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Wu G, Wang Q, Wang D, Xiong F, Liu W, Chen J, Wang B, Huang W, Wang X, Chen Y. Targeting polycomb repressor complex 2-mediated bivalent promoter epigenetic silencing of secreted frizzled-related protein 1 inhibits cholangiocarcinoma progression. Clin Transl Med 2023; 13:e1502. [PMID: 38050190 PMCID: PMC10696163 DOI: 10.1002/ctm2.1502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/19/2023] [Accepted: 11/24/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Cholangiocarcinoma (CCA) refers to a collection of malignancies that are associated with a dismal prognosis. Currently, surgical resection is the only way to cure patients with CCA. Available systemic therapy is limited to gemcitabine plus cisplatin; however, this treatment is palliative in nature. Therefore, there is still a need to explore new effective therapeutic targets to intervene against CCA. METHODS We analyzed the expression of EZH2 and the prognosis of patients in CCA. The proliferation, migration and invasion of CCA cells after gene knockdown and overexpression were examined and validated by a xenograft model and a primary CCA mouse model with corresponding gene intervention. Targeting DNA methylation, and RNA-sequencing-based transcriptomic analysis in EZH2 and SUZ12 knockout CCA cells was performed. Bisulfite sequencing polymerase chain reaction (PCR), chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) and reverse-ChIP assays were performed for research purposes. RESULTS Increased expression of EZH2 in CCA exhibited a significantly poorer prognosis. DNA hypomethylation of the promoter and increased mRNA levels of secreted frizzled-related protein 1 (SFRP1) were observed in CCA cells following the inhibition of polycomb repressor complex 2 (PRC2), which was achieved through a knockout of EZH2, SUZ12 and EED, respectively, or treatment with GSK126 and GSK343. Targeting the SFRP1 promoter DNA hypermethylation with dCas9-DNMT3a decreased the mRNA level of SFRP1. The expression of SFRP1 is regulated by both H3K27me3 and DNA methylation and H3K27me3 plays a crucial role in promoting SFRP1 promotor DNA methylation. GSK343 is a small molecule inhibitor that targets the catalytic activity of EZH2. It effectively inhibits the progression and development of subcutaneous xenografts and primary CCA mouse models. CONCLUSION Overall, our data strongly suggested that targeting PRC2 promotes the expression of SFRP1, thereby inhibiting the progression of CCA. KEY POINTS/HEADLIGHTS Cholangiocarcinoma (CCA) exhibits elevated expression of EZH2, SUZ12 and EED, resulting in increased levels of H3K27me3. Targeting polycomb repressor complex 2 (PRC2) leads to the removal of H3K27me3 from the secreted frizzled-related protein 1 (SFRP1) promoter and DNA hypomethylation, thereby activating the transcription of SFRP1. Inhibiting PRC2, including the use of EZH2 inhibitors, holds promise as a potential strategy for developing anti-cancer drugs for CCA.
