1
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Nandadasa S, Szafron JM, Pathak V, Murtada SI, Kraft CM, O'Donnell A, Norvik C, Hughes C, Caterson B, Domowicz MS, Schwartz NB, Tran-Lundmark K, Veigl M, Sedwick D, Philipson EH, Humphrey JD, Apte SS. Vascular dimorphism ensured by regulated proteoglycan dynamics favors rapid umbilical artery closure at birth. eLife 2020; 9:e60683. [PMID: 32909945 PMCID: PMC7529456 DOI: 10.7554/elife.60683] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/09/2020] [Indexed: 01/29/2023] Open
Abstract
The umbilical artery lumen closes rapidly at birth, preventing neonatal blood loss, whereas the umbilical vein remains patent longer. Here, analysis of umbilical cords from humans and other mammals identified differential arterial-venous proteoglycan dynamics as a determinant of these contrasting vascular responses. The umbilical artery, but not the vein, has an inner layer enriched in the hydrated proteoglycan aggrecan, external to which lie contraction-primed smooth muscle cells (SMC). At birth, SMC contraction drives inner layer buckling and centripetal displacement to occlude the arterial lumen, a mechanism revealed by biomechanical observations and confirmed by computational analyses. This vascular dimorphism arises from spatially regulated proteoglycan expression and breakdown. Mice lacking aggrecan or the metalloprotease ADAMTS1, which degrades proteoglycans, demonstrate their opposing roles in umbilical vascular dimorphism, including effects on SMC differentiation. Umbilical vessel dimorphism is conserved in mammals, suggesting that differential proteoglycan dynamics and inner layer buckling were positively selected during evolution.
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Affiliation(s)
- Sumeda Nandadasa
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research InstituteClevelandUnited States
| | - Jason M Szafron
- Department of Biomedical Engineering, Yale UniversityNew HavenUnited States
| | - Vai Pathak
- Case Comprehensive Cancer Center, Case Western Reserve UniversityClevelandUnited States
| | - Sae-Il Murtada
- Department of Biomedical Engineering, Yale UniversityNew HavenUnited States
| | - Caroline M Kraft
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research InstituteClevelandUnited States
| | - Anna O'Donnell
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research InstituteClevelandUnited States
| | - Christian Norvik
- Department of Experimental Medical Science and Wallenberg Center for Molecular Medicine, Lund UniversityLundSweden
| | - Clare Hughes
- The Sir Martin Evans Building, School of Biosciences, Cardiff UniversityCardiffUnited Kingdom
| | - Bruce Caterson
- The Sir Martin Evans Building, School of Biosciences, Cardiff UniversityCardiffUnited Kingdom
| | | | - Nancy B Schwartz
- Department of Pediatrics, University of ChicagoChicagoUnited States
| | - Karin Tran-Lundmark
- Department of Experimental Medical Science and Wallenberg Center for Molecular Medicine, Lund UniversityLundSweden
| | - Martina Veigl
- Case Comprehensive Cancer Center, Case Western Reserve UniversityClevelandUnited States
- Department of Medicine, Case Western Reserve UniversityClevelandUnited States
| | - David Sedwick
- Department of Medicine, Case Western Reserve UniversityClevelandUnited States
| | - Elliot H Philipson
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research InstituteClevelandUnited States
- The Women's Health Institute, Department of Obstetrics and Gynecology, Cleveland ClinicClevelandUnited States
| | - Jay D Humphrey
- Department of Biomedical Engineering, Yale UniversityNew HavenUnited States
| | - Suneel S Apte
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research InstituteClevelandUnited States
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2
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Zhao Y, Feng X, Chen Y, Selfridge JE, Gorityala S, Du Z, Wang JM, Hao Y, Cioffi G, Conlon RA, Barnholtz-Sloan JS, Saltzman J, Krishnamurthi SS, Vinayak S, Veigl M, Xu Y, Bajor DL, Markowitz SD, Meropol NJ, Eads JR, Wang Z. 5-Fluorouracil Enhances the Antitumor Activity of the Glutaminase Inhibitor CB-839 against PIK3CA-Mutant Colorectal Cancers. Cancer Res 2020; 80:4815-4827. [PMID: 32907836 DOI: 10.1158/0008-5472.can-20-0600] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/06/2020] [Accepted: 09/03/2020] [Indexed: 12/14/2022]
Abstract
