1
|
Peng H, Ishida M, Li L, Saito A, Kamiya A, Hamilton JP, Fu R, Olaru AV, An F, Popescu I, Iacob R, Dima S, Alexandrescu ST, Grigorie R, Nastase A, Berindan-Neagoe I, Tomuleasa C, Graur F, Zaharia F, Torbenson MS, Mezey E, Lu M, Selaru FM. Pseudogene INTS6P1 regulates its cognate gene INTS6 through competitive binding of miR-17-5p in hepatocellular carcinoma. Oncotarget 2016; 6:5666-77. [PMID: 25686840 PMCID: PMC4467393 DOI: 10.18632/oncotarget.3290] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/02/2015] [Indexed: 12/13/2022] Open
Abstract
The complex regulation of tumor suppressive gene and its pseudogenes play key roles in the pathogenesis of hepatocellular cancer (HCC). However, the roles played by pseudogenes in the pathogenesis of HCC are still incompletely elucidated. This study identifies the putative tumor suppressor INTS6 and its pseudogene INTS6P1 in HCC through the whole genome microarray expression. Furthermore, the functional studies – include growth curves, cell death, migration assays and in vivo studies – verify the tumor suppressive roles of INTS6 and INTS6P1 in HCC. Finally, the mechanistic experiments indicate that INTS6 and INTS6P1 are reciprocally regulated through competition for oncomiR-17-5p. Taken together, these findings demonstrate INTS6P1 and INTS6 exert the tumor suppressive roles through competing for oncomiR-17-5p. Our investigation of this regulatory circuit reveals novel insights into the underlying mechanisms of hepatocarcinogenesis.
Collapse
Affiliation(s)
- Haoran Peng
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins Hospital, Baltimore, Maryland, USA.,Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P.R. China
| | - Masaharu Ishida
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Ling Li
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Atsushi Saito
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Atsushi Kamiya
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - James P Hamilton
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Rongdang Fu
- Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P.R. China
| | - Alexandru V Olaru
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Fangmei An
- Department of Gastroenterology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu, P.R. China
| | - Irinel Popescu
- Dan Setlacec Center of General Surgery and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Razvan Iacob
- Dan Setlacec Center of General Surgery and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Simona Dima
- Dan Setlacec Center of General Surgery and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Sorin T Alexandrescu
- Dan Setlacec Center of General Surgery and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Razvan Grigorie
- Dan Setlacec Center of General Surgery and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Anca Nastase
- Dan Setlacec Center of General Surgery and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Ioana Berindan-Neagoe
- Department of Immunology, The Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Department of Functional Genomics, The Oncology Institute Ion Chiricuta, Cluj Napoca, Romania.,The Research Center for Functional Genomics, Biomedicine and Translational Medicine, The Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Ciprian Tomuleasa
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, The Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Department of Hematology, The Oncology Institute Ion Chiricuta, Cluj Napoca, Romania
| | - Florin Graur
- Department of Surgery, The Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Department of Surgery, Regional Institute of Gastroenterology and Hepatology "Octavian Fodor", Cluj Napoca, Romania
| | - Florin Zaharia
- Department of Surgery, The Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Department of Surgery, Regional Institute of Gastroenterology and Hepatology "Octavian Fodor", Cluj Napoca, Romania
| | - Michael S Torbenson
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Esteban Mezey
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Minqiang Lu
- Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P.R. China
| | - Florin M Selaru
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins Hospital, Baltimore, Maryland, USA.,The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| |
Collapse
|
2
|
An F, Olaru AV, Mezey E, Xie Q, Li L, Piontek KB, Selaru FM. MicroRNA-224 Induces G1/S Checkpoint Release in Liver Cancer. J Clin Med 2015; 4:1713-28. [PMID: 26343737 PMCID: PMC4600154 DOI: 10.3390/jcm4091713] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/03/2015] [Accepted: 08/12/2015] [Indexed: 02/07/2023] Open
Abstract
Profound changes in microRNA (miR) expression levels are frequently found in liver cancers compared to the normal liver. In this study, we evaluate the expression of miR-224 in human HCC and CCA, as well as its downstream targets and affected pathways. We show that miR-224 is upregulated in a large cohort of human CCA, similar to its upregulation in human HCC. For the purpose of studying the roles of miR-224 in HCC and CCA, we enforced miR-224 expression in cells. mRNA arrays followed by Ingenuity Pathway Analysis (IPA)-identified putative molecules and pathways downstream of miR-224. Phenotypically, we report that enforced expression of miR-224 increases the growth rate of normal cholangiocytes, CCA cell lines, and HCC cell lines. In addition, we identified, in an unbiased fashion, that one of the major biologic processes affected by miR-224 is Gap1 (G1) to Synthesis (S) transition checkpoint release. We next identified p21, p15, and CCNE1 as downstream targets of miR-224 and confirmed the coordinated downregulation results in the increased phosphorylation of Retinoblastoma (Rb) with resulting G1/S checkpoint release. Our data suggest that miR-224 is a master regulator of cell cycle progression, and that its overexpression results in G1/S checkpoint release followed by accelerated cell growth.
Collapse
Affiliation(s)
- Fangmei An
- Department of Gastroenterology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214002, China.
| | - Alexandru V Olaru
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins Hospital, Baltimore, MD, 21205, USA.
| | - Esteban Mezey
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins Hospital, Baltimore, MD, 21205, USA.
| | - Qing Xie
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Ling Li
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins Hospital, Baltimore, MD, 21205, USA.
| | - Klaus B Piontek
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins Hospital, Baltimore, MD, 21205, USA.
| | - Florin M Selaru
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins Hospital, Baltimore, MD, 21205, USA.
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins Hospital, Baltimore, MD, 21287, USA.
