1
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Chi P, Qin LX, Camacho N, Kelly CM, D'Angelo SP, Dickson MA, Gounder MM, Keohan ML, Movva S, Nacev BA, Rosenbaum E, Thornton KA, Crago AM, Francis JH, Martindale M, Phelan HT, Biniakewitz MD, Lee CJ, Singer S, Hwang S, Berger MF, Chen Y, Antonescu CR, Tap WD. Phase Ib Trial of the Combination of Imatinib and Binimetinib in Patients with Advanced Gastrointestinal Stromal Tumors. Clin Cancer Res 2022; 28:1507-1517. [PMID: 35110417 PMCID: PMC9012681 DOI: 10.1158/1078-0432.ccr-21-3909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/06/2022] [Accepted: 01/31/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE This phase Ib trial was designed to evaluate the safety and early efficacy signal of the combination of imatinib and binimetinib in patients with imatinib-resistant advanced gastrointestinal stromal tumors (GISTs). PATIENTS AND METHODS This trial used a standard 3 + 3 design to determine the recommended phase II dose (RP2D). Additional patients were enrolled on an expansion cohort at the RP2D enriching for succinate dehydrogenase (SDH)-deficient GISTs to explore potential efficacy. RESULTS The trial enrolled nine patients in the dose-escalation cohort and 14 in the dose-expansion cohort including six with SDH-deficient GISTs. Imatinib 400 mg daily with binimetinib 45 mg twice daily was established as the RP2D. Dose-limiting toxicity (DLT) was asymptomatic grade 4 creatinine phosphokinase (CPK) elevation. The most common non-DLT grade 3/4 toxicity was asymptomatic CPK elevation (69.6%). Other common ≥grade 2 toxicities included peripheral edema (17.4%), acneiform rash (21.7%), anemia (30.4%), hypophosphatemia (39.1%), and aspartate aminotransferase (AST) increase (17.4%). Two serious adverse events occurred (grade 2 dropped head syndrome and grade 3 central retinal vein occlusion). No unexpected toxicities were observed. Limited clinical activity was observed in KIT-mutant GIST. For SDH-deficient GISTs, one of five had confirmed RECIST1.1 partial response (PR). The median progression-free survival (mPFS) in patients with SDH-deficient GIST was 45.1 months [95% confidence interval (CI), 15.8-not estimable (NE)]; the median overall survival (mOS) was not reached (95% CI, 31.6 months-NE). One patient with a refractory metastatic SDH-deficient GIST had an exceptional pathologic response and durable clinical benefit. CONCLUSIONS The combination of imatinib and binimetinib is safe with manageable toxicity and has encouraging activity in SDH-deficient but not imatinib-refractory KIT/PDGFRA-mutant GISTs. The observed clinical benefits provide a motivation for a larger trial of the combination strategy in SDH-deficient GISTs.
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Affiliation(s)
- Ping Chi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Li-Xuan Qin
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Niedzica Camacho
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ciara M. Kelly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Sandra P. D'Angelo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Mark A. Dickson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Mrinal M. Gounder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Mary L. Keohan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Sujana Movva
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Benjamin A. Nacev
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Evan Rosenbaum
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Katherine A. Thornton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Aimee M. Crago
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Surgery, Weill Cornell Medical College, New York, New York
| | - Jasmine H. Francis
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Ophthalmology, Weill Cornell Medical College, New York, New York
| | - Moriah Martindale
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Haley T. Phelan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Cindy J. Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samuel Singer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Surgery, Weill Cornell Medical College, New York, New York
| | - Sinchun Hwang
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F. Berger
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | | | - William D. Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
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Banerjee S, Yoon H, Ting S, Tang CM, Yebra M, Wenzel AT, Yeerna H, Mesirov JP, Wechsler-Reya RJ, Tamayo P, Sicklick JK. KIT low Cells Mediate Imatinib Resistance in Gastrointestinal Stromal Tumor. Mol Cancer Ther 2021; 20:2035-2048. [PMID: 34376580 PMCID: PMC8492542 DOI: 10.1158/1535-7163.mct-20-0973] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/06/2021] [Accepted: 06/30/2021] [Indexed: 11/16/2022]
Abstract
Gastrointestinal stromal tumor (GIST) is commonly driven by oncogenic KIT mutations that are effectively targeted by imatinib (IM), a tyrosine kinase inhibitor (TKI). However, IM does not cure GIST, and adjuvant therapy only delays recurrence in high-risk tumors. We hypothesized that GIST contains cells with primary IM resistance that may represent a reservoir for disease persistence. Here, we report a subpopulation of CD34+KITlow human GIST cells that have intrinsic IM resistance. These cells possess cancer stem cell-like expression profiles and behavior, including self-renewal and differentiation into CD34+KIThigh progeny that are sensitive to IM treatment. We also found that TKI treatment of GIST cell lines led to induction of stem cell-associated transcription factors (OCT4 and NANOG) and concomitant enrichment of the CD34+KITlow cell population. Using a data-driven approach, we constructed a transcriptomic-oncogenic map (Onco-GPS) based on the gene expression of 134 GIST samples to define pathway activation during GIST tumorigenesis. Tumors with low KIT expression had overexpression of cancer stem cell gene signatures consistent with our in vitro findings. Additionally, these tumors had activation of the Gas6/AXL pathway and NF-κB signaling gene signatures. We evaluated these targets in vitro and found that primary IM-resistant GIST cells were effectively targeted with either single-agent bemcentinib (AXL inhibitor) or bardoxolone (NF-κB inhibitor), as well as with either agent in combination with IM. Collectively, these findings suggest that CD34+KITlow cells represent a distinct, but targetable, subpopulation in human GIST that may represent a novel mechanism of primary TKI resistance, as well as a target for overcoming disease persistence following TKI therapy.
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Affiliation(s)
- Sudeep Banerjee
- Department of Surgery, Division of Surgical Oncology, University of California, San Diego, California
- Department of Surgery, University of California, Los Angeles, California
- Moores Cancer Center, University of California, San Diego, California
| | - Hyunho Yoon
- Department of Surgery, Division of Surgical Oncology, University of California, San Diego, California
- Moores Cancer Center, University of California, San Diego, California
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Stephanie Ting
- Moores Cancer Center, University of California, San Diego, California
- Department of Medicine, Division of Medical Genetics, University of California, San Diego, California
| | - Chih-Min Tang
- Department of Surgery, Division of Surgical Oncology, University of California, San Diego, California
- Moores Cancer Center, University of California, San Diego, California
| | - Mayra Yebra
- Department of Surgery, Division of Surgical Oncology, University of California, San Diego, California
- Moores Cancer Center, University of California, San Diego, California
| | - Alexander T Wenzel
- Moores Cancer Center, University of California, San Diego, California
- Department of Medicine, Division of Medical Genetics, University of California, San Diego, California
| | - Huwate Yeerna
- Moores Cancer Center, University of California, San Diego, California
- Department of Medicine, Division of Medical Genetics, University of California, San Diego, California
| | - Jill P Mesirov
- Moores Cancer Center, University of California, San Diego, California
- Department of Medicine, Division of Medical Genetics, University of California, San Diego, California
| | | | - Pablo Tamayo
- Moores Cancer Center, University of California, San Diego, California
- Department of Medicine, Division of Medical Genetics, University of California, San Diego, California
- UCSD Center for Novel Therapeutics, La Jolla, California
| | - Jason K Sicklick
- Department of Surgery, Division of Surgical Oncology, University of California, San Diego, California.