PIK3CA encodes the p110α catalytic subunit of PI3K and is frequently mutated in human cancers, including ∼30% of colorectal cancer. Oncogenic mutations in PIK3CA render colorectal cancers more dependent on glutamine. Here we report that the glutaminase inhibitor CB-839 preferentially inhibits xenograft growth of PIK3CA-mutant, but not wild-type (WT), colorectal cancers. Moreover, the combination of CB-839 and 5-fluorouracil (5-FU) induces PIK3CA-mutant tumor regression in xenograft models. CB-839 treatment increased reactive oxygen species and caused nuclear translocation of Nrf2, which in turn upregulated mRNA expression of uridine phosphorylase 1 (UPP1). UPP1 facilitated the conversion of 5-FU to its active compound, thereby enhancing the inhibition of thymidylate synthase. Consistently, knockout of UPP1 abrogated the tumor inhibitory effect of combined CB-839 and 5-FU administration. A phase I clinical trial showed that the combination of CB-839 and capecitabine, a prodrug of 5-FU, was well tolerated at biologically-active doses. Although not designed to test efficacy, an exploratory analysis of the phase I data showed a trend that PIK3CA-mutant patients with colorectal cancer might derive greater benefit from this treatment strategy as compared with PIK3CA WT patients with colorectal cancer. These results effectively demonstrate that targeting glutamine metabolism may be an effective approach for treating patients with PIK3CA-mutant colorectal cancers and warrants further clinical evaluation. SIGNIFICANCE: Preclinical and clinical trial data suggest that the combination of CB-839 with capecitabine could serve as an effective treatment for PIK3CA-mutant colorectal cancers.
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Affiliation(s)
- Yiqing Zhao
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
| | - Xiujing Feng
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
| | - Yicheng Chen
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
| | - J Eva Selfridge
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio.,Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | | | - Zhanwen Du
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
| | - Janet M Wang
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Yujun Hao
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
| | - Gino Cioffi
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Ronald A Conlon
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio.,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Joel Saltzman
- Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Smitha S Krishnamurthi
- Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Shaveta Vinayak
- Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Martina Veigl
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Yan Xu
- Department of Chemistry, Cleveland State University, Cleveland, Ohio
| | - David L Bajor
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio.,Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Sanford D Markowitz
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio.,Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Neal J Meropol
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio.,Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Flatiron Health, New York, New York
| | - Jennifer R Eads
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio. .,Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zhenghe Wang
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio. .,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
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3
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Thiagarajan PS, Wu X, Zhang W, Shi I, Bagai R, Leahy P, Feng Y, Veigl M, Lindner D, Danielpour D, Yin L, Rosell R, Bivona TG, Zhang Z, Ma PC. Transcriptomic-metabolomic reprogramming in EGFR-mutant NSCLC early adaptive drug escape linking TGFβ2-bioenergetics-mitochondrial priming. Oncotarget 2018; 7:82013-82027. [PMID: 27852038 PMCID: PMC5347670 DOI: 10.18632/oncotarget.13307] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 10/28/2016] [Indexed: 11/25/2022] Open
Abstract
The impact of EGFR-mutant NSCLC precision therapy is limited by acquired resistance despite initial excellent response. Classic studies of EGFR-mutant clinical resistance to precision therapy were based on tumor rebiopsies late during clinical tumor progression on therapy. Here, we characterized a novel non-mutational early adaptive drug-escape in EGFR-mutant lung tumor cells only days after therapy initiation, that is MET-independent. The drug-escape cell states were analyzed by integrated transcriptomic and metabolomics profiling uncovering a central role for autocrine TGFβ2 in mediating cellular plasticity through profound cellular adaptive Omics reprogramming, with common mechanistic link to prosurvival mitochondrial priming. Cells undergoing early adaptive drug escape are in proliferative-metabolic quiescent, with enhanced EMT-ness and stem cell signaling, exhibiting global bioenergetics suppression including reverse Warburg, and are susceptible to glutamine deprivation and TGFβ2 inhibition. Our study further supports a preemptive therapeutic targeting of bioenergetics and mitochondrial priming to impact early drug-escape emergence using EGFR precision inhibitor combined with broad BH3-mimetic to interrupt BCL-2/BCL-xL together, but not BCL-2 alone.