| |
Collapse
|
3
|
Gultepe E, Yamanaka S, Laflin KE, Kadam S, Shim Y, Olaru AV, Khashab MA, Kalloo AN, Gracias DH, Selaru FM, Selaru FM. Biologic tissue sampling with untethered microgrippers. Gastroenterology 2013; 144:691-3. [PMID: 23399954 PMCID: PMC3626272 DOI: 10.1053/j.gastro.2013.01.066] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 01/23/2013] [Accepted: 01/29/2013] [Indexed: 12/02/2022]
Affiliation(s)
- Evin Gultepe
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, 3400 N. Charles St. Baltimore, MD 21218, USA
| | - Sumitaka Yamanaka
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins, University, 720 Rutland Ave, Baltimore, MD 21205, USA
| | - Kate E. Laflin
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, 3400 N. Charles St. Baltimore, MD 21218, USA
| | - Sachin Kadam
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, 3400 N. Charles St. Baltimore, MD 21218, USA
| | - YooSun Shim
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, 3400 N. Charles St. Baltimore, MD 21218, USA
| | - Alexandru V. Olaru
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins, University, 720 Rutland Ave, Baltimore, MD 21205, USA
| | - Mouen A. Khashab
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins, University, 720 Rutland Ave, Baltimore, MD 21205, USA
| | - Anthony N. Kalloo
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins, University, 720 Rutland Ave, Baltimore, MD 21205, USA
| | - David H. Gracias
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, 3400 N. Charles St. Baltimore, MD 21218, USA,Department of Chemistry, The Johns Hopkins University, Baltimore, 3400 N. Charles St., Baltimore, MD 21218, USA,To whom correspondence should be addressed., ,
| | - Florin M. Selaru
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins, University, 720 Rutland Ave, Baltimore, MD 21205, USA,To whom correspondence should be addressed., ,
| | | |
Collapse
|
4
|
Cheng Y, Jin Z, Agarwal R, Ma K, Yang J, Ibrahim S, Olaru AV, David S, Ashktorab H, Smoot DT, Duncan MD, Hutcheon DF, Abraham JM, Meltzer SJ, Mori Y. LARP7 is a potential tumor suppressor gene in gastric cancer. J Transl Med 2012; 92:1013-9. [PMID: 22488152 PMCID: PMC3446825 DOI: 10.1038/labinvest.2012.59] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We previously reported frequent truncating mutations of the RNA-binding protein gene, La ribonucleoprotein domain family, member-7 (LARP7) in gastric cancers (GCs) with frequent microsatellite instability. LARP7 negatively regulates positive transcription elongation factor-b (p-TEFb) by binding to and stabilizing 7sk RNA. p-TEFb has been linked to proliferation and de-differentiation in various tissues. Therefore, we reasoned that loss of LARP7 may contribute to gastric tumorigenesis. In this study, we evaluated LARP7 mRNA expression in 18 GCs, their corresponding non-neoplastic gastric tissues (N(GC)), and 18 normal gastric tissues from healthy individuals (N(N)). We also assessed the effects of transient small interfering (siRNA)-mediated LARP7 knockdown in immortalized non-neoplastic gastric epithelial cells. LARP7 mRNA was significantly decreased in GCs (median 2.5) relative to N(N)s (median 14.9, P<0.01) as well as relative to their corresponding N(GC)s (median 8.1, P<0.01). Transfection of an siRNA directed against LARP7 (anti-LARP7 siRNA) into non-neoplastic gastric epithelial cells decreased 7sk levels by 72% relative to a control siRNA (P<0.01). Furthermore, anti-LARP7 siRNA transfection increased cell proliferation by 23% (P<0.01) and cell migration by 22% (P<0.001) relative to control siRNA transfection. Taken together, these findings suggest that LARP7 downregulation occurs early during gastric tumorigenesis and may promote gastric tumorigenesis via p-TEFb dysregulation.
Collapse
Affiliation(s)
- Yulan Cheng
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; Baltimore, Maryland, USA
| | - Zhe Jin
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; Baltimore, Maryland, USA
| | - Rachana Agarwal
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; Baltimore, Maryland, USA
| | - Ke Ma
- University Maryland at College Park; Baltimore, Maryland, USA
| | - Jian Yang
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; Baltimore, Maryland, USA
| | - Soibrahim Ibrahim
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; Baltimore, Maryland, USA
| | - Alexandru V. Olaru
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; Baltimore, Maryland, USA
| | - Stefan David
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; Baltimore, Maryland, USA
| | - Hassan Ashktorab
- Department of Medicine and Cancer Center, Division of Gastroenterology, Howard University College of Medicine; Washington D.C., District of Columbia, USA
| | - Duane T. Smoot
- Department of Surgery, Johns Hopkins Bayview Medical Center; Baltimore, Maryland, USA
| | - Mark D. Duncan
- Department of Surgery, Johns Hopkins Bayview Medical Center; Baltimore, Maryland, USA
| | - David F. Hutcheon
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; Baltimore, Maryland, USA
| | - John M. Abraham
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; Baltimore, Maryland, USA
| | - Stephen J. Meltzer
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; Baltimore, Maryland, USA
| | - Yuriko Mori
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; Baltimore, Maryland, USA
| |
Collapse
|
5
|
Yamanaka S, Olaru AV, An F, Luvsanjav D, Jin Z, Agarwal R, Tomuleasa C, Popescu I, Alexandrescu S, Dima S, Chivu M, Montgomery EA, Torbenson M, Meltzer SJ, Selaru FM. MicroRNA-21 inhibits Serpini1, a gene with novel tumour suppressive effects in gastric cancer. Dig Liver Dis 2012; 44:589-96. [PMID: 22464652 PMCID: PMC3360813 DOI: 10.1016/j.dld.2012.02.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 02/16/2012] [Accepted: 02/24/2012] [Indexed: 12/11/2022]
Abstract
BACKGROUND A thorough understanding of gastric cancer at the molecular level is urgently needed. One prominent oncogenic microRNA, miR-21, was previously reported to be upregulated in gastric cancer. METHODS We performed an unbiased search for downstream messenger RNA targets of miR-21, based on miR-21 dysregulation, by using human tissue specimens and the MKN28 human gastric carcinoma cell line. Molecular techniques include microRNA microarrays, cDNA microarrays, qRT-PCR for miR and mRNA expression, transfection of MKN28 with miR-21 inhibitor or Serpini1 followed by Western blotting, cell cycle analysis by flow cytometry and luciferase reporter assay. RESULTS This search identified Serpini1 as a putative miR-21 target. Luciferase assays demonstrated direct interaction between miR-21 and Serpini1 3'UTR. miR-21 and Serpini1 expression levels were inversely correlated in a subgroup of gastric cancers, suggesting a regulatory mechanism that included both of these molecules. Furthermore, Serpini1 induced growth retardation of MKN28 and induced vigorous G1/S arrest suggesting its potential tumour-suppressive function in the stomach. CONCLUSION Taken together, these data suggest that in a subgroup of gastric cancers, miR-21 is upregulated, inducing downregulation of Serpini1, which in turn releases the G1-S transition checkpoint, with the end result being increased tumour growth.