- Moores Cancer Center, University of California, San Diego, California
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Zhao Y, Liu X, Xiao K, Wang L, Li Y, Kan M, Jiang Z. Clinicopathological value of long non-coding RNA profiles in gastrointestinal stromal tumor. PeerJ 2021; 9:e11946. [PMID: 34557343 PMCID: PMC8420874 DOI: 10.7717/peerj.11946] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) have been implicated in diagnosis and prognosis in various cancers. However, few lncRNA signatures have been established for prediction of gastrointestinal stromal tumors (GIST). We aimed to explore a lncRNA signature profile that associated with clinical relevance by mining data from Gene Expression Ominus (GEO) and Surveillance, Epidemiology, and End Results (SEER) Program. Methods Using a lncRNA-mining approach, we performed non-negative matrix factorization (NMF) consensus algorithm in Gastrointestinal stromal tumors (GISTs) cohorts (61 patients from GSE8167 and GSE17743) to cluster LncRNA expression profiles. Comparative markers selection, and Gene Set Enrichment Analysis (GSEA) algorithm were performed between distinct molecular subtypes of GIST. The survival rate of GIST patients from SEER stratified by gender were compared by Kaplan-Meier method and log-rank analysis. lncRNA-mRNA co-expression analysis was performed by Pearson correlation coefficients (PCC) using R package LINC. Somatic copy number alterations of GIST patients (GSE40966) were analyzed via web server GenePattern GISTIC2 algorithm. Results A total of four lncRNA molecular subtypes of GIST were identified with distinct biological pathways and clinical characteristics. LncRNA expression profiles well clustered the GIST samples into small size (<5 mm) and large size tumors (>5 mm), which is a fundamental index for GIST malignancy diagnosis. Several lncRNAs with abundant expression (LRRC75A-AS1, HYMAI, NEAT1, XIST and FTX) were closely associated with tumor size, which may suggest to be biomarkers for the GIST malignancy. Particularly, LRRC75A-AS1 was positively associated with tumor diameters and suggested an oncogene in GIST. Co-expression analysis suggested that chromosome region 17p11.2-p12 may contribute to the oncogenic process in malignant GIST. Interestingly, the gender had a strong influence on clustering by lncRNA expression profile. Data from the Surveillance, Epidemiology, and End Results (SEER) Program were further explored and 7983 patients who were diagnosed with GISTs from 1973 to 2014 were enrolled for analysis. The results also showed the favorable prognosis for female patients. The survival rate between male and female with GIST was statistically significant (P < 0.0001). Gene set enrichment analysis (GSEA) indicated distinct pathways between female and male, and malignant GIST was associated with several cancer metabolism and cell cycle associated pathways. Conclusions This lncRNAs-based classification for GISTs may provide a molecular classification applicable to individual GIST that has implications to influence lncRNA markers selection and prediction of tumor progression.
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Affiliation(s)
- Yan Zhao
- Clinical Medical College of Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu Province, China
| | - Xinxin Liu
- Department of Gastrointestinal Surgery, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, Jiangsu Province, China
| | - Keshuai Xiao
- Department of General Surgery, Yangzhou Hongquan Hospital, Yangzhou, Jiangsu Province, China
| | - Liwen Wang
- Department of Gastrointestinal Surgery, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, Jiangsu Province, China
| | - Yuping Li
- Department of Gastrointestinal Surgery, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, Jiangsu Province, China
| | - Mingyun Kan
- Department of Gastrointestinal Surgery, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, Jiangsu Province, China
| | - Zhiwei Jiang
- Department of Gastrointestinal Surgery, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, Jiangsu Province, China
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4
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Ju KC, Zhang B, Hu YL, Feng Y, Li XH, Liu YF, Li P, Mao QS, Xue WJ. High expression of G protein subunit gamma 13 is associated with poor prognosis of gastrointestinal stromal tumor. Pathol Res Pract 2020; 216:153143. [PMID: 32853961 DOI: 10.1016/j.prp.2020.153143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/07/2020] [Accepted: 07/24/2020] [Indexed: 12/18/2022]
Abstract
The G protein subunit gamma 13 (GNG13) plays an important role in olfaction, vision, and biological behavior. However, our knowledge of the relationship between GNG13 expression and the clinicopathological features of gastrointestinal tumors is insufficient. Therefore, we used the Oncomine database to evaluate the expression of GNG13 mRNA in gastric cancer, the result showed that there was no significant difference in the expression of GNG13 between gastric cancer and adjacent normal tissues, and GNG13 mRNA expression was assessed in 32 matched pairs of Gastrointestinal adenocarcinoma tissues and adjacent normal tissues as well as 32 matched pairs of gastrointestinal stromal tumor (GIST) and adjacent normal tissues by quantitative reverse transcription-polymerase chain reaction analysis. The results suggested that GNG13 is upregulated in gastrointestinal stromal tumors. Immunohistochemical analysis was used to detect the GNG13 in the tissues of 123 patients with GIST. High cytoplasmic expression of GNG13, which was observed in 65.85 % of GIST patients, significantly correlated with mitotic index(P = 0.036) and tumor size(P = 0.024). Multiple logistic regression analysis showed that the expression of GNG13 was significantly associated with tumor size. Kaplan-Meier analysis indicated that high GNG13 expression was associated with poor prognosis of GIST. Multivariate Cox regression analysis indicated that the expression of GNG13, mitotic index and tumor size were independent adverse prognostic factors of GIST. These findings suggest that GNG13 is associated with the malignant phenotype of GIST and may serve as a marker of poor prognosis.
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Affiliation(s)
- Ke-Cheng Ju
- Department of Gastrointestinal Surgery, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China; Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China
| | - Bin Zhang
- Department of Infectious Diseases, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China
| | - Yi-Lin Hu
- Department of Gastrointestinal Surgery, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China; Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China
| | - Ying Feng
- Department of Gastrointestinal Surgery, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China; Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China
| | - Xiao-Hong Li
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China
| | - Yi-Fei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China
| | - Peng Li
- Department of Gastrointestinal Surgery, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China
| | - Qin-Sheng Mao
- Department of Gastrointestinal Surgery, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China.
| | - Wan-Jiang Xue
- Department of Gastrointestinal Surgery, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China; Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China.