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Affiliation(s)
- Guanhua Wu
- Department of Biliary‐Pancreatic SurgeryTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanP. R. China
| | - Qi Wang
- Department of Biliary‐Pancreatic SurgeryTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanP. R. China
| | - Da Wang
- Department of Biliary‐Pancreatic SurgeryTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanP. R. China
| | - Fei Xiong
- Department of Biliary‐Pancreatic SurgeryTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanP. R. China
| | - Wenzheng Liu
- Department of Biliary‐Pancreatic SurgeryTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanP. R. China
| | - Junsheng Chen
- Department of Biliary‐Pancreatic SurgeryTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanP. R. China
| | - Bing Wang
- Department of Biliary‐Pancreatic SurgeryTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanP. R. China
| | - Wenhua Huang
- Department of EmergencyTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanP. R. China
| | - Xin Wang
- Departement of Pediatric SurgeryWuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanP. R. China
| | - Yongjun Chen
- Department of Biliary‐Pancreatic SurgeryTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanP. R. China
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Stubbe BE, Madsen PH, Larsen AC, Krarup HB, Pedersen IS, Hansen CP, Johansen JS, Henriksen SD, Thorlacius-Ussing O. Promoter hypermethylation of SFRP1 as a prognostic and potentially predictive blood-based biomarker in patients with stage III or IV pancreatic ductal adenocarcinoma. Pancreatology 2023; 23:512-521. [PMID: 37230892 DOI: 10.1016/j.pan.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma remains one of the major causes of cancer-related mortality globally. Unfortunately, current prognostic biomarkers are limited, and no predictive biomarkers exist. This study examined promoter hypermethylation of secreted frizzled-related protein 1 (phSFRP1) in cfDNA as a prognostic biomarker and predictor of treatment effect in patients with metastatic FOLFIRINOX-treated PDAC and locally advanced PDAC. METHODS We performed methylation-specific PCR of the SFRP1 genes' promoter region, based on bisulfite treatment. Survival was assessed as time-to-event data using the pseudo-observation method and analyzed with Kaplan-Meier curves and generalized linear regressions. RESULTS The study included 52 patients with FOLFIRINOX-treated metastatic PDAC. Patients with unmethylated (um) SFRP1 (n = 29) had a longer median overall survival (15.7 months) than those with phSFRP1 (6.8 months). In crude regression, phSFRP1 was associated with an increased risk of death of 36.9% (95% CI 12.0%-61.7%) and 19.8% (95% CI 1.9-37.6) at 12 and 24-months, respectively. In supplementary regression analysis, interaction terms between SFRP1 methylation status and treatment were significant, indicating reduced benefit of chemotherapy. Forty-four patients with locally advanced PDAC were included. phSFRP1 was associated with an increased risk of death at 24-months CONCLUSIONS: This indicates that phSFRP1 is a clinically useful prognostic biomarker in metastatic PDAC and possibly in locally advanced PDAC. Together with existing literature, results could indicate the value of cfDNA-measured phSFRP1 as a predictive biomarker of standard palliative chemotherapy in patients with metastatic PDAC. This could facilitate personalized treatment of patients with metastatic PDAC.
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Affiliation(s)
- Benjamin E Stubbe
- Department of Gastrointestinal Surgery, Aalborg University Hospital, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Denmark.
| | - Poul H Madsen
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Molecular Diagnostics, Aalborg University Hospital, Denmark
| | - Anders C Larsen
- Department of Gastrointestinal Surgery, Aalborg University Hospital, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Denmark
| | - Henrik B Krarup
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Molecular Diagnostics, Aalborg University Hospital, Denmark
| | - Inge S Pedersen
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Molecular Diagnostics, Aalborg University Hospital, Denmark; Department of Clinical Medicine, Aalborg University, Denmark
| | - Carsten P Hansen
- Department of Surgery, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Julia S Johansen
- Department of Medicine, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Stine D Henriksen
- Department of Gastrointestinal Surgery, Aalborg University Hospital, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Denmark
| | - Ole Thorlacius-Ussing
- Department of Gastrointestinal Surgery, Aalborg University Hospital, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Denmark
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García-Ortiz MV, Cano-Ramírez P, Toledano-Fonseca M, Cano MT, Inga-Saavedra E, Rodríguez-Alonso RM, Guil-Luna S, Gómez-España MA, Rodríguez-Ariza A, Aranda E. Circulating NPTX2 methylation as a non-invasive biomarker for prognosis and monitoring of metastatic pancreatic cancer. Clin Epigenetics 2023; 15:118. [PMID: 37481552 PMCID: PMC10362605 DOI: 10.1186/s13148-023-01535-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/16/2023] [Indexed: 07/24/2023] Open
Abstract
BACKGROUND Pancreatic cancer is the most lethal cancer with a dismal prognosis mainly due to diagnosis at advanced stage and ineffective treatments. CA19-9 levels and computed tomography (CT) imaging are the main standard criteria for evaluating disease progression and treatment response. In this study we explored liquid biopsy-based epigenetic biomarkers for prognosis and monitoring disease in patients with metastatic pancreatic ductal adenocarcinoma (mPDAC). METHODS Plasma samples were collected from 44 mPDAC patients at the time of diagnosis, and in 15 of them, additional samples were obtained during follow-up of the disease. After cell-free DNA (cfDNA), isolation circulating levels of methylated NPTX2, SPARC, BMP3, SFRP1 and TFPI2 genes were measured using digital droplet PCR (ddPCR). BEAMing technique was performed for quantitation of RAS mutations in cfDNA, and CA19-9 was measured using standard techniques. RESULTS NPTX2 was the most highly and frequently methylated gene in cfDNA samples from mPDAC patients. Higher circulating NPTX2 methylation levels at diagnosis were associated with poor prognosis and efficiently stratified patients for prediction of overall survival (6.06% cut-off, p = 0.0067). Dynamics of circulating NPTX2 methylation levels correlated with disease progression and response to therapy and predicted better than CA19-9 the evolution of disease in mPDAC patients. Remarkably, in many cases the disease progression detected by CT scan was anticipated by an increase in circulating NPTX2 methylation levels. CONCLUSIONS Our study supports circulating NPTX2 methylation levels as a promising liquid biopsy-based clinical tool for non-invasive prognosis, monitoring disease evolution and response to treatment in mPDAC patients.