Collapse
Affiliation(s)
- Sumitaka Yamanaka
- Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alexandru V. Olaru
- Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fangmei An
- Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Delgermaa Luvsanjav
- Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zhe Jin
- Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rachana Agarwal
- Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ciprian Tomuleasa
- Department of Cancer Immunology, Prof. Dr. Ion Chiricuta Comprehensive Cancer Center and Iuliu Hatieganu University of Medicine and Pharmacy, Romania
| | - Irinel Popescu
- Clinic of General Surgery and Liver Transplantation "Dan Setlacec", Fundeni Clinical Institute of Digestive Diseases and Liver Transplantation, Bucharest, Romania
| | - Sorin Alexandrescu
- Clinic of General Surgery and Liver Transplantation "Dan Setlacec", Fundeni Clinical Institute of Digestive Diseases and Liver Transplantation, Bucharest, Romania
| | - Simona Dima
- Clinic of General Surgery and Liver Transplantation "Dan Setlacec", Fundeni Clinical Institute of Digestive Diseases and Liver Transplantation, Bucharest, Romania
| | - Mihaela Chivu
- Clinic of General Surgery and Liver Transplantation "Dan Setlacec", Fundeni Clinical Institute of Digestive Diseases and Liver Transplantation, Bucharest, Romania
| | | | - Michael Torbenson
- Department of Pathology, Johns Hopkins University Hospital, Baltimore, MD, USA
| | - Stephen J. Meltzer
- Department of Pathology, Johns Hopkins University Hospital, Baltimore, MD, USA
| | - Florin M. Selaru
- Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
6
|
Olaru AV, Cheng Y, Agarwal R, Yang J, David S, Abraham JM, Yu W, Lazarev M, Brant SR, Marohn MR, Hutcheon DF, Harpaz N, Meltzer SJ, Mori Y, Mori Y. Unique patterns of CpG island methylation in inflammatory bowel disease-associated colorectal cancers. Inflamm Bowel Dis 2012; 18:641-8. [PMID: 21830278 PMCID: PMC3214229 DOI: 10.1002/ibd.21826] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 06/20/2011] [Indexed: 12/20/2022]
Abstract
BACKGROUND CpG island (CGI) hypermethylation at discrete loci is a prevalent cancer-promoting abnormality in sporadic colorectal carcinomas (S-CRCs). We investigated genome-wide CGI methylation in inflammatory bowel disease (IBD)-associated CRCs (IBD-CRCs). METHODS Methylation microarray analyses were conducted on seven IBD-CRCs, 17 S-CRCs, and eight normal control colonic tissues from patients without CRC or IBD. CGI methylator phenotype (CIMP), a surrogate marker for widespread cancer-specific CGI hypermethylation, was examined in 30 IBD-CRCs and 43 S-CRCs. RESULTS The genome-wide CGI methylation pattern of IBD-CRCs was CIMP status-dependent. Based on methylation array data profiling of all autosomal loci, CIMP(+) IBD-CRCs grouped together with S-CRCs, while CIMP(-) IBD-CRCs grouped together with control tissues. CIMP(-) IBD-CRCs demonstrated less methylation than did age-matched CIMP(-) S-CRCs at autosomal CGIs (z-score -0.17 vs. 0.09, P = 3 × 10(-3)) and CRC-associated hypermethylation target CGIs (z-score -0.43 vs. 0.68, P = 1 × 10(-4)). Age-associated hypermethylation target CGIs were significantly overrepresented in CGIs that were hypermethylated in S-CRCs (P = 1 × 10(-192)), but not in CGIs that were hypermethylated in IBD-CRCs (P = 0.11). In contrast, KRAS mutation prevalence was similar between IBD-CRCs and S-CRCs. Notably, CIMP(+) prevalence was significantly higher in older than in younger IBD-CRC cases (50.0 vs. 4.2, P = 0.02), but not in S-CRC cases (9.7 vs. 16.7, P = 0.92). CONCLUSIONS Cancer-specific CGI hypermethylation and age-associated CGI hypermethylation are diminished in IBD-CRCs relative to S-CRCs, while the KRAS mutation rate is comparable between these cancers. CGI hypermethylation appears to play only a minor role in IBD-associated carcinogenesis. We speculate that aging, rather than inflammation per se, promotes CIMP(+) CRCs in IBD patients.
Collapse
Affiliation(s)
- Alexandru V. Olaru
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Yulan Cheng
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Rachana Agarwal
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Jian Yang
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Stefan David
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - John M. Abraham
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Wayne Yu
- Sidney Kimmel Comprehensive Cancer Center, DNA Microarray Core Facility, Johns Hopkins University School of Medicine; 1503 E. Jefferson Street, Baltimore, Maryland 21287
| | - Mark Lazarev
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Steven R. Brant
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Michael R. Marohn
- Department of Surgery, Johns Hopkins University School of Medicine; 600 N. Wolfe Street, Baltimore MD 21207
| | - David F. Hutcheon
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Noam Harpaz
- Department of Pathology, Mount Sinai School of Medicine; One Gustave L. Levy Place, New York, New York 10029
| | - Stephen J. Meltzer
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205, Department of Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center; 1503 E. Jefferson Street, Baltimore, Maryland 21287
| | - Yuriko Mori
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | | |
Collapse
|
7
|
Agarwal R, Jin Z, Yang J, Mori Y, Song JH, Kumar S, Sato M, Cheng Y, Olaru AV, Abraham JM, Verma A, Meltzer SJ. Epigenomic program of Barrett's-associated neoplastic progression reveals possible involvement of insulin signaling pathways. Endocr Relat Cancer 2012; 19:L5-9. [PMID: 22194443 PMCID: PMC3688264 DOI: 10.1530/erc-11-0364] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
8
|
Olaru AV, Ghiaur G, Yamanaka S, Luvsanjav D, An F, Popescu I, Alexandrescu S, Allen S, Pawlik TM, Torbenson M, Georgiades C, Roberts LR, Gores GJ, Ferguson-Smith A, Almeida MI, Calin GA, Mezey E, Selaru FM. MicroRNA down-regulated in human cholangiocarcinoma control cell cycle through multiple targets involved in the G1/S checkpoint. Hepatology 2011; 54:2089-98. [PMID: 21809359 PMCID: PMC3212606 DOI: 10.1002/hep.24591] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
UNLABELLED MicroRNAs (miRs) recently emerged as prominent regulators of cancer processes. In the current study we aimed at elucidating regulatory pathways and mechanisms through which miR-494, one of the miR species found to be down-regulated in cholangiocarcinoma (CCA), participates in cancer homeostasis. miR-494 was identified as down-regulated in CCA based on miR arrays. Its expression was verified with quantitative real-time reverse-transcription polymerase chain reaction (qRT-PCR). To enforce miR expression, we employed both transfection methods, as well as a retroviral construct to stably overexpress miR-494. Up-regulation of miR-494 in cancer cells decreased growth, consistent with a functional role. mRNA arrays of cells treated with miR-494, followed by pathway analysis, suggested that miR-494 impacts cell cycle regulation. Cell cycle analyses demonstrated that miR-494 induces a significant G1/S checkpoint reinforcement. Further analyses demonstrated that miR-494 down-regulates multiple molecules involved in this transition checkpoint. Luciferase reporter assays demonstrated a direct interaction between miR-494 and the 3'-untranslated region of cyclin-dependent kinase 6 (CDK6). Last, xenograft experiments demonstrated that miR-494 induces a significant cancer growth retardation in vivo. CONCLUSION Our findings demonstrate that miR-494 is down-regulated in CCA and that its up-regulation induces cancer cell growth retardation through multiple targets involved in the G1-S transition. These findings support the paradigm that miRs are salient cellular signaling pathway modulators, and thus represent attractive therapeutic targets. miR-494 emerges as an important regulator of CCA growth and its further study may lead to the development of novel therapeutics.