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5
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Flavahan WA, Drier Y, Johnstone SE, Hemming ML, Tarjan DR, Hegazi E, Shareef SJ, Javed NM, Raut CP, Eschle BK, Gokhale PC, Hornick JL, Sicinska ET, Demetri GD, Bernstein BE. Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs. Nature 2019; 575:229-233. [PMID: 31666694 PMCID: PMC6913936 DOI: 10.1038/s41586-019-1668-3] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 09/10/2019] [Indexed: 12/22/2022]
Abstract
Epigenetic aberrations are widespread in cancer, yet the underlying
mechanisms and causality remain poorly understood1-3.
A subset of gastrointestinal stromal tumors (GISTs) lack canonical kinase
mutations but instead have succinate dehydrogenase (SDH)-deficiency and global
DNA hyper-methylation4,5. Here we associate this hyper-methylation
with changes in genome topology that activate oncogenic programs. To investigate
epigenetic alterations systematically, we mapped DNA methylation, CTCF
insulators, enhancers, and chromosome topology in KIT-mutant,
PDGFRA-mutant, and SDH-deficient GISTs. Although these
respective subtypes shared similar enhancer landscapes, we identified hundreds
of putative insulators where DNA methylation replaced CTCF binding in
SDH-deficient GISTs. We focused on a disrupted insulator that normally
partitions a core GIST super-enhancer from the FGF4 oncogene.
Recurrent loss of this insulator alters locus topology in SDH-deficient GISTs,
allowing aberrant physical interaction between enhancer and oncogene.
CRISPR-mediated excision of the corresponding CTCF motifs in an SDH-intact GIST
model disrupted the boundary and strongly up-regulated FGF4
expression. We also identified a second recurrent insulator loss event near the
KIT oncogene, which is also highly expressed across
SDH-deficient GISTs. Finally, we established a patient-derived xenograft (PDX)
from an SDH-deficient GIST that faithfully maintains the epigenetics of the
parental tumor, including hyper-methylation and insulator defects. This PDX
model is highly sensitive to FGF receptor (FGFR) inhibitor, and more so to
combined FGFR and KIT inhibition, validating the functional significance of the
underlying epigenetic lesions. Our study reveals how epigenetic alterations can
drive oncogenic programs in the absence of canonical kinase mutations, with
implications for mechanistic targeting of aberrant pathways in cancers.
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Affiliation(s)
- William A Flavahan
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yotam Drier
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,The Lautenberg Center for Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University, Jerusalem, Israel.
| | - Sarah E Johnstone
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew L Hemming
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School Boston, Boston, MA, USA
| | - Daniel R Tarjan
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Esmat Hegazi
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sarah J Shareef
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nauman M Javed
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chandrajit P Raut
- Department of Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Benjamin K Eschle
- Experimental Therapeutics Core, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Prafulla C Gokhale
- Experimental Therapeutics Core, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ewa T Sicinska
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - George D Demetri
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School Boston, Boston, MA, USA. .,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
| | - Bradley E Bernstein
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
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6
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Wang WJ, Li HT, Yu JP, Li YM, Han XP, Chen P, Yu WW, Chen WK, Jiao ZY, Liu HB. Identification of key genes and associated pathways in KIT/PDGFRA wild‑type gastrointestinal stromal tumors through bioinformatics analysis. Mol Med Rep 2018; 18:4499-4515. [PMID: 30221743 PMCID: PMC6172374 DOI: 10.3892/mmr.2018.9457] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 08/23/2018] [Indexed: 12/20/2022] Open
Abstract
Gastrointestinal stromal tumors (GISTs) are the most common type of mesenchymal tumor in the gastrointestinal tract. The present study aimed to identify the potential candidate biomarkers that may be involved in the pathogenesis and progression of v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (KIT)/platelet-derived growth factor receptor α (PDGFRA) wild-type GISTs. A joint bioinformatics analysis was performed to identify the differentially expressed genes (DEGs) in wild-type GIST samples compared with KIT/PDGFRA mutant GIST samples. Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs was conducted using Database for Annotation, Visualization and Integrated Discovery and KEGG Orthology-Based Annotation System (KOBAS) online tools, respectively. Protein-protein interaction (PPI) networks of the DEGs were constructed using Search Tool for the Retrieval of Interacting Genes online tool and Cytoscape, and divided into sub-networks using the Molecular Complex Detection (MCODE) plug-in. Furthermore, enrichment analysis of DEGs in the modules was analyzed with KOBAS. In total, 546 DEGs were identified, including 238 upregulated genes primarily enriched in ‘cell adhesion’, ‘biological adhesion’, ‘cell-cell signaling’, ‘PI3K-Akt signaling pathway’ and ‘ECM-receptor interaction’, while the 308 downregulated genes were predominantly involved in ‘inflammatory response’, ‘sterol metabolic process’ and ‘fatty acid metabolic process’, ‘small GTPase mediated signal transduction’, ‘cAMP signaling pathway’ and ‘proteoglycans in cancer’. A total of 25 hub genes were obtained and four modules were mined from the PPI network, and sub-networks also revealed these genes were primarily involved in significant pathways, including ‘PI3K-Akt signaling pathway’, ‘proteoglycans in cancer’, ‘pathways in cancer’, ‘Rap1 signaling pathway’, ‘ECM-receptor interaction’, ‘phospholipase D signaling pathway’, ‘ras signaling pathway’ and ‘cGMP-PKG signaling pathway’. These results suggested that several key hub DEGs may serve as potential candidate biomarkers for wild-type GISTs, including phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit γ, insulin like growth factor 1 receptor, hepatocyte growth factor, thrombospondin 1, Erb-B2 receptor tyrosine kinase 2 and matrix metallopeptidase 2. However, further experiments are required to confirm these results.