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Affiliation(s)
- María Victoria García-Ortiz
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Seville, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
| | - Pablo Cano-Ramírez
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Seville, Spain
| | - Marta Toledano-Fonseca
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Seville, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
| | - María Teresa Cano
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Seville, Spain
- Medical Oncology Department, Reina Sofía University Hospital, Córdoba, Spain
| | - Elizabeth Inga-Saavedra
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Seville, Spain
- Medical Oncology Department, Reina Sofía University Hospital, Córdoba, Spain
| | | | - Silvia Guil-Luna
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Seville, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
- Department of Anatomy and Comparative Pathology, University of Córdoba, Córdoba, Spain
| | - María Auxiliadora Gómez-España
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Seville, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
- Medical Oncology Department, Reina Sofía University Hospital, Córdoba, Spain
| | - Antonio Rodríguez-Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Seville, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
- Medical Oncology Department, Reina Sofía University Hospital, Córdoba, Spain
| | - Enrique Aranda
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Seville, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
- Medical Oncology Department, Reina Sofía University Hospital, Córdoba, Spain
- Department of Medicine, Faculty of Medicine, University of Córdoba, Córdoba, Spain
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Rasmussen LS, Winther SB, Chen IM, Weber B, Ventzel L, Liposits G, Johansen JS, Detlefsen S, Egendal I, Shim S, Christensen S, Pfeiffer P, Ladekarl M. A randomized phase II study of full dose gemcitabine versus reduced dose gemcitabine and nab-paclitaxel in vulnerable patients with non-resectable pancreatic cancer (DPCG-01). BMC Cancer 2023; 23:552. [PMID: 37328835 DOI: 10.1186/s12885-023-11035-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 05/31/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND According to current evidence, the best treatment for fit patients with non-resectable pancreatic cancer (PC) is combination chemotherapy, whereas frail patients are recommended gemcitabine (Gem) monotherapy. Randomized controlled trials in colorectal cancer and a post-hoc analysis of gemcitabine and nab-paclitaxel (GemNab) in PC suggest, however, that reduced dose of combination chemotherapy may be feasible and more efficient compared to monotherapy in frail patients. The aim of this study is to investigate whether reduced dose GemNab is superior to full dose Gem in patients with resectable PC, who are not candidates for full dose combination chemotherapy in first line. METHODS The Danish Pancreas Cancer Group (DPCG)-01 trial is a national multicenter prospective randomized phase II trial. A total of 100 patients in ECOG performance status 0-2 with non-resectable PC, not candidate for full dose combination chemotherapy in first line, but eligible for full dose Gem, will be included. Patients are randomized 1:1 to either full dose Gem or GemNab in 80% of recommended dose. The primary endpoint is progression-free survival. Secondary endpoints are overall survival, overall response rate, quality of life, toxicity and rate of hospitalizations during treatment. The correlation between blood inflammatory markers, including YKL-40 and IL-6, circulating tumor DNA, and tissue biomarkers of resistance to chemotherapy and outcome will be explored. Finally, the study will include measures of frailty (G8, modified G8, and chair-stand-test) to assess whether scoring would enable a personalized allocation to different treatments or indicates a possibility for interventions. DISCUSSION Single-drug treatment with Gem has for frail patients with non-resectable PC been the main treatment option for more than thirty years, but the impact on outcome is modest. If improved results and sustained tolerability with reduced dose combination chemotherapy can be shown, this could change the future practice for this increasing group of patients. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT05841420. Secondary Identifying No: N-20210068. EudraCT No: 2021-005067-52. PROTOCOL VERSION 1.5, 16-MAY-2023.