Collapse
Affiliation(s)
- Alexandru V. Olaru
- Division of Gastroenterology and Hepatology, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Gabriel Ghiaur
- Division of Hematology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Sumitaka Yamanaka
- Division of Gastroenterology and Hepatology, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Delgermaa Luvsanjav
- Division of Gastroenterology and Hepatology, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Fangmei An
- Division of Gastroenterology and Hepatology, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Irinel Popescu
- Clinic of General Surgery and Liver Transplantation “Dan Setlacec”, Fundeni Clinical Institute of Digestive Diseases and Liver Transplantation, Bucharest, Romania
| | - Sorin Alexandrescu
- Clinic of General Surgery and Liver Transplantation “Dan Setlacec”, Fundeni Clinical Institute of Digestive Diseases and Liver Transplantation, Bucharest, Romania
| | - Sarah Allen
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Timothy M. Pawlik
- Department of Surgery, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Michael Torbenson
- Department of Pathology, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | | | - Lewis R. Roberts
- Divisions of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Gregory J. Gores
- Divisions of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Anne Ferguson-Smith
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Maria I. Almeida
- Department of Experimental Therapeutics, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - George A. Calin
- Department of Experimental Therapeutics, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Esteban Mezey
- Division of Gastroenterology and Hepatology, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Florin M. Selaru
- Division of Gastroenterology and Hepatology, Johns Hopkins Hospital, Baltimore, Maryland, USA,To whom correspondence should be addressed: Florin M. Selaru, MD, Johns Hopkins Hospital, 720 Rutland Ave, Ross Research Building Suite 950, Baltimore, MD, 21205
| |
Collapse
|
9
|
Ito T, Sato F, Kan T, Cheng Y, David S, Agarwal R, Paun BC, Jin Z, Olaru AV, Hamilton JP, Selaru FM, Yang J, Matsumura N, Shimizu K, Abraham JM, Shimada Y, Mori Y, Meltzer SJ. Polo-like kinase 1 regulates cell proliferation and is targeted by miR-593* in esophageal cancer. Int J Cancer 2011; 129:2134-46. [PMID: 21170987 PMCID: PMC3176391 DOI: 10.1002/ijc.25874] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 11/19/2010] [Indexed: 12/13/2022]
Abstract
Polo-like kinase 1 (PLK1) is overexpressed in various human cancers. However, the biological functions and the post-transcriptional regulations of PLK1 in esophageal cancer (EC) are still unknown. The purposes of our study are to determine whether PLK1 can be a molecular target of EC therapy and to identify a microRNA (miRNA) targeting PLK1. We performed loss-of-function and gain-of-function experiments regarding cell proliferation, cell cycle, apoptosis, in vivo tumor formation and luciferase reporter assays, using siRNAs against PLK1 and miRNA. PLK1 protein was expressed in all 11 EC cell lines, but not in normal esophageal epithelial cells (HEEpiC). Knockdown of PLK1 in EC cells induced G2/M arrest (p < 0.001) in cell cycle assay and reduced cell proliferation (p = 0.019) and tumor formation ability in vivo (p < 0.0001). MiR-593*, identified as a miRNA targeting PLK1 by a database search, was less expressed especially in six EC cell lines than HEEpiC cells. Moreover, miR-593* expression level was inversely correlated with PLK1 mRNA level in 48 clinical tissue specimens of EC (p = 0.006). Introduction of synthetic miR-593* suppressed PLK1 expression by 69-73%, reduced cell proliferation (p = 0.008) and increased cell proportion of G2/M phase (p = 0.01) in HSA/c (an EC cells), whereas a miR-593* inhibitor upregulated PLK1 expression by 11-55%. Additionally, luciferase assay demonstrated that miR-593* interacted two binding sites in the PLK1 3'-UTR and reduced 56.8-71.5% of luciferase activity by degrading luciferase mRNA in HSA/c cells. In conclusion, PLK1 is post-transcriptionally regulated by miR-593* and could be a promising molecular target for EC treatment.
Collapse
Affiliation(s)
- Tetsuo Ito
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Fumiaki Sato
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Nanobio Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Takatsugu Kan
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Yulan Cheng
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stefan David
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rachana Agarwal
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Bogdan C. Paun
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Zhe Jin
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alexandru V. Olaru
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - James P. Hamilton
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Florin M. Selaru
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jian Yang
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nobutoshi Matsumura
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kazuharu Shimizu
- Department of Nanobio Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - John M. Abraham
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Yutaka Shimada
- Department of Surgery and Science, Graduate School of Medicine and Pharmaceutical Sciences Research, University of Toyama, Toyama, Japan
| | - Yuriko Mori
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stephen J. Meltzer
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| |
Collapse
|
10
|
Mori Y, Olaru AV, Cheng Y, Agarwal R, Yang J, Luvsanjav D, Yu W, Selaru FM, Hutfless S, Lazarev M, Kwon JH, Brant SR, Marohn MR, Hutcheon DF, Duncan MD, Goel A, Meltzer SJ. Novel candidate colorectal cancer biomarkers identified by methylation microarray-based scanning. Endocr Relat Cancer 2011; 18:465-78. [PMID: 21636702 PMCID: PMC3464012 DOI: 10.1530/erc-11-0083] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA hypermethylation is a common epigenetic abnormality in colorectal cancers (CRCs) and a promising class of CRC screening biomarkers. We conducted a genome-wide search for novel neoplasia-specific hypermethylation events in the colon. We applied methylation microarray analysis to identify loci hypermethylated in 17 primary CRCs relative to eight non-neoplastic colonic mucosae (NCs) from neoplasia-free subjects. These CRC-associated hypermethylation events were then individually evaluated for their ability to discriminate neoplastic from non-neoplastic cases, based on real-time quantitative methylation-specific PCR (qMSP) assays in 113 colonic tissues: 51 CRCs, nine adenomas, 19 NCs from CRC patients (CRC-NCs), and 34 NCs from neoplasia-free subjects (control NCs). A strict microarray data filtering identified 169 candidate CRC-associated hypermethylation events. Fourteen of these 169 loci were evaluated using qMSP assays. Ten of these 14 methylation events significantly distinguished CRCs from age-matched control NCs (P<0.05 by receiver operator characteristic curve analysis); methylation of visual system homeobox 2 (VSX2) achieved the highest discriminative accuracy (83.3% sensitivity and 92.3% specificity, P<1×10(-6)), followed by BEN domain containing 4 (BEND4), neuronal pentraxin I (NPTX1), ALX homeobox 3 (ALX3), miR-34b, glucagon-like peptide 1 receptor (GLP1R), BTG4, homer homolog 2 (HOMER2), zinc finger protein 583 (ZNF583), and gap junction protein, gamma 1 (GJC1). Adenomas were significantly discriminated from control NCs by hypermethylation of VSX2, BEND4, NPTX1, miR-34b, GLP1R, and HOMER2 (P<0.05). CRC-NCs were significantly distinguished from control NCs by methylation of ALX3 (P<1×10(-4)). In conclusion, systematic methylome-wide analysis has identified ten novel methylation events in neoplastic and non-neoplastic colonic mucosae from CRC patients. These potential biomarkers significantly discriminate CRC patients from controls. Thus, they merit further evaluation in stool- and circulating DNA-based CRC detection studies.