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Affiliation(s)
- Wen-Jie Wang
- Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Hong-Tao Li
- Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Jian-Ping Yu
- Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Yu-Min Li
- Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Xiao-Peng Han
- Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Peng Chen
- Department of General Surgery, Lanzhou General Hospital of Chinese People's Liberation Army, Lanzhou, Gansu 730050, P.R. China
| | - Wen-Wen Yu
- Department of General Surgery, Lanzhou General Hospital of Chinese People's Liberation Army, Lanzhou, Gansu 730050, P.R. China
| | - Wei-Kai Chen
- Department of General Surgery, Lanzhou General Hospital of Chinese People's Liberation Army, Lanzhou, Gansu 730050, P.R. China
| | - Zuo-Yi Jiao
- Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Hong-Bin Liu
- Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu 730030, P.R. China
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7
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Hedgehog pathway dysregulation contributes to the pathogenesis of human gastrointestinal stromal tumors via GLI-mediated activation of KIT expression. Oncotarget 2018; 7:78226-78241. [PMID: 27793025 PMCID: PMC5346634 DOI: 10.18632/oncotarget.12909] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 10/13/2016] [Indexed: 12/20/2022] Open
Abstract
Gastrointestinal stromal tumors (GIST) arise within the interstitial cell of Cajal (ICC) lineage due to activating KIT/PDGFRA mutations. Both ICC and GIST possess primary cilia (PC), which coordinate PDGFRA and Hedgehog signaling, regulators of gastrointestinal mesenchymal development. Therefore, we hypothesized that Hedgehog signaling may be altered in human GIST and controls KIT expression. Quantitative RT-PCR, microarrays, and next generation sequencing were used to describe Hedgehog/PC-related genes in purified human ICC and GIST. Genetic and pharmacologic approaches were employed to investigate the effects of GLI manipulation on KIT expression and GIST cell viability. We report that Hedgehog pathway and PC components are expressed in ICC and GIST and subject to dysregulation during GIST oncogenesis, irrespective of KIT/PDGFRA mutation status. Using genomic profiling, 10.2% of 186 GIST studied had potentially deleterious genomic alterations in 5 Hedgehog-related genes analyzed, including in the PTCH1 tumor suppressor (1.6%). Expression of the predominantly repressive GLI isoform, GLI3, was inversely correlated with KIT mRNA levels in GIST cells and non-KIT/non-PDGFRA mutant GIST. Overexpression of the 83-kDa repressive form of GLI3 or small interfering RNA-mediated knockdown of the activating isoforms GLI1/2 reduced KIT mRNA. Treatment with GLI1/2 inhibitors, including arsenic trioxide, significantly increased GLI3 binding to the KIT promoter, decreased KIT expression, and reduced viability in imatinib-sensitive and imatinib-resistant GIST cells. These data offer new evidence that genes necessary for Hedgehog signaling and PC function in ICC are dysregulated in GIST. Hedgehog signaling activates KIT expression irrespective of mutation status, offering a novel approach to treat imatinib-resistant GIST.
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Boonstra PA, Gietema JA, Suurmeijer AJH, Groves MR, de Assis Batista F, Schuuring E, Reyners AKL. Tyrosine kinase inhibitor sensitive PDGFRΑ mutations in GIST: Two cases and review of the literature. Oncotarget 2017; 8:109836-109847. [PMID: 29312652 PMCID: PMC5752565 DOI: 10.18632/oncotarget.22663] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 10/30/2017] [Indexed: 12/31/2022] Open
Abstract
Gastrointestinal stromal tumors (GISTs) are rare mesenchymal malignancies of the gastrointestinal tract. Most GISTs harbor a c-KIT (80%) or a PDGFRα (10%) mutation that leads to constitutive activation of the tyrosine kinase receptor. Response to treatment with tyrosine kinase inhibitors (TKIs) is dependent on mutational status of the tumor. The most common mutation in PDGFRα, D842V, is known to be imatinib resistant. Almost all other PDGFRα mutations are imatinib sensitive. We describe two patients with a PDGFRα exon 18 mutated GIST responding to treatment with TKIs. One of these patients has a p.M844_S847 deletion, not previously described in relation with TKI treatment response. Mutations in circulating tumor DNA were detectable with digital droplet PCR in serial plasma samples taken during treatment and correlated with treatment response of both patients. Computer 3D-modeling of the PDGFRα kinase domain of these two variants revealed no direct interference in imatinib or sunitinib binding and no effect in its activity in contrast to the reported structure of the imatinib resistant D842V mutation. An overview is given of the literature regarding the evidence of patients with different PDGFRα mutated GISTs on response to TKIs. The findings emphasize the use of mutational analysis in GIST to provide patients personalized treatment. Detection of mutations in plasma is feasible and can provide real-time information concerning treatment response. We suggest to register GIST patients with these uncommon mutations in a prospective international database to understand the tumor biology and obtain more evidence of such mutations to predict treatment response.
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Affiliation(s)
- Pieter A Boonstra
- University of Groningen, University Medical Center Groningen, Department of Medical Oncology, Hanzeplein, Groningen, The Netherlands
| | - Jourik A Gietema
- University of Groningen, University Medical Center Groningen, Department of Medical Oncology, Hanzeplein, Groningen, The Netherlands
| | - Albert J H Suurmeijer
- University of Groningen, University Medical Center Groningen, Department of Pathology, Hanzeplein, Groningen, The Netherlands
| | - Matthew R Groves
- University of Groningen, Faculty of Science and Engineering, Antonius Deusinglaan, Groningen, The Netherlands
| | - Fernando de Assis Batista
- University of Groningen, Faculty of Science and Engineering, Antonius Deusinglaan, Groningen, The Netherlands
| | - Ed Schuuring
- University of Groningen, University Medical Center Groningen, Department of Pathology, Hanzeplein, Groningen, The Netherlands
| | - Anna K L Reyners
- University of Groningen, University Medical Center Groningen, Department of Medical Oncology, Hanzeplein, Groningen, The Netherlands
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Joglekar-Javadekar M, Van Laere S, Bourne M, Moalwi M, Finetti P, Vermeulen PB, Birnbaum D, Dirix LY, Ueno N, Carter M, Rains J, Ramachandran A, Bertucci F, van Golen KL. Characterization and Targeting of Platelet-Derived Growth Factor Receptor alpha (PDGFRA) in Inflammatory Breast Cancer (IBC). Neoplasia 2017; 19:564-573. [PMID: 28609680 PMCID: PMC5470553 DOI: 10.1016/j.neo.2017.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 03/09/2017] [Accepted: 03/13/2017] [Indexed: 01/05/2023] Open
Abstract
PURPOSE: Inflammatory breast cancer (IBC) is arguably the deadliest form of breast cancer due to its rapid onset and highly invasive nature. IBC carries 5- and 10-year disease-free survival rates of ~45% and <20%, respectively. Multiple studies demonstrate that in comparison with conventional breast cancer, IBC has a unique molecular identity. Here, we have identified platelet-derived growth factor receptor alpha (PDGFRA) as being uniquely expressed and active in IBC patient tumor cells. EXPERIMENTAL DESIGN: Here we focus on characterizing and targeting PDGFRA in IBC. Using gene expression, we analyzed IBC patient samples and compared them with non-IBC patient samples. Further, using IBC cells in culture, we determined the effect of small molecules inhibitors in both in vitro and in vivo assays. RESULTS: In IBC patients, we show more frequent PDGFRA activation signature than non-IBC samples. In addition, the PDGFRA activation signature is associated with shorter metastasis-free survival in both uni- and multivariate analyses. We also demonstrate that IBC cells express active PDGFRA. Finally, we show that PDGFRA targeting by crenolanib (CP-868-596), but not imatinib (STI571), two small molecule inhibitors, interferes with IBC cell growth and emboli formation in vitro and tumor growth in vivo. CONCLUSIONS: Our data suggest that PDGFRA may be a promising target for therapy in IBC.