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Affiliation(s)
- Praveena S Thiagarajan
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.,Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Xiaoliang Wu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China & Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Sara Crile Allen and James Frederick Allen Comprehensive Lung Cancer Program, Eminent Scholar in Lung Cancer Research, WVU Cancer Institute, West Virginia University, Morgantown, WV, USA
| | - Wei Zhang
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.,Sara Crile Allen and James Frederick Allen Comprehensive Lung Cancer Program, Eminent Scholar in Lung Cancer Research, WVU Cancer Institute, West Virginia University, Morgantown, WV, USA
| | - Ivy Shi
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Rakesh Bagai
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Patrick Leahy
- Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - Yan Feng
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Martina Veigl
- Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - Daniel Lindner
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.,Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - David Danielpour
- Case Comprehensive Cancer Center, Cleveland, OH, USA.,Department of Pharmacology, and Department of Biochemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Lihong Yin
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Rafael Rosell
- Catalan Institute of Oncology, Badalona, Spain.,Spanish Lung Cancer Group, Badalona, Spain
| | - Trever G Bivona
- Department of Medicine, Division of Hematology/ Oncology, Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Zhenfeng Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China & Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Patrick C Ma
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.,Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Sara Crile Allen and James Frederick Allen Comprehensive Lung Cancer Program, Eminent Scholar in Lung Cancer Research, WVU Cancer Institute, West Virginia University, Morgantown, WV, USA
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4
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Sun X, Chandar AK, Canto MI, Thota PN, Brock M, Shaheen NJ, Beer DG, Wang JS, Falk GW, Iyer PG, Abrams JA, Venkat-Ramani M, Veigl M, Miron A, Willis J, Patil DT, Nalbantoglu I, Guda K, Markowitz SD, Zhu X, Elston R, Chak A. Genomic regions associated with susceptibility to Barrett's esophagus and esophageal adenocarcinoma in African Americans: The cross BETRNet admixture study. PLoS One 2017; 12:e0184962. [PMID: 29073141 PMCID: PMC5657624 DOI: 10.1371/journal.pone.0184962] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 09/04/2017] [Indexed: 12/20/2022] Open
Abstract
Background Barrett’s esophagus (BE) and esophageal adenocarcinoma (EAC) are far more prevalent in European Americans than in African Americans. Hypothesizing that this racial disparity in prevalence might represent a genetic susceptibility, we used an admixture mapping approach to interrogate disease association with genomic differences between European and African ancestry. Methods Formalin fixed paraffin embedded samples were identified from 54 African Americans with BE or EAC through review of surgical pathology databases at participating Barrett’s Esophagus Translational Research Network (BETRNet) institutions. DNA was extracted from normal tissue, and genotyped on the Illumina OmniQuad SNP chip. Case-only admixture mapping analysis was performed on the data from both all 54 cases and also on a subset of 28 cases with high genotyping quality. Haplotype phases were inferred with Beagle 3.3.2, and local African and European ancestries were inferred with SABER plus. Disease association was tested by estimating and testing excess European ancestry and contrasting it to excess African ancestry. Results Both datasets, the 54 cases and the 28 cases, identified two admixture regions. An association of excess European ancestry on chromosome 11p reached a 5% genome-wide significance threshold, corresponding to -log10(P) = 4.28. A second peak on chromosome 8q reached -log10(P) = 2.73. The converse analysis examining excess African ancestry found no genetic regions with significant excess African ancestry associated with BE and EAC. On average, the regions on chromosomes 8q and 11p showed excess European ancestry of 15% and 20%, respectively. Conclusions Chromosomal regions on 11p15 and 8q22-24 are associated with excess European ancestry in African Americans with BE and EAC. Because GWAS have not reported any variants in these two regions, low frequency and/or rare disease associated variants that confer susceptibility to developing BE and EAC may be driving the observed European ancestry association evidence.