Collapse
Affiliation(s)
- Yuriko Mori
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, 720 Rutland Avenue, Baltimore, Maryland 21205, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Song JH, Cheng Y, Yang J, Wu W, Mori Y, Olaru AV, Bootwalla M, Sharpf R, Meltzer SJ. Abstract 4960: Circulating miRNAs as noninvasive biomarkers in esophageal adenocarcinoma patients. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-4960] [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
Esophageal adenocarcinoma (EAC) is one of the most rapidly increasing cancers in the United States and throughout the developed world. The current primary screening method for EAC is gastrointestinal endoscopy (EGD), and this method is unsuitable and impractical for population-based screening or detection of asymptomatic EAC. Moreover, thus far, only a few reports have described altered miR expression in EAC, none of which were carried out in serum or plasma. We discovered a panel of noninvasive circulating microRNA (miR) biomarkers to promote earlier detection of EAC. We extracted total RNA from serum of each subject and hybridized it to fixed-probe miR microarrays in 12 sera each from EAC patients, subjects with normal EGDs, and 12 matched EAC tissues and normal esophageal tissues from EAC patients. Data was extracted and normalized using Feature Extraction Software 9.3 and GeneSpring software (Agilent) and subsequently analyzed by classification trees, multiple leave-one-out cross-validation, and relative influence plots. We selected the most influential miRs for validation by quantitative RT-PCR assays. Our preliminary miR findings indicate that several miRs show dramatic and significant differences in serum levels between EAC and normal control subjects. An ROC curve assembled based on aggregate data yielded an area under the curve (AUC) = 0.885, with sensitivity = 92% and specificity = 83%. We conclude that a panel consisting of several miRs is likely to discriminate asymptomatic EAC patients from normal subjects, leading to earlier diagnosis and improved prognosis.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4960. doi:10.1158/1538-7445.AM2011-4960
Collapse
Affiliation(s)
| | - Yulan Cheng
- 1Johns Hopkins School of Medicine, Baltimore, MD
| | - Jian Yang
- 1Johns Hopkins School of Medicine, Baltimore, MD
| | - Wenjing Wu
- 1Johns Hopkins School of Medicine, Baltimore, MD
| | - Yuriko Mori
- 1Johns Hopkins School of Medicine, Baltimore, MD
| | | | | | | | | |
Collapse
|
12
|
Olaru AV, Selaru FM, Mori Y, Vazquez C, David S, Paun B, Cheng Y, Jin Z, Yang J, Agarwal R, Abraham JM, Dassopoulos T, Harris M, Bayless TM, Kwon J, Harpaz N, Livak F, Meltzer SJ. Dynamic changes in the expression of MicroRNA-31 during inflammatory bowel disease-associated neoplastic transformation. Inflamm Bowel Dis 2011; 17:221-31. [PMID: 20848542 PMCID: PMC3006011 DOI: 10.1002/ibd.21359] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Patients with inflammatory bowel disease (IBD) are at increased risk of developing colorectal cancer. Aberrant microRNA (miR) expression has been linked to carcinogenesis; however, no reports document a relationship between IBD-related neoplasia (IBDN) and altered miR expression. In the current study we sought to identify specific miR dysregulation along the normal-inflammation-cancer axis. METHODS miR microarrays and quantitative reverse-transcriptase polymerase chain reaction (RT-PCR) were used to detect dysregulated miRs. Receiver operating characteristic curve analysis was employed to test for potential usefulness of miR-31 as a disease marker of IBDNs. In silico prediction analysis, Western blot, and luciferase activity measurement were employed for target identification. RESULTS Several dysregulated miRs were identified between chronically inflamed mucosae and dysplasia arising in IBD. MiR-31 expression increases in a stepwise fashion during progression from normal to IBD to IBDN and accurately discriminated IBDNs from normal or chronically inflamed tissues in IBD patients. Finally, we identified factor inhibiting hypoxia inducible factor 1 as a direct target of miR-31. CONCLUSIONS Our study reveals specific miR dysregulation as chronic inflammation progresses to dysplasia. MiR-31 expression levels increase with disease progression and accurately discriminates between distinct pathological entities that coexist in IBD patients. The novel effect of miR-31 on regulating factor inhibiting hypoxia inducible factor 1 expression provides a new insight on the pathogenesis of IBDN.
Collapse
Affiliation(s)
- Alexandru V. Olaru
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, MD, 21287
| | - Florin M. Selaru
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, MD, 21287
| | - Yuriko Mori
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, MD, 21287
| | - Christine Vazquez
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, MD, 21287
| | - Stefan David
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, MD, 21287
| | - Bogdan Paun
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, MD, 21287
| | - Yulan Cheng
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, MD, 21287
| | - Zhe Jin
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, MD, 21287
| | - Jian Yang
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, MD, 21287
| | - Rachana Agarwal
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, MD, 21287
| | - John M. Abraham
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, MD, 21287
| | | | - Mary Harris
- The Institute for Digestive Health & Liver Disease at Mercy Hospital, Baltimore, MD
| | - Theodore M. Bayless
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, MD, 21287
| | - John Kwon
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, MD, 21287
| | - Noam Harpaz
- Division of Gastrointestinal Pathology, Department of Pathology, Mount Sinai School of Medicine, New York, NY
| | - Ferenc Livak
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD
| | - Stephen J. Meltzer
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, MD, 21287
| |
Collapse
|
13
|
Jin Z, Selaru FM, Cheng Y, Kan T, Agarwal R, Mori Y, Olaru AV, Yang J, David S, Hamilton JP, Abraham JM, Harmon J, Duncan M, Montgomery EA, Meltzer SJ. MicroRNA-192 and -215 are upregulated in human gastric cancer in vivo and suppress ALCAM expression in vitro. Oncogene 2010; 30:1577-85. [PMID: 21119604 DOI: 10.1038/onc.2010.534] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The dismal outcome of gastric cancer patients highlights the need for diagnostic biomarkers and effective therapeutic targets, such as microRNAs. We sought to discover microRNAs involved in gastric cancer, and to elucidate their downstream target mechanisms. Both cultured gastric epithelial cells (HFE145 and NCI-N87) and primary human gastric tissues (31 non-neoplastic stomach (NS) and 25 gastric carcinomas (GC)) were studied. MicroRNA microarrays and quantitative RT-PCR were applied to discover and verify differentially expressed microRNAs. in vitro cell migration and invasion, cell proliferation, cell cycle and apoptosis assays were executed to elucidate biological effects of microRNA-192 and -215. Western blotting and luciferase assays were performed to confirm direct messenger RNA targeting by microRNA-192 and -215. MicroRNA microarray analyses revealed that 25 and 20 microRNAs were upregulated and downregulated in GC vs NS, respectively. Expression levels of both microRNA-192 and -215 were significantly higher in GC than in NS (P<0.05). Luciferase assays suggested that microRNA-215 inhibits activated leukocyte cell adhesion molecule (ALCAM) expression at the posttranscriptional level. In addition, expression levels of ALCAM were significantly lower in GC than in NS. Mimics and inhibitors, respectively, of microRNA-192 or -215 exerted no effect on cell cycle or apoptosis in the immortalized normal gastric cell line HFE145 or the gastric cancer cell line NCI-N87. However, mimics of microRNA-192 or -215 significantly increased growth rates in HFE145 cells, whereas inhibitors of microRNA-192 or -215 caused significant decreases in growth rates in NCI-N87 cells. ALCAM knockdown by an ALCAM-specific siRNA significantly increased cell growth in HFE145 cells. Both transfection of mimics of microRNA-192 or -215 and ALCAM knockdown by an ALCAM-specific siRNA significantly increased the migration of HFE145 cells. In conclusion, in gastric cancer, both microRNA-192 and -215 are overexpressed in vivo and exert cell growth and migration-promoting effects in vitro, thus representing potential microRNAs with a role in cancer in the human stomach.