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Affiliation(s)
- Madhura Joglekar-Javadekar
- The Laboratory for Cytoskeletal Physiology, Department of Biological Sciences, The University of Delaware, Newark, DE; The Center for Translational Cancer Research, The University of Delaware, Newark, DE
| | - Steven Van Laere
- Center for Oncological Research, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Michael Bourne
- The Laboratory for Cytoskeletal Physiology, Department of Biological Sciences, The University of Delaware, Newark, DE; The Center for Translational Cancer Research, The University of Delaware, Newark, DE
| | - Manal Moalwi
- The Laboratory for Cytoskeletal Physiology, Department of Biological Sciences, The University of Delaware, Newark, DE; The Center for Translational Cancer Research, The University of Delaware, Newark, DE
| | - Pascal Finetti
- Department of Molecular Oncology, Centre de Recherche en Cancérologie de Marseille, INSERM UMR1068, CNRS UMR725, Institut Paoli-Calmettes (IPC), Marseille, France
| | - Peter B Vermeulen
- Center for Oncological Research, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Daniel Birnbaum
- Department of Molecular Oncology, Centre de Recherche en Cancérologie de Marseille, INSERM UMR1068, CNRS UMR725, Institut Paoli-Calmettes (IPC), Marseille, France
| | - Luc Y Dirix
- Center for Oncological Research, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Naoto Ueno
- Breast Cancer Translational Research Laboratory, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Breast Medical Oncology, Morgan Welch Inflammatory Breast Cancer Research Program, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | - Francois Bertucci
- Department of Molecular Oncology, Centre de Recherche en Cancérologie de Marseille, INSERM UMR1068, CNRS UMR725, Institut Paoli-Calmettes (IPC), Marseille, France
| | - Kenneth L van Golen
- The Laboratory for Cytoskeletal Physiology, Department of Biological Sciences, The University of Delaware, Newark, DE; The Center for Translational Cancer Research, The University of Delaware, Newark, DE; The Helen F. Graham Cancer Center, Newark, DE.
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Bertucci F, Finetti P, Mamessier E, Pantaleo MA, Astolfi A, Ostrowski J, Birnbaum D. PDL1 expression is an independent prognostic factor in localized GIST. Oncoimmunology 2015; 4:e1002729. [PMID: 26155391 DOI: 10.1080/2162402x.2014.1002729] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 12/22/2014] [Accepted: 12/23/2014] [Indexed: 01/18/2023] Open
Abstract
Gastrointestinal stromal tumors (GIST) are the most frequently occurring digestive sarcomas. The prognosis of localized GIST is heterogeneous, notably for patients with an Armed Forces Institute of Pathology (AFIP) intermediate or high risk of relapse. Despite imatinib effectiveness, it is crucial to develop therapies able to overcome the resistance mechanisms. The immune system represents an attractive prognostic and therapeutic target. The Programmed cell Death 1 (PD1)/programmed cell death ligand 1 (PDL1) pathway is a key inhibitor of the immune response; recently, anti-PD1 and anti-PDL1 drugs showed very promising results in patients with solid tumors. However, PDL1 expression has never been studied in GIST. Our objective was to analyze PDL1 expression in a large series of clinical samples. We analyzed mRNA expression data of 139 operated imatinib-untreated localized GIST profiled using DNA microarrays and searched for correlations with histoclinical features including postoperative metastatic relapse. PDL1 expression was heterogeneous across tumors and was higher in AFIP low-risk than in high-risk samples, and in samples without than with metastatic relapse. PDL1 expression was associated with immunity-related parameters such as T-cell-specific and CD8+ T-cell-specific gene expression signatures and probabilities of activation of interferon α (IFNα), IFNγ, and tumor necrosis factor α (TNFα) pathways, suggesting positive correlation with a cytotoxic T-cell response. In multivariate analysis, the PDL1-low group was associated with a higher metastatic risk independently of the AFIP classification and the KIT mutational status. In conclusion, PDL1 expression refines the prediction of metastatic relapse in localized GIST and might improve our ability to better tailor adjuvant imatinib. In the metastatic setting, PDL1 expression might guide the use of PDL1 inhibitors, alone or associated with tyrosine kinase inhibitors.
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Key Words
- AFIP, Armed Forces Institute of Pathology
- DNA microarray
- FDR, false discovery rate
- GEO, gene expression omnibus
- GES, gene expression signatures
- GIST
- GIST, gastrointestinal stromal tumors
- GO, gene ontology
- IHC, immunohistochemistry
- ISH, in situ hybridization
- MFS, metastasis-free survival
- MHC, major histocompatibility complex
- NCBI, National Center for Biotechnology Information
- NK cells, natural killer cells
- PCA, principal component analysis
- PD1, programmed cell death 1
- PDGFRA, platelet-derived growth factor receptor α
- PDL1
- PDL1, programmed cell death ligand 1
- REMARK, REcommendations for tumor MARKer
- RMA, robust multichip average
- ROC, receiver operating characteristic
- TILs, tumor-infiltrating lymphocytes
- Treg, regulatory T cells
- WT, wild type
- gene expression
- immune response
- prognosis
- qRT-PCR, quantitative reverse transcription-polymerase chain reaction
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Affiliation(s)
- François Bertucci
- Department of Molecular Oncology; Institut Paoli-Calmettes; Centre de Recherche en Cancérologie de Marseille ; UMR1068 Inserm; Marseille, France ; Aix-Marseille University ; Marseille, France ; French Sarcoma Group ; Lyon, France
| | - Pascal Finetti
- Department of Molecular Oncology; Institut Paoli-Calmettes; Centre de Recherche en Cancérologie de Marseille ; UMR1068 Inserm; Marseille, France
| | - Emilie Mamessier
- Department of Molecular Oncology; Institut Paoli-Calmettes; Centre de Recherche en Cancérologie de Marseille ; UMR1068 Inserm; Marseille, France
| | - Maria Abbondanza Pantaleo
- Department of Specialized, Experimental and Diagnostic Medicine; Sant'Orsola-Malpighi Hospital ; Bologna, Italy
| | - Annalisa Astolfi
- Giorgio Prodi Cancer Research Center; University of Bologna ; Bologna, Italy
| | - Jerzy Ostrowski
- Department of Gastroenterology and Hepatology; Cancer Center-Institute and Medical Center of Postgraduate Education ; Warsaw, Poland
