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Conemans EB, Lodewijk L, Moelans CB, Offerhaus GJA, Pieterman CRC, Morsink FH, Dekkers OM, de Herder WW, Hermus AR, van der Horst-Schrivers AN, Drent ML, Bisschop PH, Havekes B, Brosens LAA, Dreijerink KMA, Borel Rinkes IHM, Timmers HTM, Valk GD, Vriens MR. DNA methylation profiling in MEN1-related pancreatic neuroendocrine tumors reveals a potential epigenetic target for treatment. Eur J Endocrinol 2018; 179:153-160. [PMID: 29903750 DOI: 10.1530/eje-18-0195] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/14/2018] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Epigenetic changes contribute to pancreatic neuroendocrine tumor (PanNET) development. Hypermethylation of promoter DNA as a cause of tumor suppressor gene silencing is a well-established oncogenic mechanism that is potentially reversible and therefore an interesting therapeutic target. Multiple endocrine neoplasia type 1 (MEN1) is the most frequent cause of inherited PanNETs. The aim of this study was to determine promoter methylation profiles in MEN1-related PanNETs. DESIGN AND METHODS Methylation-specific multiplex ligation-dependent probe amplification was used to assess promoter methylation of 56 tumor suppressor genes in MEN1-related (n = 61) and sporadic (n = 34) PanNETs. Differences in cumulative methylation index (CMI), individual methylation percentages and frequency of promoter hypermethylation between subgroups were analyzed. RESULTS We found promoter methylation of a large number of potential tumor suppressor genes. CMI (median CMI: 912 vs 876, P = 0.207) was the same in MEN1-related and sporadic PanNETs. We found higher methylation percentages of CASP8 in MEN1-related PanNETs (median: 59% vs 16.5%, P = 0.002). In MEN1-related non-functioning PanNETs, the CMI was higher in larger PanNETs (>2 cm) (median: 969.5 vs 838.5; P = 0.021) and in PanNETs with liver metastases (median: 1036 vs 869; P = 0.013). Hypermethylation of MGMT2 was more frequent in non-functioning PanNETs compared to insulinomas (median: 44.7% vs 8.3%; P = 0.022). Hypermethylation of the Von Hippel-Lindau gene promoter was observed in one MEN1-related PanNET and was associated with loss of protein expression. CONCLUSION Promoter hypermethylation is a frequent event in MEN1-related and sporadic PanNETs. Targeting DNA methylation could be of therapeutic value in MEN1 patients with advanced PanNETs.
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Affiliation(s)
- E B Conemans
- Departments of Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
- Departments of Internal Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Departments of Section Endocrinology, Department of Internal Medicine, VU University Medical Center, Amsterdam, The Netherlands
| | - L Lodewijk
- Departments of Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - C B Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - G J A Offerhaus
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - C R C Pieterman
- Departments of Internal Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - F H Morsink
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - O M Dekkers
- Departments of Endocrinology and Metabolism and Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - W W de Herder
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - A R Hermus
- Department of Endocrinology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - M L Drent
- Departments of Section Endocrinology, Department of Internal Medicine, VU University Medical Center, Amsterdam, The Netherlands
| | - P H Bisschop
- Department of Endocrinology and Metabolism, Academic Medical Center, Amsterdam, The Netherlands
| | - B Havekes
- Division of Endocrinology, Department of Internal Medicine, Maastricht University Medical Center, Maastricht, The Netherlands
| | - L A A Brosens
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - K M A Dreijerink