Collapse
Affiliation(s)
- Z Jin
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Kan T, Paun BC, Mori Y, Sato F, Jin Z, Hamilton JP, Ito T, Cheng Y, David S, Olaru AV, Yang J, Agarwal R, Abraham JM, Meltzer SJ. Rarity of Somatic Mutation and Frequency of Normal Sequence Variation Detected in Sporadic Colon Adenocarcinoma Using High-Throughput cDNA Sequencing. Bioinform Biol Insights 2009; 1:1-16. [PMID: 18389087 PMCID: PMC2287164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We performed high-throughput cDNA sequencing in colorectal adenocarcinoma and matching normal colorectal epithelium. All six hundred three genes in the UCSC database that were expressed in colon cancers and contained open reading frames of 1000 nucleotides or less were selected for study (total basepairs/bp, 366,686). 304,350 of these 366,686 bp (83.0%) were amplified and sequenced successfully. Seventy-eight sequence variants present in germline (i.e. normal) as well as matching somatic (i.e. tumor) DNA were discovered, yielding a frequency of 1 variant per 3,902 bp. Fifty-one of these sequence variants were homozygous (26 synonymous, 25 non-synonymous), while 27 were heterozygous (11 synonymous, 16 non-synonymous). Cancer tissue contained only one sequence-altered allele of the gene ATP50, which was present heterozygously alongside the wild-type allele in matching normal epithelium. Despite this relatively large number of bp and genes sequenced, no somatic mutations unique to tumor were found. High-throughput cDNA sequencing is a practical approach for detecting novel sequence variations and alterations in human tumors, such as those of the colon.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Stephen J. Meltzer
- Correspondence: Stephen J. Meltzer, M.D., Professor of Medicine and Oncology, Division of Gastroenterology, Department of Medicine, The Johns Hopkins University School of Medicine 1503 E. Jefferson Street, Rm. 112, Baltimore, MD 21287. Tel: 410-502-6071; Fax: 410-502-1329;
| |
Collapse
|
15
|
Agarwal R, Mori Y, Cheng Y, Jin Z, Olaru AV, Hamilton JP, David S, Selaru FM, Yang J, Abraham JM, Montgomery E, Morin PJ, Meltzer SJ. Silencing of claudin-11 is associated with increased invasiveness of gastric cancer cells. PLoS One 2009; 4:e8002. [PMID: 19956721 PMCID: PMC2776495 DOI: 10.1371/journal.pone.0008002] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [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: 08/03/2009] [Accepted: 10/23/2009] [Indexed: 12/13/2022] Open
Abstract
Background Claudins are membrane proteins that play critical roles in tight junction (TJ) formation and function. Members of the claudin gene family have been demonstrated to be aberrantly regulated, and to participate in the pathogenesis of various human cancers. In the present study, we report that claudin-11 (CLDN11) is silenced in gastric cancer via hypermethylation of its promoter region. Methodology/Principal Findings Levels of CLDN11 methylation and mRNA expression were measured in primary gastric cancer tissues, noncancerous gastric mucosae, and cell lines of gastric origin using quantitative methylation-specific PCR (qMSP) and quantitative reverse transcriptase-PCR (qRT-PCR), respectively. Analyses of paired gastric cancers and adjacent normal gastric tissues revealed hypermethylation of the CLDN11 promoter region in gastric cancers, and this hypermethylation was significantly correlated with downregulation of CLDN11 expression vs. normal tissues. The CLDN11 promoter region was also hypermethylated in all gastric cancer cell lines tested relative to immortalized normal gastric epithelial cells. Moreover, CLDN11 mRNA expression was inversely correlated with its methylation level. Treatment of CLDN11-nonexpressing gastric cancer cells with 5-aza-2′-deoxycytidine restored CLDN11 expression. Moreover, siRNA-mediated knockdown of CLDN11 expression in normal gastric epithelial cells increased their motility and invasiveness. Conclusions/Significance These data suggest that hypermethylation of CLDN11, leading to downregulated expression, contributes to gastric carcinogenesis by increasing cellular motility and invasiveness. A further understanding of the mechanisms underlying the role of claudin proteins in gastric carcinogenesis will likely help in the identification of novel approaches for diagnosis and therapy of gastric cancer.
Collapse
Affiliation(s)
- Rachana Agarwal
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Jin Z, Cheng Y, Gu W, Zheng Y, Sato F, Mori Y, Olaru AV, Paun BC, Yang J, Kan T, Ito T, Hamilton JP, Selaru FM, Agarwal R, David S, Abraham JM, Wolfsen HC, Wallace MB, Shaheen NJ, Washington K, Wang J, Canto MI, Bhattacharyya A, Nelson MA, Wagner PD, Romero Y, Wang KK, Feng Z, Sampliner RE, Meltzer SJ. A multicenter, double-blinded validation study of methylation biomarkers for progression prediction in Barrett's esophagus. Cancer Res 2009; 69:4112-5. [PMID: 19435894 DOI: 10.1158/0008-5472.can-09-0028] [Citation(s) in RCA: 177] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Esophageal adenocarcinoma risk in Barrett's esophagus (BE) is increased 30- to 125-fold versus the general population. Among all BE patients, however, neoplastic progression occurs only once per 200 patient-years. Molecular biomarkers are therefore needed to risk-stratify patients for more efficient surveillance endoscopy and to improve the early detection of progression. We therefore performed a retrospective, multicenter, double-blinded validation study of eight BE progression prediction methylation biomarkers. Progression or nonprogression were determined at 2 years (tier 1) and 4 years (tier 2). Methylation was assayed in 145 nonprogressors and 50 progressors using real-time quantitative methylation-specific PCR. Progressors were significantly older than nonprogressors (70.6 versus 62.5 years; P < 0.001). We evaluated a linear combination of the eight markers, using coefficients from a multivariate logistic regression analysis. Areas under the ROC curve (AUC) were high in the 2-year, 4-year, and combined data models (0.843, 0.829, and 0.840; P < 0.001, <0.001, and <0.001, respectively). In addition, even after rigorous overfitting correction, the incremental AUCs contributed by panels based on the 8 markers plus age versus age alone were substantial (Delta-AUC = 0.152, 0.114, and 0.118, respectively) in all 3 models. A methylation biomarker-based panel to predict neoplastic progression in BE has potential clinical value in improving both the efficiency of surveillance endoscopy and the early detection of neoplasia.
Collapse
Affiliation(s)
- Zhe Jin
- Gastroenterology Division, Johns Hopkins University, Baltimore, MD 21287, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Kan T, Sato F, Ito T, Matsumura N, David S, Cheng Y, Agarwal R, Paun BC, Jin Z, Olaru AV, Selaru FM, Hamilton JP, Yang J, Abraham JM, Mori Y, Meltzer SJ. The miR-106b-25 polycistron, activated by genomic amplification, functions as an oncogene by suppressing p21 and Bim. Gastroenterology 2009; 136:1689-700. [PMID: 19422085 PMCID: PMC2887605 DOI: 10.1053/j.gastro.2009.02.002] [Citation(s) in RCA: 214] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
BACKGROUND & AIMS Barrett's esophagus (BE) is a highly premalignant disease that predisposes to the development of esophageal adenocarcinoma (EAC); however, the involvement of microRNAs (miRs) in BE-EAC carcinogenic progression is not known. METHODS Esophageal cultured cells (HEEpiC, QhTRT, ChTRT, GihTRT, and OE-33) and esophageal tissues (22 normal epithelia, 24 BE, and 22 EAC) were studied. MiR microarrays and quantitative reverse-transcription polymerase chain reaction (RT-PCR) were employed to explore and verify differentially expressed miRs. Quantitative genomic PCR was performed to study copy number variation at the miR-106b-25 polycistron and MCM7 gene locus on chromosome 7q22.1. In vitro cell proliferation, cell cycle, and apoptosis assays and in vivo tumorigenesis experiments were performed to elucidate biologic effects of the miR-106b-25 polycistron. Western blotting and luciferase assays were performed to confirm direct messenger RNA (mRNA) targeting by the miR-106b-25 polycistron. RESULTS The miR-106b-25 polycistron exerted potential proliferative, antiapoptotic, cell cycle-promoting effects in vitro and tumorigenic activity in vivo. MiRs-93 and -106b targeted and inhibited p21, whereas miR-25 targeted and inhibited Bim. This polycistron was upregulated progressively at successive stages of neoplasia, in association with genomic amplification and overexpression of MCM7. In addition, miRs-93 and -106b decreased p21 mRNA, whereas miR-25 did not alter Bim mRNA, suggesting the following discrete miR effector mechanisms: (1) for p21, mRNA degradation; (2) for Bim, translational inhibition. CONCLUSIONS The miR-106b-25 polycistron is activated by genomic amplification and is potentially involved in esophageal neoplastic progression and proliferation via suppression of 2 target genes: p21 and Bim.