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Affiliation(s)
- Xiangqing Sun
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States of America
| | - Apoorva K. Chandar
- Division of Gastroenterology and Hepatology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Marcia I. Canto
- Division of Gastroenterology and Hepatology, Johns Hopkins Medical Institutions, Baltimore, MD, United States of America
| | - Prashanthi N. Thota
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH, United States of America
| | - Malcom Brock
- Department of Cardiology and Thoracic Surgery, Johns Hopkins Medical Institutions, Baltimore, MD, United States of America
| | - Nicholas J. Shaheen
- Center for Esophageal Diseases & Swallowing, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States of America
| | - David G. Beer
- Thoracic Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI, United States of America
| | - Jean S. Wang
- Division of Gastroenterology, Washington University School of Medicine, St Louis, MO, United States of America
| | - Gary W. Falk
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United states of America
| | - Prasad G. Iyer
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America
| | - Julian A. Abrams
- Department of Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Medha Venkat-Ramani
- Division of Gastroenterology and Hepatology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Martina Veigl
- Division of General Medical Sciences (Oncology), Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Alexander Miron
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Joseph Willis
- Department of Pathology, University Hospitals Case Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Deepa T. Patil
- Department of Pathology, Cleveland Clinic, Cleveland, OH, United States of America
| | - Ilke Nalbantoglu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Kishore Guda
- Division of General Medical Sciences (Oncology), Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Sanford D. Markowitz
- Division of Oncology and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States of America
| | - Robert Elston
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States of America
| | - Amitabh Chak
- Division of Gastroenterology and Hepatology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
- Division of General Medical Sciences (Oncology), Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
- * E-mail:
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5
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Fink SP, Myeroff L, Kariv R, Platzer P, Xin B, Mikkola D, Lawrence E, Morris N, Nosrati A, Willson J, Willis J, Veigl M, Barnholtz-Sloan J, Wang Z, Markowitz S. Abstract 3126: CEMIP, a secreted protein highly induced in colon cancer and associated with poor patient survival. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-3126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Colorectal cancer is the second leading cause of cancer death among adult Americans. Tumor stage still remains the clinical standard for determining prognosis of colon cancer patients and for selecting individuals for treatment with adjuvant chemotherapy. Genes induced in colon cancer provide novel candidate biomarkers of tumor phenotype and aggressiveness. The goal of this study was to identify genes whose expression is dramatically up-regulated in colon neoplasia even at the early stages of the disease, and with the potential to be new prognostic markers of patient outcome and/or targets for new therapies.
Methods: We used expression microarrays, real-time PCR, Western blot, and immunohistochemistry to identify CEMIP (originally named KIAA1199/CCSP1) induction in colon cancer, and characterized the biological properties of the corresponding protein in cell-line and mouse xenografts. Sandwich ELISA was developed to determine CEMIP plasma levels in patients with colon cancer. Prognostic importance of gene induction was demonstrated by real-time PCR measurement of gene expression in colon cancer cases of known clinical outcome.
Results: We originally identified CEMIP as a novel transcript that is induced an average of 54-fold in colon cancer, with a similar increase in protein level. We find that CEMIP is a secreted protein and that plasma levels of CEMIP in colon cancer patients is increased compared to normal subjects (P = 0.05). Knocking out CEMIP in a human colon cancer cell line markedly reduced growth of tumor xenografts implanted in athymic mice. Tumors that did grow had increased deposition of hyaluronan, linking CEMIP participation in hyaluronan degradation to the modulation of tumor phenotype. Human stage III colon cancer cases with greater than average increased tumor CEMIP expression had a median survival time of 37 months, versus greater than 140 months for colon cancer cases with below average CEMIP expression (P = 0.004). Similarly, among combined stage II plus III colon cancer cases, median survival decreased by 92 months for CEMIP high versus low expressing tumors (P = 0.0003).
Conclusions: CEMIP is highly expressed in colon neoplasia and is a novel member of the colon cancer secreted proteome making it a candidate serological marker of early human colon neoplasia. CEMIP facilitates tumor growth, and high CEMIP correlates with poor outcome in stage III and in stages II plus III combined cohorts. CEMIP may have utility as both a prognostic marker of colon cancer outcome, and as a potential therapeutic target.