| | - Daniel Birnbaum
- Department of Molecular Oncology; Institut Paoli-Calmettes; Centre de Recherche en Cancérologie de Marseille ; UMR1068 Inserm; Marseille, France
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Zovak M, Boban M, Boban L, Cicek S, Madzar Z, Belev B, Tomas D. Significance of surgery for prognosis of GIST in cohort from transitional healthcare settings. Int J Surg 2014; 12:1167-71. [PMID: 25091396 DOI: 10.1016/j.ijsu.2014.07.275] [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: 04/07/2014] [Accepted: 07/29/2014] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Despite significant improvement in survival of gastrointestinal stromal tumors (GIST) due to use of tyrosine kinase inhibitors, surgery still represents the important part of clinical management. The aim of our study was to retrospectively analyze prognosis of GIST depending on the success of surgical treatments and utilization of chemotherapy in transitional country with relatively limited resources. METHODS cohort of consecutive patients operated for GIST in tertiary medical center, within time frame 1999-2012. RESULTS 54 patients, in age range 20-85 years (63.3 ± 14.7), male to female ratio 28 (51.9%):26 (48.1%), respectively. Complete excision with clean resection margins (R0) was obtained in 44 (81.5%)of total patients i.e. 44/47 (93.6%) of localized GISTs. Mean follow up was 3.9 ± 3.3 years and 19 patients (35.2%) received imatinib. Rate of overall survival was 40 (74.1%), disease-free survival 31 (57.4%) and 20 (37.0%) experienced recidivism. Follow-up parameters showed significant difference in connection with utilization of imatinib, completeness of resection and existence of metastatic disease (all p < 0.05). ROC analyzes revealed critical value of Ki-67 > 9% as significant predictor of long-term mortality; sensitivity 64.3% [95%CI = 35.1-87.2]; specificity 75.0% [58.8-87.3]; (AUC = 0.693; p = 0.049). CONCLUSION Rate of complete resections in studied sample of patients from transitional background was overall peer comparable with reports from the developed countries. On the other hand, relatively dominant prognostic position of surgical treatments might be consequence of limited utilization of adjuvant treatment with tyrosine kinase inhibitors.
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Affiliation(s)
- Mario Zovak
- Department of Surgery, University Hospital Center "Sestre Milosrdnice" Zagreb, Croatia; Medical and Dental School University of Zagreb, Croatia.
| | - Marko Boban
- Department of Internal Medicine, Medical School University of Osijek, Croatia
| | - Ljubica Boban
- Department of Pediatrics, Children's Hospital Zagreb, Croatia; Medical School University of Zagreb, Croatia
| | - Slaven Cicek
- Department of Surgery, University Hospital Center "Sestre Milosrdnice" Zagreb, Croatia; Medical and Dental School University of Zagreb, Croatia
| | - Zrinko Madzar
- Department of Surgery, University Hospital Center "Sestre Milosrdnice" Zagreb, Croatia; Medical and Dental School University of Zagreb, Croatia
| | - Borislav Belev
- Department of Clinical Oncology, University Hospital Center "Rebro", Zagreb, Croatia; Medical and Dental School University of Zagreb, Croatia
| | - Davor Tomas
- Department of Clinical Pathology, University Hospital Center "Sestre Milosrdnice" Zagreb, Croatia; Medical School University of Zagreb, Croatia
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12
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High-resolution melting analysis is a sensitive diagnostic tool to detect imatinib-resistant and imatinib-sensitive PDGFRA exon 18 mutations in gastrointestinal stromal tumors. Hum Pathol 2014; 45:573-82. [DOI: 10.1016/j.humpath.2013.10.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 10/10/2013] [Accepted: 10/19/2013] [Indexed: 01/01/2023]
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13
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Kelly L, Bryan K, Kim SY, Janeway KA, Killian JK, Schildhaus HU, Miettinen M, Helman L, Meltzer PS, van de Rijn M, Debiec-Rychter M, O’Sullivan M. Post-transcriptional dysregulation by miRNAs is implicated in the pathogenesis of gastrointestinal stromal tumor [GIST]. PLoS One 2013; 8:e64102. [PMID: 23717541 PMCID: PMC3663836 DOI: 10.1371/journal.pone.0064102] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 04/09/2013] [Indexed: 12/12/2022] Open
Abstract
In contrast to adult mutant gastrointestinal stromal tumors [GISTs], pediatric/wild-type GISTs remain poorly understood overall, given their lack of oncogenic activating tyrosine kinase mutations. These GISTs, with a predilection for gastric origin in female patients, show limited response to therapy with tyrosine kinase inhibitors and generally pursue a more indolent course, but still may prove fatal. Defective cellular respiration appears to underpin tumor development in these wild-type cases, which as a group lack expression of succinate dehydrogenase [SDH] B, a surrogate marker for respiratory chain metabolism. Yet, only a small subset of the wild-type tumors show mutations in the genes coding for the SDH subunits [SDHx]. To explore additional pathogenetic mechanisms in these wild-type GISTs, we elected to investigate post-transcriptional regulation of these tumors by conducting microRNA (miRNA) profiling of a mixed cohort of 73 cases including 18 gastric pediatric wild-type, 25 (20 gastric, 4 small bowel and 1 retroperitoneal) adult wild-type GISTs and 30 gastric adult mutant GISTs. By this approach we have identified distinct signatures for GIST subtypes which correlate tightly with clinico-pathological parameters. A cluster of miRNAs on 14q32 show strikingly different expression patterns amongst GISTs, a finding which appears to be explained at least in part by differential allelic methylation of this imprinted region. Small bowel and retroperitoneal wild-type GISTs segregate with adult mutant GISTs and express SDHB, while adult wild-type gastric GISTs are dispersed amongst adult mutant and pediatric wild-type cases, clustering in this situation on the basis of SDHB expression. Interestingly, global methylation analysis has recently similarly demonstrated that these wild-type, SDHB-immunonegative tumors show a distinct pattern compared with KIT and PDGFRA mutant tumors, which as a rule do express SDHB. All cases with Carney triad within our cohort cluster together tightly.