Collapse
Affiliation(s)
- Takatsugu Kan
- Division of Gastroenterology, Departments of Medicine and Oncology, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Fumiaki Sato
- Department of Nanobio Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Tetsuo Ito
- Division of Gastroenterology, Departments of Medicine and Oncology, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | | | - Stefan David
- Division of Gastroenterology, Departments of Medicine and Oncology, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Yulan Cheng
- Division of Gastroenterology, Departments of Medicine and Oncology, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Rachana Agarwal
- Division of Gastroenterology, Departments of Medicine and Oncology, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Bogdan C. Paun
- Division of Gastroenterology, Departments of Medicine and Oncology, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Zhe Jin
- Division of Gastroenterology, Departments of Medicine and Oncology, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Alexandru V. Olaru
- Division of Gastroenterology, Departments of Medicine and Oncology, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Florin M. Selaru
- Division of Gastroenterology, Departments of Medicine and Oncology, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - James P. Hamilton
- Division of Gastroenterology, Departments of Medicine and Oncology, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Jian Yang
- Division of Gastroenterology, Departments of Medicine and Oncology, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - John M. Abraham
- Division of Gastroenterology, Departments of Medicine and Oncology, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Yuriko Mori
- Division of Gastroenterology, Departments of Medicine and Oncology, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Stephen J. Meltzer
- Division of Gastroenterology, Departments of Medicine and Oncology, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland,Correspondence: Stephen J. Meltzer, Division of Gastroenterology, Department of Medicine, Johns Hopkins University School of Medicine, 1503 East Jefferson Street Rm 112, Baltimore, MD 21287. Phone: 410-502-6071; Fax: 410-502-1329; E-mail:
| |
Collapse
|
18
|
Selaru FM, Olaru AV, Kan T, David S, Cheng Y, Mori Y, Yang J, Paun B, Jin Z, Agarwal R, Hamilton JP, Abraham J, Georgiades C, Alvarez H, Vivekanandan P, Yu W, Maitra A, Torbenson M, Thuluvath PJ, Gores GJ, LaRusso NF, Hruban R, Meltzer SJ. MicroRNA-21 is overexpressed in human cholangiocarcinoma and regulates programmed cell death 4 and tissue inhibitor of metalloproteinase 3. Hepatology 2009; 49:1595-601. [PMID: 19296468 PMCID: PMC3124086 DOI: 10.1002/hep.22838] [Citation(s) in RCA: 218] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
UNLABELLED Cholangiocarcinomas (CCAs) are aggressive cancers, with high mortality and poor survival rates. Only radical surgery offers patients some hope of cure; however, most patients are not surgical candidates because of late diagnosis secondary to relatively poor accuracy of diagnostic means. MicroRNAs (miRs) are involved in every cancer examined, but they have not been evaluated in primary CCA. In this study, miR arrays were performed on five primary CCAs and five normal bile duct specimens (NBDs). Several miRs were dysregulated and miR-21 was overexpressed in CCAs. miR-21 differential expression in these 10 specimens was verified by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). To validate these findings, qRT-PCR for miR-21 was then performed on 18 additional primary CCAs and 12 normal liver specimens. MiR-21 was 95% sensitive and 100% specific in distinguishing between CCA and normal tissues, with an area under the receiver operating characteristic curve of 0.995. Inhibitors of miR-21 increased protein levels of programmed cell death 4 (PDCD4) and tissue inhibitor of metalloproteinases 3 (TIMP3). Notably, messenger RNA levels of TIMP3 were significantly lower in CCAs than in normals. CONCLUSIONS MiR-21 is overexpressed in human CCAs. Furthermore, miR-21 may be oncogenic, at least in part, by inhibiting PDCD4 and TIMP3. Finally, these data suggest that TIMP3 is a candidate tumor suppressor gene in the biliary tree.
Collapse
Affiliation(s)
- Florin M. Selaru
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University, Baltimore, MD, 1503 E Jefferson St, Room 106, Baltimore, MD, 21287
| | - Alexandru V. Olaru
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University, Baltimore, MD, 1503 E Jefferson St, Room 106, Baltimore, MD, 21287
| | - Takatsugu Kan
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University, Baltimore, MD, 1503 E Jefferson St, Room 106, Baltimore, MD, 21287
| | - Stefan David
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University, Baltimore, MD, 1503 E Jefferson St, Room 106, Baltimore, MD, 21287
| | - Yulan Cheng
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University, Baltimore, MD, 1503 E Jefferson St, Room 106, Baltimore, MD, 21287
| | - Yuriko Mori
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University, Baltimore, MD, 1503 E Jefferson St, Room 106, Baltimore, MD, 21287
| | - Jian Yang
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University, Baltimore, MD, 1503 E Jefferson St, Room 106, Baltimore, MD, 21287
| | - Bogdan Paun
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University, Baltimore, MD, 1503 E Jefferson St, Room 106, Baltimore, MD, 21287
| | - Zhe Jin
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University, Baltimore, MD, 1503 E Jefferson St, Room 106, Baltimore, MD, 21287
| | - Rachana Agarwal
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University, Baltimore, MD, 1503 E Jefferson St, Room 106, Baltimore, MD, 21287
| | - James P. Hamilton
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University, Baltimore, MD, 1503 E Jefferson St, Room 106, Baltimore, MD, 21287
| | - John Abraham
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University, Baltimore, MD, 1503 E Jefferson St, Room 106, Baltimore, MD, 21287
| | | | - Hector Alvarez
- Division of Pathology, Johns Hopkins University, Baltimore, MD
| | | | - Wayne Yu
- Division of Oncology, Johns Hopkins University, Baltimore, MD
| | - Anirban Maitra
- Division of Pathology, Johns Hopkins University, Baltimore, MD, Division of Oncology, Johns Hopkins University, Baltimore, MD
| | | | - Paul J. Thuluvath
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University, Baltimore, MD, 1503 E Jefferson St, Room 106, Baltimore, MD, 21287
| | - Gregory J. Gores
- Division of Gastroenterology and Hepatology, Center for Basic Research in Digestive Diseases, Mayo Clinic College of Medicine, Rochester, MN
| | - Nicholas F. LaRusso
- Division of Gastroenterology and Hepatology, Center for Basic Research in Digestive Diseases, Mayo Clinic College of Medicine, Rochester, MN
| | - Ralph Hruban
- Division of Pathology, Johns Hopkins University, Baltimore, MD
| | - Stephen J. Meltzer
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University, Baltimore, MD, 1503 E Jefferson St, Room 106, Baltimore, MD, 21287
| |
Collapse
|
19
|
David S, Olaru AV, Paun BC, Jin Z, Meltzer SJ, Selaru FM. The interplay between microRNA‐21 and endothelin receptor B (EDNRB) in gastric cancer. FASEB J 2009. [DOI: 10.1096/fasebj.23.1_supplement.lb205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Stefan David
- Medicine, GastroenterologyJohns Hopkins UniversityBaltimoreMD