Citation Format: Stephen P. Fink, Lois Myeroff, Revital Kariv, Petra Platzer, Baozhong Xin, Debra Mikkola, Earl Lawrence, Nathan Morris, Arman Nosrati, James Willson, Joseph Willis, Martina Veigl, Jill Barnholtz-Sloan, Zhenghe Wang, Sanford Markowitz. CEMIP, a secreted protein highly induced in colon cancer and associated with poor patient survival. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3126.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - James Willson
- 2University of Texas Southwestern Medical Center, Dallas, TX
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6
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Markowitz SD, Nock NL, Schmit SL, Stadler ZK, Joseph V, Zhang L, Willis JE, Scacheri P, Veigl M, Adams MD, Raskin L, Sullivan JF, Stratton K, Shia J, Ellis N, Rennert HS, Manschreck C, Li L, Offit K, Elston RC, Rennert G, Gruber SB. A Germline Variant on Chromosome 4q31.1 Associates with Susceptibility to Developing Colon Cancer Metastasis. PLoS One 2016; 11:e0146435. [PMID: 26751797 PMCID: PMC4709047 DOI: 10.1371/journal.pone.0146435] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/03/2015] [Indexed: 12/02/2022] Open
Abstract
We tested for germline variants showing association to colon cancer metastasis using a genome-wide association study that compared Ashkenazi Jewish individuals with stage IV metastatic colon cancers versus those with stage I or II non-metastatic colon cancers. In a two-stage study design, we demonstrated significant association to developing metastatic disease for rs60745952, that in Ashkenazi discovery and validation cohorts, respectively, showed an odds ratio (OR) = 2.3 (P = 2.73E-06) and OR = 1.89 (P = 8.05E-04) (exceeding validation threshold of 0.0044). Significant association to metastatic colon cancer was further confirmed by a meta-analysis of rs60745952 in these datasets plus an additional Ashkenazi validation cohort (OR = 1.92; 95% CI: 1.28–2.87), and by a permutation test that demonstrated a significantly longer haplotype surrounding rs60745952 in the stage IV samples. rs60745952, located in an intergenic region on chromosome 4q31.1, and not previously associated with cancer, is, thus, a germline genetic marker for susceptibility to developing colon cancer metastases among Ashkenazi Jews.
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Affiliation(s)
- Sanford D. Markowitz
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, United States of America
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail: (SDM); (GR); (SBG)
| | - Nora L. Nock
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Stephanie L. Schmit
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Zsofia K. Stadler
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Vijai Joseph
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Lu Zhang
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Joseph E. Willis
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Peter Scacheri
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, United States of America
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Martina Veigl
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Mark D. Adams
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Leon Raskin
- Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, Tennessee, United States of America
| | - John F. Sullivan
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Kelly Stratton
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Jinru Shia
- Department of Pathology, Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, United States of America
| | - Nathan Ellis
- The University of Arizona Cancer Center, Tucson, Arizona, United States of America
| | - Hedy S. Rennert
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
- Clalit Health Services, National Cancer Control Center, Haifa, Israel
- Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Christopher Manschreck
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Li Li
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Robert C. Elston
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Gadi Rennert
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
- Clalit Health Services, National Cancer Control Center, Haifa, Israel
- Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- * E-mail: (SDM); (GR); (SBG)
| | - Stephen B. Gruber
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- * E-mail: (SDM); (GR); (SBG)
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7
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Chen X, Veigl M, Barnholtz-Sloan J, Xin W, Chen Y, Dorth J. Prediction of Response to Chemoradiation by Gene Expression Profiling in Esophageal Squamous Cell Carcinoma. Int J Radiat Oncol Biol Phys 2015. [DOI: 10.1016/j.ijrobp.2015.07.527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Liu Y, Koyutürk M, Maxwell S, Xiang M, Veigl M, Cooper RS, Tayo BO, Li L, LaFramboise T, Wang Z, Zhu X, Chance MR. Discovery of common sequences absent in the human reference genome using pooled samples from next generation sequencing. BMC Genomics 2014; 15:685. [PMID: 25129063 PMCID: PMC4148959 DOI: 10.1186/1471-2164-15-685] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 08/04/2014] [Indexed: 11/16/2022] Open
Abstract
Background Sequences up to several megabases in length have been found to be present in individual genomes but absent in the human reference genome. These sequences may be common in populations, and their absence in the reference genome may indicate rare variants in the genomes of individuals who served as donors for the human genome project. As the reference genome is used in probe design for microarray technology and mapping short reads in next generation sequencing (NGS), this missing sequence could be a source of bias in functional genomic studies and variant analysis. One End Anchor (OEA) and/or orphan reads from paired-end sequencing have been used to identify novel sequences that are absent in reference genome. However, there is no study to investigate the distribution, evolution and functionality of those sequences in human populations. Results To systematically identify and study the missing common sequences (micSeqs), we extended the previous method by pooling OEA reads from large number of individuals and applying strict filtering methods to remove false sequences. The pipeline was applied to data from phase 1 of the 1000 Genomes Project. We identified 309 micSeqs that are present in at least 1% of the human population, but absent in the reference genome. We confirmed 76% of these 309 micSeqs by comparison to other primate genomes, individual human genomes, and gene expression data. Furthermore, we randomly selected fifteen micSeqs and confirmed their presence using PCR validation in 38 additional individuals. Functional analysis using published RNA-seq and ChIP-seq data showed that eleven micSeqs are highly expressed in human brain and three micSeqs contain transcription factor (TF) binding regions, suggesting they are functional elements. In addition, the identified micSeqs are absent in non-primates and show dynamic acquisition during primate evolution culminating with most micSeqs being present in Africans, suggesting some micSeqs may be important sources of human diversity. Conclusions 76% of micSeqs were confirmed by a comparative genomics approach. Fourteen micSeqs are expressed in human brain or contain TF binding regions. Some micSeqs are primate-specific, conserved and may play a role in the evolution of primates. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-685) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu Liu
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, USA.
