, Poh W, Herman JG, Karnitz LM, Kaufmann SH, Chen A, Karp JE. A Phase 1 Study of the PARP Inhibitor Veliparib in Combination with Temozolomide in Acute Myeloid Leukemia. Clin Cancer Res 2017; 23:697-706. [PMID: 27503200 PMCID: PMC5290001 DOI: 10.1158/1078-0432.ccr-16-0984] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 06/23/2016] [Accepted: 07/17/2016] [Indexed: 11/16/2022]
Abstract
PURPOSE In preclinical studies, the PARP inhibitor veliparib enhanced the antileukemic action of temozolomide through potentiation of DNA damage. Accordingly, we conducted a phase 1 study of temozolomide with escalating doses of veliparib in patients with relapsed, refractory acute myeloid leukemia (AML) or AML arising from aggressive myeloid malignancies. EXPERIMENTAL DESIGN Patients received veliparib [20-200 mg once a day on day 1 and twice daily on days 4-12 in cycle 1 (days 1-8 in cycle ≥2)] and temozolomide [150-200 mg/m2 daily on days 3-9 in cycle 1 (days 1-5 in cycle ≥2)] every 28 to 56 days. Veliparib pharmacokinetics and pharmacodynamics [ability to inhibit poly(ADP-ribose) polymer (PAR) formation and induce H2AX phosphorylation] were assessed. Pretreatment levels of MGMT and PARP1 protein, methylation of the MGMT promoter, and integrity of the Fanconi anemia pathway were also examined. RESULTS Forty-eight patients were treated at seven dose levels. Dose-limiting toxicities were oral mucositis and esophagitis lasting >7 days. The MTD was veliparib 150 mg twice daily with temozolomide 200 mg/m2 daily. The complete response (CR) rate was 17% (8/48 patients). Veliparib exposure as well as inhibition of PAR polymer formation increased dose proportionately. A veliparib-induced increase in H2AX phosphorylation in CD34+ cells was observed in responders. Three of 4 patients with MGMT promoter methylation achieved CR. CONCLUSIONS Veliparib plus temozolomide is well tolerated, with activity in advanced AML. Further evaluation of this regimen and of treatment-induced phosphorylation of H2AX and MGMT methylation as potential response predictors appears warranted. Clin Cancer Res; 23(3); 697-706. ©2016 AACR.
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Affiliation(s)
- Ivana Gojo
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Hospital, Baltimore, Maryland.
| | - Jan H Beumer
- Cancer Therapeutics Program, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Keith W Pratz
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Hospital, Baltimore, Maryland
| | - Michael A McDevitt
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Hospital, Baltimore, Maryland
| | - Maria R Baer
- Department of Medicine, University of Maryland Greenebaum Cancer Center, Baltimore, Maryland
| | - Amanda L Blackford
- Department of Statistics, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Hospital, Baltimore, Maryland
| | - B Douglas Smith
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Hospital, Baltimore, Maryland
| | - Steven D Gore
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Hospital, Baltimore, Maryland
| | - Hetty E Carraway
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Hospital, Baltimore, Maryland
| | - Margaret M Showel
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Hospital, Baltimore, Maryland
| | - Mark J Levis
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Hospital, Baltimore, Maryland
| | - Amy E Dezern
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Hospital, Baltimore, Maryland
| | - Douglas E Gladstone
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Hospital, Baltimore, Maryland
| | - Jiuping Jay Ji
- Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Support Directorate, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland
| | - Lihua Wang
- Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Support Directorate, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland
| | - Robert J Kinders
- Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Support Directorate, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland
| | - Marie Pouquet
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ismail Ali-Walbi
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Michelle A Rudek
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Hospital, Baltimore, Maryland
| | - Weijie Poh
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Hospital, Baltimore, Maryland
| | - James G Herman
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Hospital, Baltimore, Maryland
| | - Larry M Karnitz
- Division of Oncology Research and Department of Molecular Pharmacology, Mayo Clinic, Rochester, Minnesota
| | - Scott H Kaufmann
- Division of Oncology Research and Department of Molecular Pharmacology, Mayo Clinic, Rochester, Minnesota
| | - Alice Chen
- Cancer Therapy Evaluation Program, NCI, Rockville, Maryland
| | - Judith E Karp
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Hospital, Baltimore, Maryland
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Connolly RM, Li H, Jankowitz RC, Zhang Z, Rudek MA, Jeter SC, Slater SA, Powers P, Wolff AC, Fetting JH, Brufsky A, Piekarz R, Ahuja N, Laird PW, Shen H, Weisenberger DJ, Cope L, Herman JG, Somlo G, Garcia AA, Jones PA, Baylin SB, Davidson NE, Zahnow CA, Stearns V. Combination Epigenetic Therapy in Advanced Breast Cancer with 5-Azacitidine and Entinostat: A Phase II National Cancer Institute/Stand Up to Cancer Study. Clin Cancer Res 2016; 23:2691-2701. [PMID: 27979916 DOI: 10.1158/1078-0432.ccr-16-1729] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/27/2016] [Accepted: 11/19/2016] [Indexed: 01/20/2023]
Abstract
Purpose: In breast cancer models, combination epigenetic therapy with a DNA methyltransferase inhibitor and a histone deacetylase inhibitor led to reexpression of genes encoding important therapeutic targets, including the estrogen receptor (ER). We conducted a multicenter phase II study of 5-azacitidine and entinostat in women with advanced hormone-resistant or triple-negative breast cancer (TNBC).Experimental Design: Patients received 5-azacitidine 40 mg/m2 (days 1-5, 8-10) and entinostat 7 mg (days 3, 10) on a 28-day cycle. Continuation of epigenetic therapy was offered with the addition of endocrine therapy at the time of progression [optional continuation (OC) phase]. Primary endpoint was objective response rate (ORR) in each cohort. We hypothesized that ORR would be ≥20% against null of 5% using Simon two-stage design. At least one response was required in 1 of 13 patients per cohort to continue accrual to 27 per cohort (type I error, 4%; power, 90%).Results: There was one partial response among 27 women with hormone-resistant disease (ORR = 4%; 95% CI, 0-19), and none in 13 women with TNBC. One additional partial response was observed in the OC phase in the hormone-resistant cohort (n = 12). Mandatory tumor samples were obtained pre- and posttreatment (58% paired) with either up- or downregulation of ER observed in approximately 50% of posttreatment biopsies in the hormone-resistant, but not TNBC cohort.Conclusions: Combination epigenetic therapy was well tolerated, but our primary endpoint was not met. OC phase results suggest that some women benefit from epigenetic therapy and/or reintroduction of endocrine therapy beyond progression, but further study is needed. Clin Cancer Res; 23(11); 2691-701. ©2016 AACR.
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Affiliation(s)
- Roisin M Connolly
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Huili Li
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | | | - Zhe Zhang
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Michelle A Rudek
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Stacie C Jeter
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Shannon A Slater
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Penny Powers
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Antonio C Wolff
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - John H Fetting
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Adam Brufsky
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - Richard Piekarz
- Cancer Therapy Evaluation Program (CTEP), NCI, Bethesda, Maryland
| | - Nita Ahuja
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Peter W Laird
- Van Andel Research Institute, Grand Rapids, Michigan
| | - Hui Shen
- Van Andel Research Institute, Grand Rapids, Michigan
| | | | - Leslie Cope
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - James G Herman
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | | | | | - Peter A Jones
- Van Andel Research Institute, Grand Rapids, Michigan
| | - Stephen B Baylin
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Nancy E Davidson
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - Cynthia A Zahnow
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Vered Stearns
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland.
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