| | | | - Bogdan C Paun
- Medicine, GastroenterologyJohns Hopkins UniversityBaltimoreMD
| | - Zhe Jin
- Medicine, GastroenterologyJohns Hopkins UniversityBaltimoreMD
| | | | - Florin M Selaru
- Medicine, GastroenterologyJohns Hopkins UniversityBaltimoreMD
| |
Collapse
|
20
|
Kan T, Paun BC, Mori Y, Sato F, Jin Z, Hamilton JP, Ito T, Cheng Y, David S, Olaru AV, Yang J, Agarwal R, Abraham JM, Meltzer SJ. Rarity of Somatic Mutation and Frequency of Normal Sequence Variation Detected in Sporadic Colon Adenocarcinoma Using High-Throughput cDNA Sequencing. Bioinform Biol Insights 2007. [DOI: 10.1177/117793220700100001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
We performed high-throughput cDNA sequencing in colorectal adenocarcinoma and matching normal colorectal epithelium. All six hundred three genes in the UCSC database that were expressed in colon cancers and contained open reading frames of 1000 nucleotides or less were selected for study (total basepairs/bp, 366,686). 304,350 of these 366,686 bp (83.0%) were amplified and sequenced successfully. Seventy-eight sequence variants present in germline (i.e. normal) as well as matching somatic (i.e. tumor) DNA were discovered, yielding a frequency of 1 variant per 3,902 bp. Fifty-one of these sequence variants were homozygous (26 synonymous, 25 non-synonymous), while 27 were heterozygous (11 synonymous, 16 non-synonymous). Cancer tissue contained only one sequence-altered allele of the gene ATP50, which was present heterozygously alongside the wild-type allele in matching normal epithelium. Despite this relatively large number of bp and genes sequenced, no somatic mutations unique to tumor were found. High-throughput cDNA sequencing is a practical approach for detecting novel sequence variations and alterations in human tumors, such as those of the colon.
Collapse
Affiliation(s)
- Takatsugu Kan
- Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287
| | - Bogdan C. Paun
- Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287
| | - Yuriko Mori
- Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287
| | - Fumiaki Sato
- Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287
| | - Zhe Jin
- Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287
| | - James P. Hamilton
- Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287
| | - Tetsuo Ito
- Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287
| | - Yulan Cheng
- Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287
| | - Stefan David
- Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287
| | - Alexandru V. Olaru
- Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287
| | - Jian Yang
- Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287
| | - Rachana Agarwal
- Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287
| | - John M. Abraham
- Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287
| | - Stephen J. Meltzer
- Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287
| |
Collapse
|
21
|
Selaru FM, Wang S, Yin J, Schulmann K, Xu Y, Mori Y, Olaru AV, Sato F, Hamilton JP, Abraham JM, Schneider P, Greenwald BD, Brabender J, Meltzer SJ. Beyond Field Effect: Analysis of Shrunken Centroids in Normal Esophageal Epithelia Detects Concomitant Esophageal Adenocarcinoma. Bioinform Biol Insights 2007; 1:127-136. [PMID: 18425214 PMCID: PMC2323355 DOI: 10.4137/bbi.s311] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [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] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND AND AIMS: Because of the extremely low neoplastic progression rate in Barrett's esophagus, it is difficult to diagnose patients with concomitant adenocarcinoma early in their disease course. If biomarkers existed in normal squamous esophageal epithelium to identify patients with concomitant esophageal adenocarcinoma, potential applications would be far-reaching. The aim of the current study was to identify global gene expression patterns in normal esophageal epithelium capable of revealing simultaneous esophageal adenocarcinoma, even located remotely in the esophagus. METHODS: Tissues comprised normal esophageal epithelia from 9 patients with esophageal adenocarcinoma, 8 patients lacking esophageal adenocarcinoma or Barrett's, and 6 patients with Barrett's esophagus alone. cDNA microarrays were performed, and pattern recognition in each of these subgroups was achieved using shrunken nearest centroid predictors. RESULTS: Our method accurately discriminated normal esophageal epithelia of 8/8 patients without esophageal adenocarcinoma or Barrett's esophagus and of 6/6 patients with Barrett's esophagus alone from normal esophageal epithelia of 9/9 patients with Barrett's esophagus and concomitant esophageal adenocarcinoma. Moreover, we identified genes differentially expressed between the above subgroups. Thus, based on their corresponding normal esophageal epithelia alone, our method accurately diagnosed patients who had concomitant esophageal adenocarcinoma. CONCLUSIONS: These global gene expression patterns, along with individual genes culled from them, represent potential biomarkers for the early diagnosis of esophageal adenocarcinoma from normal esophageal epithelia. Genes discovered in normal esophagus that are differentially expressed in patients with vs. without esophageal adenocarcinoma merit further pursuit in molecular genetic, functional, and therapeutic interventional studies.
Collapse
Affiliation(s)
- Florin M. Selaru
- Gastroenterology Division, Department of Medicine, the Johns Hopkins University School of Medicine, Baltimore, MD 21231
| | - Suna Wang
- Gastroenterology Division, Department of Medicine, University of Maryland School of Medicine and Baltimore VA Hospital and Greenebaum Cancer Center, Baltimore, MD 21201
| | - Jing Yin
- Gastroenterology Division, Department of Medicine, University of Maryland School of Medicine and Baltimore VA Hospital and Greenebaum Cancer Center, Baltimore, MD 21201
| | - Karsten Schulmann
- Division of Gastroenterology, Department of Medicine, Ruhr-University Bochum, Bochum, Germany
| | - Yan Xu
- Gastroenterology Division, Department of Medicine, University of Maryland School of Medicine and Baltimore VA Hospital and Greenebaum Cancer Center, Baltimore, MD 21201
| | - Yuriko Mori
- Gastroenterology Division, Department of Medicine, the Johns Hopkins University School of Medicine, Baltimore, MD 21231
| | - Alexandru V. Olaru
- Gastroenterology Division, Department of Medicine, the Johns Hopkins University School of Medicine, Baltimore, MD 21231
| | - Fumiaki Sato
- Gastroenterology Division, Department of Medicine, the Johns Hopkins University School of Medicine, Baltimore, MD 21231
| | - James P. Hamilton
- Gastroenterology Division, Department of Medicine, the Johns Hopkins University School of Medicine, Baltimore, MD 21231
| | - John M. Abraham
- Gastroenterology Division, Department of Medicine, the Johns Hopkins University School of Medicine, Baltimore, MD 21231
| | - Paul Schneider
- Department of Visceral and Vascular Surgery, University of Cologne, Germany
| | - Bruce D. Greenwald
- Gastroenterology Division, Department of Medicine, University of Maryland School of Medicine and Baltimore VA Hospital and Greenebaum Cancer Center, Baltimore, MD 21201
| | - Jan Brabender
- Department of Visceral and Vascular Surgery, University of Cologne, Germany
| | - Stephen J. Meltzer
- Gastroenterology Division, Department of Medicine, the Johns Hopkins University School of Medicine, Baltimore, MD 21231
| |
Collapse
|