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Yu X, Guda K, Willis J, Veigl M, Wang Z, Markowitz S, Adams MD, Sun S. How do alignment programs perform on sequencing data with varying qualities and from repetitive regions? BioData Min 2012; 5:6. [PMID: 22709551 PMCID: PMC3414812 DOI: 10.1186/1756-0381-5-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 06/18/2012] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Next-generation sequencing technologies generate a significant number of short reads that are utilized to address a variety of biological questions. However, quite often, sequencing reads tend to have low quality at the 3' end and are generated from the repetitive regions of a genome. It is unclear how different alignment programs perform under these different cases. In order to investigate this question, we use both real data and simulated data with the above issues to evaluate the performance of four commonly used algorithms: SOAP2, Bowtie, BWA, and Novoalign. METHODS The performance of different alignment algorithms are measured in terms of concordance between any pair of aligners (for real sequencing data without known truth) and the accuracy of simulated read alignment. RESULTS Our results show that, for sequencing data with reads that have relatively good quality or that have had low quality bases trimmed off, all four alignment programs perform similarly. We have also demonstrated that trimming off low quality ends markedly increases the number of aligned reads and improves the consistency among different aligners as well, especially for low quality data. However, Novoalign is more sensitive to the improvement of data quality. Trimming off low quality ends significantly increases the concordance between Novoalign and other aligners. As for aligning reads from repetitive regions, our simulation data show that reads from repetitive regions tend to be aligned incorrectly, and suppressing reads with multiple hits can improve alignment accuracy. CONCLUSIONS This study provides a systematic comparison of commonly used alignment algorithms in the context of sequencing data with varying qualities and from repetitive regions. Our approach can be applied to different sequencing data sets generated from different platforms. It can also be utilized to study the performance of other alignment programs.
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Affiliation(s)
- Xiaoqing Yu
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Kishore Guda
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Joseph Willis
- Department of Pathology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Martina Veigl
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Zhenghe Wang
- J. Craig Venter Institute, 10355 Science Center Dr, San Diego, CA, 92121, USA
| | - Sanford Markowitz
- Department of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Mark D Adams
- J. Craig Venter Institute, 10355 Science Center Dr, San Diego, CA, 92121, USA
| | - Shuying Sun
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
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Balasubramanian D, Akhtar-Zaidi B, Song L, Bartels CF, Veigl M, Beard L, Myeroff L, Guda K, Lutterbaugh J, Willis J, Crawford GE, Markowitz SD, Scacheri PC. H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites. Genome Med 2012; 4:47. [PMID: 22640407 PMCID: PMC3506913 DOI: 10.1186/gm346] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 04/13/2012] [Accepted: 05/28/2012] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND In addition to mutations, epigenetic silencing of genes has been recognized as a fundamental mechanism that promotes human carcinogenesis. To date, characterization of epigenetic gene silencing has largely focused on genes in which silencing is mediated by hypermethylation of promoter-associated CpG islands, associated with loss of the H3K4me3 chromatin mark. Far less is known about promoters lacking CpG-islands or genes that are repressed by alternative mechanisms. METHODS We performed integrative ChIP-chip, DNase-seq, and global gene expression analyses in colon cancer cells and normal colon mucosa to characterize chromatin features of both CpG-rich and CpG-poor promoters of genes that undergo silencing in colon cancer. RESULTS Epigenetically repressed genes in colon cancer separate into two classes based on retention or loss of H3K4me3 at transcription start sites. Quantitatively, of transcriptionally repressed genes that lose H3K4me3 in colon cancer (K4-dependent genes), a large fraction actually lacks CpG islands. Nonetheless, similar to CpG-island containing genes, cytosines located near the start sites of K4-dependent genes become DNA hypermethylated, and repressed K4-dependent genes can be reactivated with 5-azacytidine. Moreover, we also show that when the H3K4me3 mark is retained, silencing of CpG island-associated genes can proceed through an alternative mechanism in which repressive chromatin marks are recruited. CONCLUSIONS H3K4me3 equally protects from DNA methylation at both CpG-island and non-CpG island start sites in colon cancer. Moreover, the results suggest that CpG-rich genes repressed by loss of H3K4me3 and DNA methylation represent special instances of a more general epigenetic mechanism of gene silencing, one in which gene silencing is mediated by loss of H3K4me3 and methylation of non-CpG island promoter-associated cytosines.