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Affiliation(s)
- Louise Skau Rasmussen
- Department of Oncology and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Stine B Winther
- Department of Oncology, Odense University Hospital, Odense, Denmark
| | - Inna M Chen
- Department of Oncology, Herlev-Gentofte University Hospital, Copenhagen, Denmark
| | - Britta Weber
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Lise Ventzel
- Department of Oncology, University Hospital of Southern Denmark, Vejle, Denmark
| | - Gabor Liposits
- Department of Oncology, Gødstrup Hospital, Herning, Denmark
| | - Julia Sidenius Johansen
- Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Sönke Detlefsen
- Department of Pathology, Odense University Hospital, and Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Ida Egendal
- Center for Clinical Data Science (CLINDA), and Clinical Cancer Research Center, Aalborg University and, Aalborg University Hospital, Aalborg, Denmark
| | - Susy Shim
- Department of Oncology and Clinical Cancer Research Center, Aalborg University Hospital, and Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Signe Christensen
- Department of Oncology and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Per Pfeiffer
- Department of Oncology, Odense University Hospital, and Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Morten Ladekarl
- Department of Oncology and Clinical Cancer Research Center, Aalborg University Hospital, and Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
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Stubbe BE, Larsen AC, Madsen PH, Krarup HB, Pedersen IS, Lundbye-Christensen S, Hansen CP, Hasselby JP, Johansen AZ, Thorlacius-Ussing O, Johansen JS, Henriksen SD. Promoter hypermethylation of SFRP1 as a prognostic and potentially predictive blood-based biomarker in patients with localized pancreatic ductal adenocarcinoma. Front Oncol 2023; 13:1211292. [PMID: 37333823 PMCID: PMC10272559 DOI: 10.3389/fonc.2023.1211292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023] Open
Abstract
Introduction Current prognostic blood-based biomarkers for pancreatic adenocarcinoma (PDAC) are limited. Recently, promoter hypermethylation of SFRP1 (phSFRP1) has been linked to poor prognosis in patients with gemcitabine-treated stage IV PDAC. This study explores the effects of phSFRP1 in patients with lower stage PDAC. Methods Based on a bisulfite treatment process, the promoter region of the SFRP1 gene was analyzed with methylation-specific PCR. Kaplan-Meier curves, log-rank tests, and generalized linear regression analysis were used to assess restricted mean survival time survival at 12 and 24 months. Results The study included 211 patients with stage I-II PDAC. The median overall survival of patients with phSFRP1 was 13.1 months, compared to 19.6 months in patients with unmethylated SFRP1 (umSFRP1). In adjusted analysis, phSFRP1 was associated with a loss of 1.15 months (95%CI -2.11, -0.20) and 2.71 months (95%CI -2.71, -0.45) of life at 12 and 24 months, respectively. There was no significant effect of phSFRP1 on disease-free or progression-free survival. In stage I-II PDAC, patients with phSFRP1 have worse prognoses than patients with umSFRP1. Discussion Results could indicate that the poor prognosis may be caused by reduced benefit from adjuvant chemotherapy. SFRP1 may help guide the clinician and be a possible target for epigenetically modifying drugs.