- Departments of Internal Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Departments of Section Endocrinology, Department of Internal Medicine, VU University Medical Center, Amsterdam, The Netherlands
| | - I H M Borel Rinkes
- Departments of Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - H Th M Timmers
- Regenerative Medicine Center and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - G D Valk
- Departments of Internal Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - M R Vriens
- Departments of Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
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Baker LA, Tiriac H, Corbo V, Boj SF, Hwang CI, Chio IIC, Engle DD, Jager M, Ponz-Sarvise M, Spector MS, Gracanin A, Oni T, Yu KH, Boxtel RV, Huch M, Rivera KD, Wilson JP, Feigin ME, Öhlund D, Handly-Santana A, Ardito-Abraham CM, Ludwig M, Elyada E, Alagesan B, Biffi G, Yordanov GN, Delcuze B, Creighton B, Wright K, Park Y, Morsink FH, Molenaar IQ, Rinkes IHB, Cuppen E, Hao Y, Jin Y, Nijman IJ, Iacobuzio-Donahue C, Leach SD, Pappin DJ, Hammell M, Klimstra DS, Basturk O, Hruban RH, Offerhaus GJ, Vries RG, Clevers H, Tuveson DA. Abstract B16: Using human patient-derived organoids to identify genetic dependencies in pancreatic cancer. Clin Cancer Res 2016. [DOI: 10.1158/1557-3265.pdx16-b16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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
Pancreatic ductal adenocarcinoma (PDA) is one of the most lethal malignancies due to its late diagnosis and limited response to treatment. Tractable model systems to interrogate pathways involved in pancreatic tumorigenesis and to probe individual responses to novel therapies are urgently needed. To that end, we established methods to culture normal and neoplastic pancreatic duct cells as three-dimensional organoid cultures. Pancreatic organoids can be rapidly generated from resected tumors or fine needle biopsies, survive cryopreservation, and exhibit ductal- and disease-stage-specific characteristics. Following orthotopic transplant, neoplastic organoids recapitulated the full spectrum of tumor development by forming early-grade neoplasms that progressed to locally invasive and metastatic carcinomas, demonstrating the utility of organoids to model the stages of PDA tumorigenesis. Monolayer cell lines were generated from organoid cultures with high efficiency, creating a diverse collection of new PDA cell lines. To better understand pathways involved in PDA progression, we performed transcriptomic and proteomic analyses of murine organoids derived from normal pancreatic ducts, pancreatic intraepithelial neoplasias (PanINs), and PDAs. These datasets revealed expression changes associated with early and late pancreatic tumorigenesis. To identify genes dysregulated during pancreatic tumorigenesis whose depletion impaired human PDA cells, a CRISPR-Cas competition assay was employed. Taken together, pancreatic organoids offer a novel model system for studying pancreatic cancer biology and can be used to screen for genetic dependencies in PDA.
Citation Format: Lindsey A. Baker, Hervé Tiriac, Vincenzo Corbo, Sylvia F. Boj, Chang-il Hwang, Iok In Christine Chio, Danielle D. Engle, Myrthe Jager, Mariano Ponz-Sarvise, Mona S. Spector, Ana Gracanin, Tobiloba Oni, Kenneth H. Yu, Ruben van Boxtel, Meritxell Huch, Keith D. Rivera, John P. Wilson, Michael E. Feigin, Daniel Öhlund, Abram Handly-Santana, Christine M. Ardito-Abraham, Michael Ludwig, Ela Elyada, Brinda Alagesan, Giulia Biffi, Georgi N. Yordanov, Bethany Delcuze, Brianna Creighton, Kevin Wright, Youngkyu Park, Folkert H.M. Morsink, I. Quintus Molenaar, Inne H. Borel Rinkes, Edwin Cuppen, Yuan Hao, Ying Jin, Isaac J. Nijman, Christine Iacobuzio-Donahue, Steven D. Leach, Darryl J. Pappin, Molly Hammell, David S. Klimstra, Olca Basturk, Ralph H. Hruban, George Johan Offerhaus, Robert G.J. Vries, Hans Clevers, David A. Tuveson. Using human patient-derived organoids to identify genetic dependencies in pancreatic cancer. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr B16.