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Affiliation(s)
- Dheepa Balasubramanian
- Department of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
| | - Batool Akhtar-Zaidi
- Department of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, 9500 Euclid Ave, Cleveland, OH 44195, USA
| | - Lingyun Song
- Institute for Science and Policy, and Department of Pediatrics, Duke University, 101 Science Drive, Durham, NC 27708, USA
| | - Cynthia F Bartels
- Department of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
| | - Martina Veigl
- Case Comprehensive Cancer Center, Case Western Reserve University, 11100 Euclid Ave, Cleveland, OH 44106, USA
| | - Lydia Beard
- Case Comprehensive Cancer Center, Case Western Reserve University, 11100 Euclid Ave, Cleveland, OH 44106, USA
| | - Lois Myeroff
- Case Comprehensive Cancer Center, Case Western Reserve University, 11100 Euclid Ave, Cleveland, OH 44106, USA
| | - Kishore Guda
- Case Comprehensive Cancer Center, Case Western Reserve University, 11100 Euclid Ave, Cleveland, OH 44106, USA
| | - James Lutterbaugh
- Case Comprehensive Cancer Center, Case Western Reserve University, 11100 Euclid Ave, Cleveland, OH 44106, USA
| | - Joseph Willis
- Case Comprehensive Cancer Center, Case Western Reserve University, 11100 Euclid Ave, Cleveland, OH 44106, USA
- Department of Pathology, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - Gregory E Crawford
- Institute for Science and Policy, and Department of Pediatrics, Duke University, 101 Science Drive, Durham, NC 27708, USA
| | - Sanford D Markowitz
- Department of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, 11100 Euclid Ave, Cleveland, OH 44106, USA
- Department of Medicine, Case Western Reserve University, 10900 Euclid Ave Cleveland, OH 44106, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, 9500 Euclid Ave, Cleveland, OH 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, 11100 Euclid Ave, Cleveland, OH 44106, USA
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Li LS, Morales JC, Veigl M, Sedwick D, Greer S, Meyers M, Wagner M, Fishel R, Boothman DA. DNA mismatch repair (MMR)-dependent 5-fluorouracil cytotoxicity and the potential for new therapeutic targets. Br J Pharmacol 2009; 158:679-92. [PMID: 19775280 DOI: 10.1111/j.1476-5381.2009.00423.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The metabolism and efficacy of 5-fluorouracil (FUra) and other fluorinated pyrimidine (FP) derivatives have been intensively investigated for over fifty years. FUra and its antimetabolites can be incorporated at RNA- and DNA-levels, with RNA level incorporation provoking toxic responses in human normal tissue, and DNA-level antimetabolite formation and incorporation believed primarily responsible for tumour-selective responses. Attempts to direct FUra into DNA-level antimetabolites, based on mechanism-of-action studies, have led to gradual improvements in tumour therapy. These include the use of leukovorin to stabilize the inhibitory thymidylate synthase-5-fluoro-2'-deoxyuridine 5' monophoshate (FdUMP)-5,10-methylene tetrahydrofolate (5,10-CH(2)FH(4)) trimeric complex. FUra incorporated into DNA also contributes to antitumour activity in preclinical and clinical studies. This review examines our current state of knowledge regarding the mechanistic aspects of FUra:Gua lesion detection by DNA mismatch repair (MMR) machinery that ultimately results in lethality. MMR-dependent direct cell death signalling or futile cycle responses will be discussed. As 10-30% of sporadic colon and endometrial tumours display MMR defects as a result of human MutL homologue-1 (hMLH1) promoter hypermethylation, we discuss the use and manipulation of the hypomethylating agent, 5-fluorodeoxycytidine (FdCyd), and our ability to manipulate its metabolism using the cytidine or deoxycytidylate (dCMP) deaminase inhibitors, tetrahydrouridine or deoxytetrahydrouridine, respectively, as a method for re-expression of hMLH1 and re-sensitization of tumours to FP therapy.