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Affiliation(s)
- Benjamin Emil Stubbe
- Department of Gastrointestinal Surgery, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Anders Christian Larsen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Poul Henning Madsen
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
| | - Henrik Bygum Krarup
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
| | - Inge Søkilde Pedersen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
| | | | - Carsten Palnæs Hansen
- Department of Surgery, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Jane Preuss Hasselby
- Department of Pathology, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark
| | - Astrid Zedlitz Johansen
- Department of Oncology, Copenhagen University Hospital – Herlev and Gentofte, Herlev, Denmark
| | - Ole Thorlacius-Ussing
- Department of Gastrointestinal Surgery, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Julia Sidenius Johansen
- Department of Oncology, Copenhagen University Hospital – Herlev and Gentofte, Herlev, Denmark
- Department of Medicine, Copenhagen University Hospital – Herlev and Gentofte, Herlev, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stine Dam Henriksen
- Department of Gastrointestinal Surgery, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
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Identification and Validation of Potentially Clinically Relevant CpG Regions within the Class 2 Tumor Suppressor Gene SFRP1 in Pancreatic Cancer. Cancers (Basel) 2023; 15:cancers15030683. [PMID: 36765639 PMCID: PMC9913221 DOI: 10.3390/cancers15030683] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023] Open
Abstract
In pancreatic cancer treatment, tumor stage-dependent chemotherapies are used to prolong overall survival. By measuring DNA promoter hypermethylation in the plasma of patients with stage IV pancreatic cancer, it was recently shown that promoter DNA methylation of the tumor suppressor gene SFRP1 has a high value for predicting failure of drug treatment with gemcitabine. In this study, we therefore aimed to identify as precisely as possible the region in the SFRP1 promoter that is frequently hypermethylated in pancreatic cancer tissue. First, we used the TCGA data set to define CpG-rich regions flanking the SFRP1 transcription start site that were significantly more methylated in pancreatic cancer compared to normal pancreatic acinar tissue. A core CpG island was identified that exhibited abundant tumor DNA methylation and anti-correlation of SFRP1 mRNA expression. To validate our in silico results, we performed bisulfide conversion followed by DNA pyrosequencing of 28 matched formalin-fixed, paraffin-embedded (FFPE) pancreatic cancer cases and six pancreatic cancer cell lines. A defined block of seven CpG sites within the core CpG island was identified, which confirmed our in silico results by showing significantly higher SFRP1 methylation in pancreatic cancer specimens than in normal pancreatic tissue. By selecting this core CpG island, we were able to determine a median overall survival benefit for the low SFRP1 methylation group compared to the high SFRP1 methylation group (702 versus 517 days, p = 0.01) in the TCGA pancreatic cancer cohort. We propose a compact pyrosequencing assay that can be used in the future to further investigate the prognostic value of SFRP1 promoter hypermethylation in predicting pancreatic cancer chemoresistance. Therefore, instead of DNA analysis from blood (liquid biopsy), DNA easily extractable from cancer tissue blocks (FFPE material) could be used.
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Dahl E, Villwock S, Habenberger P, Choidas A, Rose M, Klebl BM. White Paper: Mimetics of Class 2 Tumor Suppressor Proteins as Novel Drug Candidates for Personalized Cancer Therapy. Cancers (Basel) 2022; 14:cancers14184386. [PMID: 36139547 PMCID: PMC9496810 DOI: 10.3390/cancers14184386] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/01/2022] [Accepted: 09/07/2022] [Indexed: 11/21/2022] Open
Abstract
Simple Summary A concept is presented for a new therapeutic approach, still in its early stages, which focuses on the phenotypic mimicry (“mimesis”) of proteins encoded by highly disease-relevant class 2 tumor suppressor genes that are silenced by DNA promoter methylation. Proteins derived from tumor suppressor genes are usually considered control systems of cells against oncogenic properties. Thus they represent the brakes in the “car-of-life.” Restoring this “brake function” in tumors by administering mimetic drugs may have a significant therapeutic effect. The proposed approach could thus open up a new, hitherto unexploited area of research for the development of anticancer drugs for difficult-to-treat cancers. Abstract The aim of our proposed concept is to find new target structures for combating cancers with unmet medical needs. This, unfortunately, still applies to