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Affiliation(s)
- Lorna Kelly
- Histopathology Department, School of Medicine, Trinity College Dublin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
| | - Kenneth Bryan
- Computational Biology, Systems Biology/Immunology, Animal and Grassland Research and Innovation Centre, Teagasc, Dunsany, County Meath, Ireland
| | - Su Young Kim
- Centre for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Katherine A. Janeway
- Department of Pediatric Hematology-Oncology, Dana Farber Cancer Institute and Children’s Hospital, Boston, Massachusetts, United States of America
| | - J. Keith Killian
- Centre for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | | | - Markku Miettinen
- Centre for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Lee Helman
- Centre for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Paul S. Meltzer
- Centre for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Matt van de Rijn
- Department of Pathology, Stanford University Medical Centre, Stanford, California, United States of America
| | - Maria Debiec-Rychter
- Department of Human Genetics, Catholic University Leuven and University Hospitals, Leuven, Belgium
| | - Maureen O’Sullivan
- Histopathology Department, School of Medicine, Trinity College Dublin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
- * E-mail:
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15
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Pelczar P, Zibat A, van Dop WA, Heijmans J, Bleckmann A, Gruber W, Nitzki F, Uhmann A, Guijarro MV, Hernando E, Dittmann K, Wienands J, Dressel R, Wojnowski L, Binder C, Taguchi T, Beissbarth T, Hogendoorn PC, Antonescu CR, Rubin BP, Schulz-Schaeffer W, Aberger F, van den Brink GR, Hahn H. Inactivation of Patched1 in mice leads to development of gastrointestinal stromal-like tumors that express Pdgfrα but not kit. Gastroenterology 2013; 144:134-144.e6. [PMID: 23041331 PMCID: PMC4231777 DOI: 10.1053/j.gastro.2012.09.061] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 09/25/2012] [Accepted: 09/27/2012] [Indexed: 12/30/2022]
Abstract
BACKGROUND & AIMS A fraction of gastrointestinal stromal tumor (GIST) cells overexpress the platelet-derived growth factor receptor (PDGFR)A, although most overexpress KIT. It is not known if this is because these receptor tyrosine kinases have complementary oncogenic potential, or because of heterogeneity in the cellular origin of GIST. Little also is known about why Hedgehog (HH) signaling is activated in some GIST. HH binds to and inactivates the receptor protein patched homolog (PTCH). METHODS Ptch was conditionally inactivated in mice (to achieve constitutive HH signaling) using a Cre recombinase regulated by the lysozyme M promoter. Cre-expressing cells were traced using R26R-LacZ reporter mice. Tumors were characterized by in situ hybridization, immunohistochemistry, immunoblot, and quantitative reverse-transcriptase polymerase chain reaction analyses. Cell transformation was assessed by soft agar assay. RESULTS Loss of Ptch from lysozyme M-expressing cells resulted in the development of tumors of GIST-like localization and histology; these were reduced when mice were given imatinib, a drug that targets KIT and PDGFRA. The Hh signaling pathway was activated in the tumor cells, and Pdgfrα, but not Kit, was overexpressed and activated. Lineage tracing revealed that Cre-expressing intestinal cells were Kit-negative. These cells sometimes expressed Pdgfrα and were located near Kit-positive interstitial cells of Cajal. In contrast to KIT, activation of PDGFRA increased anchorage-independent proliferation and was required for tumor formation in mice by cells with activated HH signaling. CONCLUSIONS Inactivation of Ptch in mice leads to formation of GIST-like tumors that express Pdgfrα, but not Kit. Activation of Pdgfrα signaling appears to facilitate tumorigenesis.
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Affiliation(s)
- Penelope Pelczar
- Department of Human Genetics, University Medical Center, Göttingen, Germany
| | - Arne Zibat
- Department of Human Genetics, University Medical Center, Göttingen, Germany
| | - Willemijn A. van Dop
- Tytgat Institute for Liver and Intestinal Research and Department of Gastroenterology & Hepatology, Academic Medical Center, Amsterdam, The Netherlands
| | - Jarom Heijmans
- Tytgat Institute for Liver and Intestinal Research and Department of Gastroenterology & Hepatology, Academic Medical Center, Amsterdam, The Netherlands
| | - Annalen Bleckmann
- Department of Hematology and Oncology, University Medical Center, Göttingen, Germany,Department of Medical Statistics, University Medical Center, Göttingen, Germany
| | - Wolfgang Gruber
- Department of Molecular Biology, University Salzburg, Austria
| | - Frauke Nitzki
- Department of Human Genetics, University Medical Center, Göttingen, Germany
| | - Anja Uhmann
- Department of Human Genetics, University Medical Center, Göttingen, Germany
| | - Maria V. Guijarro
- Department of Pathology, New York University School of Medicine, New York, USA
| | - Eva Hernando
- Department of Pathology, New York University School of Medicine, New York, USA
| | - Kai Dittmann
- Department of Cellular and Molecular Immunology, University Medical Center, Göttingen, Germany
| | - Jürgen Wienands
- Department of Cellular and Molecular Immunology, University Medical Center, Göttingen, Germany
| | - Ralf Dressel
- Department of Cellular and Molecular Immunology, University Medical Center, Göttingen, Germany
| | | | - Claudia Binder
- Department of Hematology and Oncology, University Medical Center, Göttingen, Germany
| | - Takahiro Taguchi
- Division of Human Health and Medical Science, Graduate School of Kuroshio Science, Kochi University, Nankoku, Japan
| | - Tim Beissbarth
- Department of Medical Statistics, University Medical Center, Göttingen, Germany
| | | | | | - Brian P. Rubin
- Departments of Anatomic Pathology and Molecular Genetics, Cleveland Clinic, Lerner Research Institute and Taussig Cancer Center, Cleveland, USA
| | | | - Fritz Aberger
- Department of Molecular Biology, University Salzburg, Austria
| | - Gijs R. van den Brink
- Tytgat Institute for Liver and Intestinal Research and Department of Gastroenterology & Hepatology, Academic Medical Center, Amsterdam, The Netherlands
| | - Heidi Hahn
- Department of Human Genetics, University Medical Center, Göttingen, Germany
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Abstract
BACKGROUND Prognosis of localised gastrointestinal stromal tumour (GIST) is heterogeneous, notably for patients with AFIP intermediate or high risk of relapse, who are candidates to adjuvant imatinib. We hypothesised that gene expression profiles might improve the prognostication and help to refine the indications for imatinib. METHODS We collected gene expression and histoclinical data of 146 pre-treatment localised GIST samples treated with surgery alone. We searched for a gene expression signature (GES) predictive for relapse-free survival (RFS) and compared its performances to that of three published prognostic proliferation-based GES (Genomic Grade Index (GGI), 16-Kinase, and CINSARC) and AFIP classification. We also analysed a data set from 28 patients with advanced GIST treated with neo-adjuvant imatinib. RESULTS We identified a 275-gene GES (gene expression signature) predictive of RFS in a learning set and validated its robustness in an independent set. However, the GGI outperformed its prognostic performances, and those of the two other signatures and the AFIP intermediate-risk classification in two independent tests sets in uni- and multivariate analyses. Importantly, GGI could split the AFIP intermediate/high-risk samples into two groups with different RFS. Genomic Grade Index 'high-risk' tumours were more proliferative and genetically unstable than 'low-risk' tumours, and more sensitive to imatinib. CONCLUSION GGI refines the prediction of RFS in localised GIST and might help tailor adjuvant imatinib.