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Affiliation(s)
- Long Shan Li
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
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Allay E, Veigl M, Gerson SL. Mice over-expressing human O6 alkylguanine-DNA alkyltransferase selectively reduce O6 methylguanine mediated carcinogenic mutations to threshold levels after N-methyl-N-nitrosourea. Oncogene 1999; 18:3783-7. [PMID: 10391687 DOI: 10.1038/sj.onc.1202697] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
While it is well known that MNU induces thymic lymphomas in the mouse, it remains unclear which pre-mutagenic lesions are responsible for lymphomagenic transformation. One lesion thought to play a critical role is O6methylguanine[O6mG]which initiates G: C to A:T transition mutations in K-ras and other oncogenes. O6alkylguanine-DNA alkyltransferase (AGT), encoded by the methylguanine methyltransferase gene [MGMT], removes the methyl group thereby preventing the mutation from occurring. When overexpressed in the thymus, MGMT protects mice from MNU-induced thymic lymphomas. To determine whether MGMT overexpression reduced G: C to A: T mutation frequency after MNU, Big Blue lacI and MGMT+/Big Blue mice were treated with MNU and analysed for mutations in the lacI and K-ras genes. The incidence of MNU-induced lymphomas was 84% in Big Blue lacI mice compared to 14% in MGMT+Big Blue lacI mice. Sixty-two per cent of the lymphomas had a GGT to GAT activating mutation in codon 12 of K-ras consistent with O6mG adduct-mediated point mutagenesis. LacI mutation frequency in thymus of MNU treated Big Blue mice was 45-fold above background whereas it was 11-fold above background in MNU treated MGMT+/Big Blue mice. Most lacI mutations were G:C to A:T transitions, implicating O6mG even in the MGMT+mice. No mutations were attributable to chromosomal aberrations or rearrangements. Thus, O6mG adducts account for the carcinogenic effect of MNU and MGMT overexpression is selectively able to reduce O6methylguanine adducts below a carcinogenic threshold. Other adducts are mutagenic but appear to contribute much less to malignant transformation or oncogene activation.
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Affiliation(s)
- E Allay
- Division of Hematology/Oncology and Ireland Cancer Center at Case Western Reserve University and University Hospital of Cleveland, Ohio 44106, USA
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Johnson SP, Veigl M, Vanaman T, Leis J. Cyanogen bromide digestion of the avian myeloblastosis virus pp19 protein: isolation of an amino-terminal peptide that binds to viral RNA. J Virol 1983; 45:876-81. [PMID: 6300441 PMCID: PMC256484 DOI: 10.1128/jvi.45.2.876-881.1983] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The avian myeloblastosis virus pp19 protein was separated from the other virus proteins by a rapid and simple purification procedure which yields milligram amounts of homogeneous protein. This protein was then fragmented by digestion with cyanogen bromide. When the mixture of the cyanogen bromide peptides was passed through a 60S avian myeloblastosis virus RNA-cellulose column, only one peptide bound with high affinity to the resin. The peptide migrated on a sodium dodecyl sulfate-polyacrylamide gel with an approximate molecular weight of 2,900 and will be referred to as the p3B peptide. This peptide was also isolated directly by chromatography of the cyanogen bromide-digested pp19 protein on a reverse-phase high-pressure liquid chromatography column. It was again the only cyanogen bromide peptide of the pp19 protein that bound to the RNA affinity resin. The p3B peptide is a basic peptide, as was seen by its rapid migration on acid-urea-polyacrylamide gels and its amino acid composition. A partial amino acid sequence analysis of the p3B peptide indicated that it was derived from the amino terminus of the intact protein. Although the p3B peptide bound to 60S RNA, it did not demonstrate the selective binding of native pp19 to regions of the RNA containing secondary structure.
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