the majority of the clinically most relevant tumor entities such as, for example, liver cancer, pancreatic cancer, and many others. Current target structures almost all belong to the class of oncogenic proteins caused by tumor-specific genetic alterations, such as activating mutations, gene fusions, or gene amplifications, often referred to as cancer “driver alterations” or just “drivers.” However, restoring the lost function of tumor suppressor genes (TSGs) could also be a valid approach to treating cancer. TSG-derived proteins are usually considered as control systems of cells against oncogenic properties; thus, they represent the brakes in the “car-of-life.” Restoring these tumor-defective brakes by gene therapy has not been successful so far, with a few exceptions. It can be assumed that most TSGs are not being inactivated by genetic alteration (class 1 TSGs) but rather by epigenetic silencing (class 2 TSGs or short “C2TSGs”). Reactivation of C2TSGs in cancer therapy is being addressed by the use of DNA demethylating agents and histone deacetylase inhibitors which act on the whole cancer cell genome. These epigenetic therapies have neither been particularly successful, probably because they are “shotgun” approaches that, although acting on C2TSGs, may also reactivate epigenetically silenced oncogenic sequences in the genome. Thus, new strategies are needed to exploit the therapeutic potential of C2TSGs, which have also been named DNA methylation cancer driver genes or “DNAme drivers” recently. Here we present a concept for a new translational and therapeutic approach that focuses on the phenotypic imitation (“mimesis”) of proteins encoded by highly disease-relevant C2TSGs/DNAme drivers. Molecular knowledge on C2TSGs is used in two complementary approaches having the translational concept of defining mimetic drugs in common: First, a concept is presented how truncated and/or genetically engineered C2TSG proteins, consisting solely of domains with defined tumor suppressive function can be developed as biologicals. Second, a method is described for identifying small molecules that can mimic the effect of the C2TSG protein lost in the cancer cell. Both approaches should open up a new, previously untapped discovery space for anticancer drugs.
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Affiliation(s)
- Edgar Dahl
- Institute of Pathology, Medical Faculty, RWTH Aachen University, D-52074 Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), D-52074 Aachen, Germany
- Correspondence:
| | - Sophia Villwock
- Institute of Pathology, Medical Faculty, RWTH Aachen University, D-52074 Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), D-52074 Aachen, Germany
| | - Peter Habenberger
- Lead Discovery Center GmbH (LDC), Otto-Hahn-Straße 15, D-44227 Dortmund, Germany
| | - Axel Choidas
- Lead Discovery Center GmbH (LDC), Otto-Hahn-Straße 15, D-44227 Dortmund, Germany
| | - Michael Rose
- Institute of Pathology, Medical Faculty, RWTH Aachen University, D-52074 Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), D-52074 Aachen, Germany
| | - Bert M. Klebl
- Lead Discovery Center GmbH (LDC), Otto-Hahn-Straße 15, D-44227 Dortmund, Germany
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DNA Methylation Malleability and Dysregulation in Cancer Progression: Understanding the Role of PARP1. Biomolecules 2022; 12:biom12030417. [PMID: 35327610 PMCID: PMC8946700 DOI: 10.3390/biom12030417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/28/2022] [Accepted: 03/04/2022] [Indexed: 02/05/2023] Open
Abstract
Mammalian genomic DNA methylation represents a key epigenetic modification and its dynamic regulation that fine-tunes the gene expression of multiple pathways during development. It maintains the gene expression of one generation of cells; particularly, the mitotic inheritance of gene-expression patterns makes it the key governing mechanism of epigenetic change to the next generation of cells. Convincing evidence from recent discoveries suggests that the dynamic regulation of DNA methylation is accomplished by the enzymatic action of TET dioxygenase, which oxidizes the methyl group of cytosine and activates transcription. As a result of aberrant DNA modifications, genes are improperly activated or inhibited in the inappropriate cellular context, contributing to a plethora of inheritable diseases, including cancer. We outline recent advancements in understanding how DNA modifications contribute to tumor suppressor gene silencing or oncogenic-gene stimulation, as well as dysregulation of DNA methylation in cancer progression. In addition, we emphasize the function of PARP1 enzymatic activity or inhibition in the maintenance of DNA methylation dysregulation. In the context of cancer remediation, the impact of DNA methylation and PARP1 pharmacological inhibitors, and their relevance as a combination therapy are highlighted.
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