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Affiliation(s)
| | - Hervé Tiriac
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | | | - Sylvia F. Boj
- 3Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, Netherlands,
| | | | | | | | - Myrthe Jager
- 3Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, Netherlands,
| | | | | | - Ana Gracanin
- 3Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, Netherlands,
| | - Tobiloba Oni
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | - Kenneth H. Yu
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | - Ruben van Boxtel
- 3Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, Netherlands,
| | - Meritxell Huch
- 3Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, Netherlands,
| | | | | | | | - Daniel Öhlund
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | | | | | | | - Ela Elyada
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | | | - Giulia Biffi
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | | | | | | | - Kevin Wright
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | - Youngkyu Park
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | | | | | | | - Edwin Cuppen
- 3Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, Netherlands,
| | - Yuan Hao
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | - Ying Jin
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | - Isaac J. Nijman
- 3Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, Netherlands,
| | | | | | | | - Molly Hammell
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | | | - Olca Basturk
- 6Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | | | - Robert G.J. Vries
- 3Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, Netherlands,
| | - Hans Clevers
- 3Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, Netherlands,
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Heerma van Voss MR, Vesuna F, Trumpi K, Brilliant J, Kodach LL, Morsink FH, Offerhaus GJA, Buerger H, van der Wall E, van Diest PJ, Raman V. Abstract 3570: Identification of the DEAD box RNA helicase DDX3 as a therapeutic target in colorectal cancer. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-3570] [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
Over 85% of colorectal cancers is driven by aberrations in the Wnt-signaling pathway. Thus, identifying druggable targets in this pathway can be beneficial for optimizing colorectal cancer treatment. Within this context, a member of the RNA helicase gene family, DDX3, has been identified to exhibit oncogenic properties in breast and lung carcinomas as well as medulloblastomas. Notably, recent studies have identified DDX3 as a multilevel activator of Wnt-signaling in both normal and transformed cells without activating mutations in the Wnt signaling pathway. In this study, we evaluated whether DDX3 also plays a role in the constitutionally activated Wnt-signaling that drives colorectal cancer and therefore could be a potential therapeutic target in this cancer type.
To determine if DDX3 is expressed in colorectal cancers, we immunohistochemically stained a cohort of 303 Dutch and German colorectal cancer patients. We found 40.4% of these tumors to overexpress DDX3 in comparison to the surrounding normal tissue. DDX3 expression was found predominantly in the cytoplasm and occasionally in the nucleus. High cytoplasmic DDX3 expression correlated with nuclear Beta-catenin expression, a marker of activated Wnt-signaling. The presence of nuclear DDX3 expression correlated with shorter overall survival (HR = 2.38, 95% CI 1.45-3.93, p < 0.001). Functionally, we validated these findings in vitro and found that inhibition of DDX3 with siRNA resulted in reduced proliferation and a G1-arrest in the HCT116 and HT29 colorectal cancer cell lines. This finding further supports the potential oncogenic role of DDX3 in colorectal cancer.
With respect to targeting DDX3, we developed a small molecule inhibitor of DDX3, referred to as RK-33. RK-33 is designed to bind to the ATP-binding site of DDX3 and abrogate its functional activity. As proof of principle, we demonstrated that RK-33 binds preferentially to DDX3 and not to DDX5 and DDX17, other members of the RNA helicase family. Moreover, RK-33 inhibited the helicase activity in an in vitro assay. Furthermore, treatment of colorectal cancer cell lines and patient derived 3D- tumor cell cultures indicated that RK-33 inhibits growth and promotes cell death with IC-50 values ranging from 2.5 to 8 uM.
To further elucidate the mechanism of RK-33, we studied if inhibition of DDX3 with RK-33 could cause inhibition of Wnt-signaling in colorectal cancer cell lines. Treatment with RK-33 indeed resulted in reduced TCF-reporter activity and lowered the mRNA expression levels of the Wnt-signaling downstream target genes AXIN-2, C-MYC, CCND1 and BIRC5A.