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17
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Spisák S, Kalmár A, Galamb O, Wichmann B, Sipos F, Péterfia B, Csabai I, Kovalszky I, Semsey S, Tulassay Z, Molnár B. Genome-wide screening of genes regulated by DNA methylation in colon cancer development. PLoS One 2012; 7:e46215. [PMID: 23049694 PMCID: PMC3462205 DOI: 10.1371/journal.pone.0046215] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 08/28/2012] [Indexed: 02/05/2023] Open
Abstract
Tumorigenesis is accompanied by changes in the DNA methylation pattern. Our aim was to test a novel approach for identification of transcripts at whole transcript level which are regulated by DNA methylation. Our approach is based on comparison of data obtained from transcriptome profiling of primary human samples and in vitro cell culture models. Epithelial cells were collected by LCM from normal, adenoma, and tumorous colonic samples. Using gene expression analysis, we identified downregulated genes in the tumors compared to normal tissues. In parallel 3000 upregulated genes were determined in HT-29 colon adenocarcinoma cell culture model after DNA demethylation treatment. Of the 2533 transcripts showing reduced expression in the tumorous samples, 154 had increased expression as a result of DNA demethylation treatment. Approximately 2/3 of these genes had decreased expression already in the adenoma samples. Expression of five genes (GCG, NMES-1, LRMP, FAM161B and PTGDR), was validated using RT-PCR. PTGDR showed ambiguous results, therefore it was further studied to verify the extent of DNA methylation and its effect on the protein level. Results confirmed that our approach is suitable for genome-wide screening of genes which are regulated or inactivated by DNA methylation. Activity of these genes possibly interferes with tumor progression, therefore genes identified can be key factors in the formation and in the progression of the disease.
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Affiliation(s)
- Sándor Spisák
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary.
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Gregory-Bryson E, Bartlett E, Kiupel M, Hayes S, Yuzbasiyan-Gurkan V. Canine and human gastrointestinal stromal tumors display similar mutations in c-KIT exon 11. BMC Cancer 2010; 10:559. [PMID: 20950418 PMCID: PMC2970610 DOI: 10.1186/1471-2407-10-559] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 10/15/2010] [Indexed: 12/24/2022] Open
Abstract
Background Gastrointestinal stromal tumors (GISTs) are common mesenchymal neoplasms in the gastrointestinal tract of humans and dogs. Little is known about the pathogenesis of these tumors. This study evaluated the role of c-KIT in canine GISTs; specifically, we investigated activating mutations in exons 8, 9, 11, 13, and 17 of c-KIT and exons 12, 14, and 18 of platelet-derived growth factor receptor, alpha polypeptide (PDGFRA), all of which have been implicated in human GISTs. Methods Seventeen canine GISTs all confirmed to be positive for KIT immunostaining were studied. Exons 8, 9, 11, 13 and 17 of c-KIT and exons 12, 14, and 18 of PDGFRA, were amplified from DNA isolated from formalin-fixed paraffin-embedded samples. Results Of these seventeen cases, six amplicons of exon 11 of c-KIT showed aberrant bands on gel electrophoresis. Sequencing of these amplicons revealed heterozygous in-frame deletions in six cases. The mutations include two different but overlapping six base pair deletions. Exons 8, 9, 13, and 17 of c-KIT and exons 12, 14, and 18 of PDGFRA had no abnormalities detected by electrophoresis and sequencing did not reveal any mutations, other than synonymous single nucleotide polymorphisms (SNPs) found in exon 11 of c-KIT and exons 12 and 14 of PDGFRA. Conclusions The deletion mutations detected in canine GISTs are similar to those previously found in the juxtamembrane domain of c-KIT in canine cutaneous mast cell tumors in our laboratory as well as to those reported in human GISTs. Interestingly, none of the other c-KIT or PDGFRA exons showed any abnormalities in our cases. This finding underlines the critical importance of c-KIT in the pathophysiology of canine GISTs. The expression of KIT and the identification of these activating mutations in c-KIT implicate KIT in the pathogenesis of these tumors. Our results indicate that mutations in c-KIT may be of prognostic significance and that targeting KIT may be a rational approach to treatment of these malignant tumors. This study further demonstrates that spontaneously occurring canine GISTs share molecular features with human GISTs and are an appropriate model for human GISTs.
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Affiliation(s)
- Emmalena Gregory-Bryson
- Comparative Medicine and Integrative Biology Program, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA
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Chi P, Chen Y, Zhang L, Guo X, Wongvipat J, Shamu T, Fletcher JA, Dewell S, Maki RG, Zheng D, Antonescu CR, Allis CD, Sawyers CL. ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours. Nature 2010; 467:849-53. [PMID: 20927104 PMCID: PMC2955195 DOI: 10.1038/nature09409] [Citation(s) in RCA: 249] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Accepted: 07/20/2010] [Indexed: 12/22/2022]
Abstract
Gastrointestinal stromal tumour (GIST) is the most common human sarcoma and is primarily defined by activating mutations in the KIT or PDGFRA receptor tyrosine kinases1,2. KIT is highly expressed in interstitial cells of Cajal (ICCs)—the presumed cell of origin for GIST—as well as in hematopoietic stem cells, melanocytes, mast cells and germ cells2,3. Yet, families harbouring germline activating KIT mutations and mice with knock-in Kit mutations almost exclusively develop ICC hyperplasia and GIST4–7, suggesting that the cellular context is important for KIT to mediated oncogenesis. Here we show that the ETS family member ETV1 is highly expressed in the subtypes of ICCs sensitive to oncogenic KIT mediated transformation8, and is required for their development. In addition, ETV1 is universally highly expressed in GISTs and is required for growth of imatinib-sensitive and resistant GIST cell lines. Transcriptome profiling and global analyses of ETV1-binding sites suggest that ETV1 is a master regulator of an ICC-GIST-specific transcription network mainly through enhancer binding. The ETV1 transcriptional program is further regulated by activated KIT, which prolongs ETV1 protein stability and cooperates with ETV1 to promote tumourigenesis. We propose that GIST arises from ICCs with high levels of endogenous ETV1 expression that, when coupled with an activating KIT mutation, drives an oncogenic ETS transcription program. This differs from other ETS-dependent tumours such as prostate cancer, melanoma, and Ewing sarcoma where genomic translocation or amplification drives aberrant ETS expression9–11 and represents a novel mechanism of oncogenic transcription factor activation.
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Affiliation(s)
- Ping Chi
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
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Gastrointestinal stromal tumours at present: an approach to burning questions. Clin Transl Oncol 2010; 12:100-12. [DOI: 10.1007/s12094-010-0476-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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