Overall, we conclude that DDX3 has an oncogenic role in colorectal cancer. Inhibition of DDX3 with the small molecule inhibitor RK-33 causes potent inhibition of Wnt-signaling and is a promising future treatment strategy in colorectal cancer.
Citation Format: Marise R. Heerma van Voss, Farhad Vesuna, Kari Trumpi, Justin Brilliant, Liudmila L. Kodach, Folkert H.M. Morsink, G. Johan A. Offerhaus, Horst Buerger, Elsken van der Wall, Paul J. van Diest, Venu Raman. Identification of the DEAD box RNA helicase DDX3 as a therapeutic target in colorectal cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3570. doi:10.1158/1538-7445.AM2015-3570
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Venu Raman
- 1Johns Hopkins Medical Institutions, Baltimore, MD
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Brosens LAA, van Hattem WA, Kools MCE, Ezendam C, Morsink FH, de Leng WWJ, Giardiello FM, Offerhaus GJA. No TGFBRII germline mutations in juvenile polyposis patients without SMAD4 or BMPR1A mutation. Gut 2009; 58:154-6. [PMID: 19091845 PMCID: PMC2703607 DOI: 10.1136/gut.2008.161232] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- L A A Brosens
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - W A van Hattem
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands,Department of Pathology, Academic Medical Center, Amsterdam, The Netherlands
| | - M C E Kools
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - C Ezendam
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - F H Morsink
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - W W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - F M Giardiello
- Department of Medicine, Division of Gastroenterology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - G J A Offerhaus
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands,Department of Pathology, Academic Medical Center, Amsterdam, The Netherlands,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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6
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van Hattem WA, Brosens LAA, de Leng WWJ, Morsink FH, Lens S, Carvalho R, Giardiello FM, Offerhaus GJA. Large genomic deletions of SMAD4, BMPR1A and PTEN in juvenile polyposis. Gut 2008; 57:623-7. [PMID: 18178612 DOI: 10.1136/gut.2007.142927] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND/AIMS Juvenile polyposis syndrome (JPS) is a rare autosomal dominant disorder characterised by multiple gastrointestinal juvenile polyps and an increased risk of colorectal cancer. This syndrome is caused by germline mutation of either SMAD4 or BMPR1A, and possibly ENG. PTEN, originally linked to Cowden syndrome and Bannayan-Riley-Ruvalcaba syndrome, has also been associated with JPS. By direct sequencing, germline mutations are found in only 30-40% of patients with a JPS phenotype. Therefore, alternative ways of inactivation of the known JPS genes, or additional genes predisposing to JPS may be involved. In this study, a comprehensive genetic analysis of SMAD4, BMPR1A, PTEN and ENG is performed through direct sequencing and multiplex ligation-dependent probe amplification (MLPA) in JPS patients. METHODS Archival material of 29 patients with JPS from 27 families was collected. Direct sequencing and MLPA analysis were performed to search for germline defects in SMAD4, BMPR1A, PTEN and ENG. RESULTS A germline defect in SMAD4, BMPR1A or PTEN was found in 13 of 27 (48.1%) unrelated JPS patients. Nine mutations (33.3%) were detected by direct sequencing, including six (22.2%) SMAD4 mutations and three (11.1%) BMPR1A mutations. MLPA identified four additional patients (14.8%) with germline hemizygous large genomic deletions, including one deletion of SMAD4, one deletion of exons 10 and 11 of BMPR1A, and two unrelated patients with deletion of both BMPR1A and PTEN. No ENG gene mutations were found. CONCLUSION Large genomic deletions of SMAD4, BMPR1A and PTEN are a common cause of JPS. Using direct sequencing and MLPA, a germline defect was detected in 48.1% of JPS patients. MLPA identified 14.8% (4/27) of these mutations. Since a substantial percentage of JPS patients carry a germline deletion and MLPA is a reliable and user-friendly technique, it is concluded that MLPA is a valuable adjunct in JPS diagnosis.
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Affiliation(s)
- W A van Hattem
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
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